Highlighted Manuscripts
Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired by recent advances in physical quantum processors, we evaluated several unconventional machine-learning (ML) strategies on actual human tumor data, namely “Ising-type” methods, whose objective function is formulated identical to simulated annealing and quantum annealing. We show the efficacy of multiple Ising-type ML algorithms for classification of multi-omics human cancer data from The Cancer Genome Atlas, comparing these classifiers to a variety of standard ML methods. Our results indicate that Ising-type ML offers superior classification performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing approaches in the biomedical sciences.
The etiology of aortic aneurysms is poorly understood, but it is associated with atherosclerosis, hypercholesterolemia, and abnormal transforming growth factor β (TGF-β) signaling in smooth muscle. Here, we investigated the interactions between these different factors in aortic aneurysm development and identified a key role for smooth muscle cell (SMC) reprogramming into a mesenchymal stem cell (MSC)-like state. SMC-specific ablation of TGF-β signaling in Apoe-/- mice on a hypercholesterolemic diet led to development of aortic aneurysms exhibiting all the features of human disease, which was associated with transdifferentiation of a subset of contractile SMCs into an MSC-like intermediate state that generated osteoblasts, chondrocytes, adipocytes, and macrophages. This combination of medial SMC loss with marked increases in non-SMC aortic cell mass induced exuberant growth and dilation of the aorta, calcification and ossification of the aortic wall, and inflammation, resulting in aneurysm development.
Smooth muscle cell (SMC) proliferation has been thought to limit the progression of thoracic aortic aneurysm and dissection (TAAD) because loss of medial cells associates with advanced disease. We investigated effects of SMC proliferation in the aortic media by conditional disruption of Tsc1, which hyperactivates mTOR complex 1. Consequent SMC hyperplasia led to progressive medial degeneration and TAAD. In addition to diminished contractile and synthetic functions, fate-mapped SMCs displayed increased proteolysis, endocytosis, phagocytosis, and lysosomal clearance of extracellular matrix and apoptotic cells. SMCs acquired a limited repertoire of macrophage markers and functions via biogenesis of degradative organelles through an mTOR/β-catenin/MITF-dependent pathway, but were distinguishable from conventional macrophages by an absence of hematopoietic lineage markers and certain immune effectors even in the context of hyperlipidemia. Similar mTOR activation and induction of a degradative SMC phenotype in a model of mild TAAD due to Fbn1 mutation greatly worsened disease with near-uniform lethality. The finding of increased lysosomal markers in medial SMCs from clinical TAAD specimens with hyperplasia and matrix degradation further supports the concept that proliferation of degradative SMCs within the media causes aortic disease, thus identifying mTOR-dependent phenotypic modulation as a therapeutic target for combating TAAD.
Atherosclerosis is a progressive vascular disease triggered by interplay between abnormal shear stress and endothelial lipid retention. A combination of these and, potentially, other factors leads to a chronic inflammatory response in the vessel wall, which is thought to be responsible for disease progression characterized by a buildup of atherosclerotic plaques. Yet molecular events responsible for maintenance of plaque inflammation and plaque growth have not been fully defined. Here we show that endothelial TGFβ signaling is one of the primary drivers of atherosclerosis-associated vascular inflammation. Inhibition of endothelial TGFβ signaling in hyperlipidemic mice reduces vessel wall inflammation and vascular permeability and leads to arrest of disease progression and regression of established lesions. These pro-inflammatory effects of endothelial TGFβ signaling are in stark contrast with its effects in other cell types and identify it as an important driver of atherosclerotic plaque growth and show the potential of cell-type specific therapeutic intervention aimed at control of this disease.
To define the role of ERK1/2 signaling in the quiescent endothelium, we induced endothelial Erk2 knockout in adult Erk1-/- mice. This resulted in a rapid onset of hypertension, a decrease in eNOS expression, and an increase in endothelin-1 plasma levels, with all mice dying within 5 wk. Immunostaining and endothelial fate mapping showed a robust increase in TGFβ signaling leading to widespread endothelial-to-mesenchymal transition (EndMT). Fibrosis affecting the cardiac conduction system was responsible for the universal lethality in these mice. Other findings included renal endotheliosis, loss of fenestrated endothelia in endocrine organs, and hemorrhages. An ensemble computational intelligence strategy, comprising deep learning and probabilistic programing of RNA-seq data, causally linked the loss of ERK1/2 in HUVECs in vitro to activation of TGFβ signaling, EndMT, suppression of eNOS, and induction of endothelin-1 expression. All in silico predictions were verified in vitro and in vivo. In summary, these data establish the key role played by ERK1/2 signaling in the maintenance of vascular normalcy.
It has long been hypothesized that aging and neurodegeneration are associated with somatic mutation in neurons; however, methodological hurdles have prevented testing this hypothesis directly. We used single-cell whole-genome sequencing to perform genome-wide somatic single-nucleotide variant (sSNV) identification on DNA from 161 single neurons from the prefrontal cortex and hippocampus of 15 normal individuals (aged 4 months to 82 years), as well as 9 individuals affected by early-onset neurodegeneration due to genetic disorders of DNA repair (Cockayne syndrome and xeroderma pigmentosum). sSNVs increased approximately linearly with age in both areas (with a higher rate in hippocampus) and were more abundant in neurodegenerative disease. The accumulation of somatic mutations with age-which we term genosenium-shows age-related, region-related, and disease-related molecular signatures and may be important in other human age-associated conditions.
Blood and lymphatic vasculatures are intimately involved in tissue oxygenation and fluid homeostasis maintenance. Assembly of these vascular networks involves sprouting, migration and proliferation of endothelial cells. Recent studies have suggested that changes in cellular metabolism are important to these processes. Although much is known about vascular endothelial growth factor (VEGF)-dependent regulation of vascular development and metabolism, little is understood about the role of fibroblast growth factors (FGFs) in this context. Here we identify FGF receptor (FGFR) signalling as a critical regulator of vascular development. This is achieved by FGF-dependent control of c-MYC (MYC) expression that, in turn, regulates expression of the glycolytic enzyme hexokinase 2 (HK2). A decrease in HK2 levels in the absence of FGF signalling inputs results in decreased glycolysis, leading to impaired endothelial cell proliferation and migration. Pan-endothelial- and lymphatic-specific Hk2 knockouts phenocopy blood and/or lymphatic vascular defects seen in Fgfr1/Fgfr3 double mutant mice, while HK2 overexpression partly rescues the defects caused by suppression of FGF signalling. Thus, FGF-dependent regulation of endothelial glycolysis is a pivotal process in developmental and adult vascular growth and development.
Featured on cover of the October 2nd 2015 issue of Science.
A Neuroscience Perspective on the potential impact in medicine and biology.
Neurons live for decades in a postmitotic state, their genomes susceptible to DNA damage.
Here we survey the landscape of somatic single-nucleotide variants (SNVs) in the human
brain.We identified thousands of somatic SNVs by single-cell sequencing of 36 neurons from
the cerebral cortex of three normal individuals. Unlike germline and cancer SNVs, which are
often caused by errors in DNA replication, neuronal mutations appear to reflect damage
during active transcription. Somatic mutations create nested lineage trees, allowing them
to be dated relative to developmental landmarks and revealing a polyclonal architecture of the
human cerebral cortex. Thus, somatic mutations in the brain represent a durable and ongoing
record of neuronal life history, from development through postmitotic function.
Biomedical research consortia are a particularly attractive means to tackle the challenges facing the scientific community. Scholarly consortia could enhance research participation and leverage the skills of diverse, highly trained and dedicated scientists toward non-traditional research. As such, research consortia could play an important part in fulfilling the NIH’s mission of “seeking fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce illness and disability".
The (i) reciprocity relations for the relative Fisher information (RFI, hereafter) and (ii) a generalized RFI–Euler theorem are selfconsistently derived from the Hellmann–Feynman theorem. These new reciprocity relations generalize the RFI–Euler theorem and constitute the basis for building up a mathematical Legendre transform structure (LTS, hereafter), akin to that of thermodynamics, that underlies the RFI scenario. This demonstrates the possibility of translating the entire mathematical structure of thermodynamics into a RFI-based theoretical framework. Virial theorems play a prominent role in this endeavor, as a Schrödinger-like equation can be associated to the RFI. Lagrange multipliers are determined invoking the RFI–LTS link and the quantum mechanical virial theorem. An appropriate ansatz allows for the inference of probability density functions (pdf’s, hereafter) and energy-eigenvalues of the above mentioned Schrödinger-like equation. The energy-eigenvalues obtained here via inference are benchmarked against established theoretical and numerical results. A principled theoretical basis to reconstruct the RFI-framework from the FIM framework is established. Numerical examples for exemplary cases are provided.
Select Research Articles
2020
Pei-Yu Chen, Lingfeng Qin, Guangxin Li, Jose Malagon-Lopez, Zheng Wang, Sonia Bergaya, Sharvari Gujja, Alexander W. Caulk, Sae-Il Murtada, Xinbo Zhang, Zhen W. Zhuang, Deepak A. Rao, Guilin Wang, Zuzana Tobiasova, Bo Jiang, Ruth R Montgomery, Lele Sun, Hongye Sun, Edward A. Fisher, Jeffrey R. Gulcher, Carlos Fernandez-Hernando, Jay D. Humphrey, George Tellides, Thomas W. Chittenden, Michael Simons. Smooth muscle cell reprogramming in aortic aneurysms. Cell Stem Cell, 2020 Apr 2;26(4):542-557.e11. doi: 10.1016/j.stem.2020.02.013 (featured article at NHLBI of NIH).
Michael Simons, Pei-Yu Chen, Thomas W. Chittenden. Resilience, disease and the age of single cell science. Aging, 2020 Feb 10;12(3):2028-2029. DOI: 10.18632/aging.
Guangxin Li, Mo Wang, Alexander W. Caulk, Nicholas A. Cilfone, Sharvari Gujja, Lingfeng Qin, Pei-Yu Chen, Zehua Chen, Sameh Yousef, Yang Jiao, Changshun He, Bo Jiang, Arina Korneva, Matthew R. Bersi, Guilin Wang, Xinran Liu, Sameet Mehta, Arnar Geirsson, Jeffrey R. Gulcher, Thomas W. Chittenden, Michael Simons, Jay D. Humphrey, George Tellides. Chronic mTOR activation induces a degradative smooth muscle cell phenotype. Journal of Clinical Investigation, 2020 Feb 10 DOI: 10.1172/JCI131048 (accompanying commissioned editorial).
2019
Pei-Yu Chen, Lingfeng Qin, Guangxin Li, Zheng Wang, James E. Dahlman, Jose Malagon-Lopez, Sharvari Gujja, Kevin J. Kauffman, Lele Sun, Hongye Sun, Xinbo Zhang, Binod Aryal, Alberto Canfran-Duque, Rebecca Liu, Pascal Kusters, Alfica Sehgal, Yang Jiao, Daniel G. Anderson, Jeffrey Gulcher, Carlos Fernandez-Hernando, Esther Lutgens, Martin A. Schwartz, Jordan S. Pober, Thomas W. Chittenden, George Tellides, and Michael Simons. Endothelial TGF-beta signaling drives vascular inflammation and atherosclerosis. Nature Metabolism, 2019 Aug 26 DOI: 10.1038/s42255-019-0102-3 (accompanying commissioned editorial).
Nicolas Ricard, Rizaldy Scott, Carmen Booth, Heino Velazquez, Nicholas Cilfone, Javier Baylon, Jeffrey Gulcher, Susan Quaggin, Thomas W. Chittenden, and Michael Simons. Endothelial ERK1/2 signaling maintains integrity of the quiescent endothelium. Journal of Experimental Medicine, 2019 Jun 13 DOI: 10.1084/jem.20182151 (accompanying commissioned editorial).
Javier Baylon, Nicholas Cilfone, Jeffrey Gulcher, Thomas W. Chittenden. Enhancing Retrosynthetic Reaction Prediction with Deep Learning using Multiscale Reaction Classification. Journal of Chemical Information and Modeling, 2019 Jan 14 DOI: 10.1021/acs.jcim.8b00801 (featured on cover).
2018
Kristin L. Ayers, Benjamin S. Glicksberg, Alastair S. Garfield3, Simonne Longerich4, Joseph A. White, Pengwei Yang, Lei Du, Thomas W. Chittenden, Jeffery R. Gulcher, Sophie Roy, Fred Fiedorek, Keith Gottesdiener, Sarah Cohen, Kari E. North, Eric E. Schadt, Shuyu D. Li1, Rong Chen, Lex H.T. Van der Ploeg. Melanocortin-4 receptor pathway dysfunction in obesity: Patient stratification aimed at MC4R agonist treatment. Journal of Clinical Endocrinology & Metabolism, 2018 May 2. doi: 10.1210/ jc.2018-00258.
Michael A. Lodato, Rachel E. Rodin, Craig L. Bohrson, Michael E. Coulter, Alison R. Barton, Minseok Kwon, Maxwell A. Sherman, Carl M. Vitzthum, Lovelace J. Luquette, Chandri Yandava, Pengwei Yang, Thomas W. Chittenden, Nicole E. Hatem, Steven C. Ryu, Mollie B. Woodworth, Peter J. Park, Christopher A. Walsh. Aging and neurodegeneration are associated with increased mutations in single human Neurons. Science, 2018 Feb 2;359(6375):555-559. doi: 10.1126/science.aao4426.
2017
Jennifer S. Fang, Brian G. Coon, Noelle Gillis, Zehua Chen, Jingyao Qiu, Thomas W. Chittenden, Janis M. Burt, Martin A. Schwartz, Karen K. Hirschi. Shear-induced Notch-Cx37-p27 axis arrests endothelial cell cycle to enable arterial specification. Nature Communications, 2017 Dec 15;8(1):2149.
Pengchun Yu, Joe K. Tung, Kerstin Wilhelm, Alexandra Dubrac, Tiago C. Alves, Jennifer S. Fang; Yi Xie, Jie Zhu, Zehua Chen, Frederik De Smet, Jiasheng Zhang, Suk-Won Jin, Lele Sun, Hongye Sun, Richard Kibbey, Karen K. Hirschi, Nissim Hay, Peter Carmeliet, Thomas W. Chittenden, Anne Eichmann, Michael Potente, Michael Simons. FGF-dependent metabolic control of vascular development. Nature, 2017 May 11;545(7653): 224-228.
2016
Banerjee, S. A biologically inspired model of distributed online communication supporting efficient search and diffusion of innovation. Interdisciplinary Description of Complex Systems, 2016;14(1):10-22.
Zehua Chen, Ryan P. Abo, Shannon T. Bailey, Jike Cui, Curt Balch, Jeffrey R. Gulcher, Thomas W. Chittenden. RNA Sequencing and Genetic Disease. Current Genetic Medicine Reports, 2016 Sep;4(3): 49-56.
Ephraim F. Trakhtenberg, Nam Pho, Kristina M. Holton, Thomas W. Chittenden, Jeffrey L. Goldberg, Lingsheng Dong. Cell types differ in global coordination of splicing and proportion of highly expressed genes. Scientific Reports, 2016 Aug 31;6:32249.
2015
Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science, 2015 Oct 2;350(6256):94-8.
Corder EH, Khalsa KP. Rejuvenation by inhibiting TGF-β1/pSmad signaling. Oncotarget 2015 Jul 10;6(19):16790-1.
Galligan JT, Martinez-Noël G, Arndt V, Hayes S, Chittenden TW, Harper JW, Howley PM. Proteomic analysis and identification of cellular interactors of the giant ubiquitin ligase HERC2. Journal of Proteome Research, 2015 Feb 6;14(2):953-66. Epub 2014 Dec 15.
Balch C, Arias-Pulido H, Banerjee S, Lancaster AK, Clark KB, Perilstein M, Hawkins B, Rhodes J, Sliz P, Wilkins J, Chittenden TW. Science and technology consortia in US biomedical research: A paradigm shift in response to unsustainable academic growth. BioEssays, 2015 Feb;37(2):119-22. Epub 2014 Nov 12.
Bailey ST, Westerling T, and Brown M. Loss estrogen-regulated microRNA expression increases HER2 signaling and is predictive of poor outcome in luminal breast cancer. Cancer Research, 2015 Jan 11;75(2):436-45.
Bailey ST, Shin H, Westerling T, Liu XS, Brown M. Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proceedings of the National Academy of Sciences, 2015;109 (44): 18060-18065.
Vogel CW, Fritzinger DC, Gorsuch WB, Stahl GL. Complement Depletion with Humanized Cobra Venom Factor: Efficacy in Preclinical Models of Vascular Diseases. Thrombosis and Haemostasis, 2015;113:548-552.
Systems neuroscience in focus: from the human brain to the global brain? Kyriazis M. Front Syst Neurosci, 2015 Feb 6;9:7.
Trakhtenberg EF, Morkin MI, Patel KH, Fernandez SG, Sang A, Shaw P, Liu X, Wang Y, Mlacker GM, Gao H, Velmeshev D, Dombrowski SM, Vitek MP, Goldberg JL. N-terminal Set-ß protein isoform induces neuronal death. J Biol Chem, (In Press).
Andereggen L, Trakhtenberg EF, Yin Y, and Benowitz LI. Neuroinflammation: New Insights into Beneficial and Detrimental Functions. Editor: Samuel David. Inflammation and Optic Nerve Regeneration, 2015; (12):189-204.
Venkatesan RC and Plastino A. Hellmann-Feynman connection for the relative Fisher information. Annals of Physics, (In Press).
2014
Venkatesan RC and Plastino A. Legendre transform structure and extremal properties of the relative Fisher information. Physics Letters A, 2014 April 4;378(20):1341–1345.
Sinadinos C, Valles-Ortega J, Boulan L, Solsona E, Tevy MF, Marquez M, Duran J, Lopez-Iglesias C, Calbó J, Blasco E, Pumarola M, Milán M, Guinovart JJ. Neuronal glycogen synthesis contributes to physiological aging. Aging Cell, 2014 Oct;13(5):935-45.
Technological integration and hyperconnectivity: Tools for promoting extreme human lifespans. Kyriazis M. Complexity, 2014 doi: 10.1002/cplx.21626.
The impracticality of biomedical rejuvenation therapies: translational and pharmacological barriers. Kyriazis M. Rejuvenation Res, 2014 Aug;17(4):390-6.
Reversal of informational entropy and the acquisition of germ-like immortality by somatic cells. Kyriazis M. Curr Aging Sci, 2014;7(1):9-16. Review.
Saez I, Duran J, Sinadinos C, Beltran A, Yanes O, Tevy MF, Martínez-Pons C, Milán M, Guinovart JJ. Neurons have an active glycogen metabolism that contributes to tolerance to hypoxia. J Cereb Blood Flow Metab, 2014 Jun;34(6):945-55.
Joshi G, Chi Y, Huang Z, Wang Y. Aβ-induced Golgi fragmentation in Alzheimer's disease enhances Aβ production. Proc Natl Acad Sci USA, 2014;111(13):E1230-9.
Trakhtenberg EF, Wang Y, Morkin MI, Fernandez SG, Mlacker GM, Shechter JM, Liu X, Patel KH, Lapins A, Yang S, Dombrowski SM, and Goldberg JL. Regulating Set-β’s subcellular localization toggles its function between inhibiting and promoting axon growth and regeneration. Journal of Neuroscience, 2014;34:7361–7374.
Joe MK, Kwon HS, Cojocaru R, Tomarev SI. Myocilin regulates cell proliferation and survival. J Biol Chem, 2014 Feb 22.
[Epub ahead of print]
Vogel CW and Fritzinger DC. Cobra Venom Factor: The Unique Component of Cobra Venom that Activates the Complement System. Toxinology, Snake Venoms, (Gopalakrishnakone, P. ed) 2014 Springer.
Vogel CW, Finnegan PW, Fritzinger DC. Humanized Cobra Venom Factor: Structure, Activity, and Therapeutic Efficacy in Preclinical Disease Models. Mol. Immunol, 2014;61: 191-203.
Baeyens N, Mulligan-Kehoe MJ, Corti F, Simon DD, Ross TD, Rhodes JM, et al. Syndecan 4 is required for endothelial alignment in flow and atheroprotective signaling. Proc Natl Acad Sci USA, 2014; 111(48):17308-13.
Ricard N, Tu L, Le Hiress M, Huertas A, Phan C, Thuillet R, et al. Increased pericyte coverage mediated by endothelial-derived fibroblast growth factor-2 and interleukin-6 is a source of smooth muscle-like cells in pulmonary hypertension. Circulation, 2014;129(15):1586-97.
Stacy MR, Yu DY, Maxfield MW, Jaba IM, Jozwik BP, Zhuang ZW, Lin BA, Hawley CL, Caracciolo CM, Pal P, Tirziu D, Sampath S, Sinusas AJ. A multimodality imaging approach for serial assessment of regional changes in lower extremity arteriogenesis and tissue perfusion in a porcine model of peripheral arterial disease. Circ Cardiovasc Imaging, 2014;7:92-99.
Nallaseth FS. Is There a Role for an Evolutionary Genetics Based Rational Health Policy In Global Biomedical, Health and Economic Policies? Mol Biol, 2014 3:1000e118.
2013
Ma W, Cojocaru R, Gotoh N, Gieser L, Villasmil R, Cogliati T, Swaroop A, Wong WT. Gene expression changes in aging retinal microglia: relationship to microglial support functions and regulation of activation. Neurobiol Aging, 2013 Oct;34(10):2310-21.
King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, Chamberlain SJ, Philpot BD, Zylka MJ. Topoisomerases facilitate transcription of long genes linked to autism. Nature, 2013 Sep 5;501(7465):58-62.
Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP Jr, Buitendijk GH, Sim X, Weeks DE, Guymer RH, Merriam JE, Francis PJ, Hannum G, Agarwal A, Armbrecht AM, Audo I, Aung T, Barile GR, Benchaboune M, Bird AC, Bishop PN, Branham KE, Brooks M, Brucker AJ, Cade WH, Cain MS, Campochiaro PA, Chan CC, Cheng CY, Chew EY, Chin KA, Chowers I, Clayton DG, Cojocaru R, Conley YP, Cornes BK, Daly MJ, Dhillon B, Edwards AO, Evangelou E, Fagerness J, Ferreyra HA, Friedman JS, Geirsdottir A, George RJ, Gieger C, Gupta N, Hagstrom SA, Harding SP, Haritoglou C, Heckenlively JR, Holz FG, Hughes G, Ioannidis JP, Ishibashi T, Joseph P, Jun G, Kamatani Y, Katsanis N, N Keilhauer C, Khan JC, Kim IK, Kiyohara Y, Klein BE, Klein R, Kovach JL, Kozak I, Lee CJ, Lee KE, Lichtner P, Lotery AJ, Meitinger T, Mitchell P, Mohand-Saïd S, Moore AT, Morgan DJ, Morrison MA, Myers CE, Naj AC, Nakamura Y, Okada Y, Orlin A, Ortube MC, Othman MI, Pappas C, Park KH, Pauer GJ, Peachey NS, Poch O, Priya RR, Reynolds R, Richardson AJ, Ripp R, Rudolph G, Ryu E, Sahel JA, Schaumberg DA, Scholl HP, Schwartz SG, Scott WK, Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson H, Sturgill-Short GM, Takahashi A, Tosakulwong N, Truitt BJ, Tsironi EE, Uitterlinden AG, van Duijn CM, Vijaya L, Vingerling JR, Vithana EN, Webster AR, Wichmann HE, Winkler TW, Wong TY, Wright AF, Zelenika D, Zhang M, Zhao L, Zhang K, Klein ML, Hageman GS, Lathrop GM, Stefansson K, Allikmets R, Baird PN, Gorin MB, Wang JJ, Klaver CC, Seddon JM, Pericak-Vance MA, Iyengar SK, Yates JR, Swaroop A, Weber BH, Kubo M, Deangelis MM, Léveillard T, Thorsteinsdottir U, Haines JL, Farrer LA, Heid IM, Abecasis GR; AMD Gene Consortium. Seven new loci associated with age-related macular degeneration. Nat Genet, 2013 Apr;45(4):433-9, 439e1-2.
Tevy MF, Giebultowicz J, Pincus Z, Mazzoccoli G, Vinciguerra M. Aging signaling pathways and circadian clock-dependent metabolic derangements. Trends Endocrinol Metab, 2013 May;24(5):229-37.
Gupta K, Madan E, Sayyid M, Arias-Pulido H, Moreno E, Kuppusamy P, Gogna R. Oxygen regulates Molecular mechanisms of Cancer. Cancer Metastasis Rev, 2013 Dec 15. [Epub ahead of print].
Altobelli G*¶, Bogdarina IG*, Stupka E, Clark AJ, Langley-Evans S. Genome-Wide Methylation and Gene Expression Changes in Newborn Rats following Maternal Protein Restriction and Reversal by Folic Acid. PLoS One, 2013 Dec 23; 8: e82989. *Equal contributors, ¶corresponding author.
Lepoivre C*, Belhocine M*, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau JC, Puthier D, Spicuglia S. Divergent transcription is associated with promoters of transcriptional regulators. BMC Genomics, 2013 Dec 23;14(1):914.*Equal contributors.
Clark KB, Hassert DL. Undecidability and opacity of metacognition in animals and humans. Front Psychol, 2013;4:171.
Clark KB. Ciliates learn to diagnose and correct classical error syndromes in mating strategies. Front Microbiol, 2013;4:229.
Clark KB, Eisenstein EM. Targeting host store-operated Ca2+ release to attenuate viral infections. Curr Top Med Chem, 2013;13(16):1916-1932.
Clark KB. New therapeutic bearings for repositioned drugs. Curr Top Med Chem, 2013;13(18):2281-2282.
Clark KB, Eisenstein EM, Krahl SE. Calcium antagonists: a ready prescription for treating infectious diseases? Curr Top Med Chem, 2013;13(18):2291-2305.
Clark KB. Biotic activity of Ca2+-modulating nontraditional antimicrobial and -viral agents. Front Microbiol, 2013;4:381.
Balch C, Nephew KP. Epigenetic targeting therapies to overcome chemotherapy resistance. Adv Exp Med Biol, 2013;754:285-311.
Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE, 2013 May 31;8(5): e64832.
Jayasinghe SN. Cell electrospinning: a novel tool for functionalising fibres, scaffolds and membranes with living cells and other advanced materials for regenerative biology and medicine. Analyst, 2013 Mar 18;138(8):2215-23.
Morteza A, Nakhjavani M, Asgarani F, Carvalho FL, Karimi R, Esteghamati A.Inconsistency in albuminuria predictors in type 2 diabetes: a comparison between neural network and conditional logistic regression. Transl Res, 2013;161:397-405.
Morteza A, Nakhjavani M, Asgarani F, Ghaneei A, Esteghamati A, Mirmiranpour H. The lost correlation between leptin and CRP in type 2 diabetes. Eur Cytokine Netw, 2013;24:53-9.
Morteza A, Nakhjavani M, Larry M, Nargesi AA, Esteghamati A. Heat shock protein 70 and albuminuria in patients with type 2 diabetes: a matched case control study. Cell Stress Chaperones, 2013 May 17.
Nallaseth FS, Anderson S. A screen for over-secretion of proteins by yeast based on a dual component cellular phosphatase and immuno-chromogenic stain for exported bacterial alkaline phosphatase reporter. Microb Cell Fact, 2013 Apr 19;12:36.
Corti F, Finetti F, Ziche M, Simons M. The syndecan-4/protein kinase Calpha pathway mediates prostaglandin E2-induced extracellular regulated kinase (ERK) activation in endothelial cells and angiogenesis in vivo. J Biol Chem, 2013; 288(18):12712-21.
Solito R, Corti F, Chen CH, Mochly-Rosen D, Giachetti A, Ziche M, et al. Mitochondrial aldehyde dehydrogenase-2 activation prevents beta-amyloid-induced endothelial cell dysfunction and restores angiogenesis. J Cell Sci, 2013;126(Pt 9):1952-61.
Jaba IM, Zhuang ZW, Li N, Jiang Y, Martin K, Sinusas AJ, Papademetris X, Simons M, Sessa W, Young L, Tirziu D. NO triggers RGS4 degradation to coordinate angiogenesis and cardiomyocyte growth. J Clin Invest, 2013;123:1718-1731.
2012
Scannell JW, Blanckley A, Boldon H, Warrington B. Diagnosing the decline in pharmaceutical R&D efficiency. Nat Rev Drug Discov, 2012 Mar 1;11(3):191-200.
Human Microbiome Project Consortium. A framework for human microbiome research. Nature, 2012 Jun 13;486(7402):215-21.
Mathew MJ, Subramanian G, Nguyen TT, Robert C, Mediannikov O, Fournier PE, Raoult D. J Bacteriol. Genome Sequence of Diplorickettsia massiliensis, an Emerging Ixodes ricinus-Associated Human Pathogen. 2012 Jun 194(12):3287.
Martinez-Noël G, Galligan JT, Sowa ME, Arndt V, Overton TM, Harper JW, Howley PM. Identification and proteomic analysis of distinct UBE3A/E6AP protein complexes. Molecular Cell Biology, 2012;32(15):3095-3106.
Duran J*, Tevy MF*, Garcia-Rocha M, Calbó J, Milán M, Guinovart JJ. Deleterious effects of neuronal accumulation of glycogen in flies and mice. EMBO Mol Med, 2012 Aug;4(8):719-29.
Qin Y, Xu J, Aysola K, Oprea G, Reddy A, Matthews R, Okoli J, Cantor A, Grizzle WE, Partridge EE, Reddy ES, Landen C, Rao VN. BRCA1 proteins regulate growth of ovarian cancer cells by tethering Ubc9. Am J Cancer Res, 2012;2(5):540-8.
Lutz D*, Wolters-Eisfeld G*, Joshi G*, Djogo N, Jakovcevski I, Schachner M, Kleene R. Generation and nuclear translocation of sumoylated transmembrane fragment of cell adhesion molecule L1. Journal of Biological Chemistry, 2012;287(21):17161-75 (*Equal contribution).
Trakhtenberg EF and Goldberg JL. The role of serotonin in axon and dendrite growth. International Review of Neurobiology: Axon Growth and Regeneration, 2012;106 (4):105-126.
Goldberg JL and Trakhtenberg EF. International Review of Neurobiology: Axon Growth and Regeneration, 2012 Volumes 106-1077: Academic Press.
Corredor RG, Trakhtenberg EF, Pita-Thomas W, Jin X, Hu Y, and Goldberg JL. Soluble adenylyl cyclase activity is necessary for retinal ganglion cell survival and axon growth. Journal of Neuroscience, 2012;32:7734-7744.
Trakhtenberg EF and Goldberg JL. Epigenetic regulation of axon and dendrite growth. Frontiers in Neuroscience, 2012; 5:1-8.
Sharma YV, Cojocaru RI, Ritter LM, Khattree N, Brooks M, Scott A, Swaroop A, Goldberg AF. Protective gene expression changes elicited by an inherited defect in photoreceptor structure. PLoS One, 2012;7(2):e31371.
Roger JE, Ranganath K, Zhao L, Cojocaru RI, Brooks M, Gotoh N, Veleri S, Hiriyanna A, Rachel RA, Campos MM, Fariss RN, Wong WT, Swaroop A.Preservation of cone photoreceptors after a rapid yet transient degeneration and remodeling in cone-only Nrl-/- mouse retina. J Neurosci, 2012 Jan 11;32(2):528-41.
Saravanamuthu SS, Le TT, Gao CY, Cojocaru RI, Pandiyan P, Liu C, Zhang J, Zelenka PS, Brown NL. Conditional ablation of the Notch2 receptor in the ocular lens. Dev Biol, 2012 Feb 15;362(2):219-29.
Fanchiang SS, Cojocaru R, Othman M, Khanna R, Brooks MJ, Smith T, Tang X, Maricic I, Swaroop A, Kumar V. Global expression profiling of peripheral Qa-1-restricted CD8αα+TCRαβ+ regulatory T cells reveals innate-like features: implications for immune-regulatory repertoire. Hum Immunol, 2012 Mar;73(3):214-22.
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Guo W, Schafer S, Greaser ML, Radke MH, Liss M, Govindarajan T, Maatz H, Schulz H, Li S, Parrish AM, et al. RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nature Medicine, 2012;18:766–773.
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Atai NA, Ryan SD, Kothary R, Breakefield XO, Nery FC. Untethering the nuclear envelope and cytoskeleton - biologically distinct dystonias arising from a common cellular dysfunction. Int J Cell Biol, 2012;2012:634214.
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Andreu N, Thomas D, Saraiva L, Ward N, Gustafsson K, Jayasinghe SN, Robertson BD. In vitro and in vivo interrogation of bio-sprayed cells. Small, 2012 Aug 20;8(16):2495-500. Epub 2012 May 31.
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Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH. The Cancer Genome Atlas Research Network. Integrated Analyses of microRNAs Demonstrate Their Widespread Influence on Gene Expression in High-Grade Serous Ovarian Carcinoma. PLoS ONE, 2012;7(3):e34546. Epub 2012 Mar 29.
*Balch C, Naegeli K, Nam S, Ballard B, Hyslop A, Melki C, Reilly E, Hur M-W, *Nephew KP (*co-corresponding authors). A unique histone deacetylase inhibitor alters microRNA expression and signal transduction in chemoresistant ovarian cancer cells. Cancer Biol Ther, 2012 Jun;13(8):681-93.
*Teng M, *Balch C, Liu Y, Li M, Huang TH-M, Wang Y, Nephew KP, Li L (*co-first authors). The influence of cis-regulatory elements on DNA methylation fidelity. PLoS ONE, 2012;7(3):e32928.
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Locasale JW. The consequences of enhanced cell autonomous glucose metabolism. Trends Endocrinol Metab, 2012 Nov;23(11):545-51.
Halley JD, Smith-Miles K, Winkler DA, Kalkan T, Huang S, Smith A. Self-organizing circuitry and emergent computation in mouse embryonic stem cells. Stem Cell Res, 2012 Mar;8(2):324-33. Epub 2011 Nov 11. Review.
Locasale JW. Metabolic rewiring drives resistance to targeted cancer therapy. Mol Syst Biol, 2012 Jul 17;8:597.
Lux MW, Bramlett BW, Ball DA, Peccoud J. Genetic design automation: engineering fantasy or scientific renewal? Trends Biotechnol, 2012;30(2): 120-126.
Chaki M*, Airik R*, Ghosh A, Giles R et al. Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell, 2012;150(3):533-48. *Equally contributed to the study.
Chaher N, Arias-Pulido H, Terki N, Qualls C, Bouzid K, Verschraegen C, Wallace AN, Royce M. Molecular and epidemiological characteristics of inflammatory breast cancer in Algerian patients. Breast Cancer Res Treat, 2012;131:437-44.
Arias-Pulido H, Chaher N, Gong Y, Qualls C, Vargas J, Lomo L, Terki N, Bouzid K, Royce M. Stromal VEGF-A preditcs worse breast cancer-specific and disease-free survival in inflammatory breast cancer. BMC Cancer, 2012;12:298.
Ramos E, Ruchala P, Goodnough JB, Kautz L, Preza GC, Nemeth E, Ganz T. Minihepcidins prevent iron overload in a hepcidin-deficient mouse model of severe hemochromatosis. Blood, 2012 [Epub ahead of print].
Xu J, Ruchala YP, Ebenstein, Li JJ, Weiss S. Stable, compact, bright biofunctional quantum dots with improved peptide coating. J Phys Chem B, 2012;116(36): 11370–11378.
Khachatoorian R, Arumugaswami V, Ruchala P, Raychaudhuri S, Maloney EM, Miao E, Dasgupta A, French SW. A cell-permeable hairpin peptide inhibits hepatitis C viral nonstructural protein 5A mediated translation and virus production. Hepatology, 2012; 55(6):1662-72.
Doss M, Ruchala P, Tecle T, Gantz D, Hartshorn A, Crouch EC, Luong H, Micewicz ED, Lehrer RI, Hartshorn KL. Hapivirins and diprovirins: novel Θ-defensin analogs with potent activity against influenza A virus. J Immunol, 2012;188(6):2759-2768.
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Retinoblastoma tumor-suppressor protein phosphorylation and inactivation depend on direct interaction with Pin1. Cell Death Differ, 2012 Jul;19(7):1152-61. doi: 10.1038/cdd.2011.202. Epub 2012 Feb 10.
Simone EA, Zern BJ, Chacko AM, Mikitsh JL, Blankemeyer ER, Muro S, Stan RV, Muzykantov VR. Endothelial targeting of polymeric nanoparticles stably labeled with the PET imaging radioisotope iodine-124. Biomaterials, 2012 Jul; 33(21):5406-13.
Wasiuk A, Dalton DK, Schpero WL, Stan RV, Conejo-Garcia JR, Noelle RJ. Mast cells impair the development of protective anti-tumor immunity. Cancer Immunol Immunother, 2012 Jun 10.
Hatanaka K, Lanahan AA, Murakami M and Simons M. Fibroblast growth factor signaling potentiates VE-cadherin stability at adherens junctions by regulating SHP2. PLoS ONE, 2012;7(5):e37600. Epub 2012 May 22.
Deharvengt SJ, Tse D, Sideleva O, McGarry C, Gunn JR, Longnecker DS, Carriere C, Stan RV. PV1 downregulation via shRNA inhibits the growth of pancreatic adenocarcinoma xenografts. J Cell Mol Med, 2012 May 9.
Fathers KE, Bell ES, Rajadurai CV, Cory S, Zhao H, Mourskaia A, Zuo D, Madore J, Monast A, Mes-Masson AM, Grosset AA, Gaboury L, Hallet M, Siegel P, Park M. Crk adaptor proteins act as key signaling integrators for breast tumorigenesis. Breast Cancer Res, 2012 May 8;14(3):R74.
Elfenbein A, Lanahan A, Zhou TX, Yamasaki A, Tkachenko E, Matsuda M and Simons M. Syndecan 4 regulates FGFR1 signaling in endothelial cells by directing macropinocytosis. Sci Signal, 2012 May 8;5(223):ra36.
Tkachenko E, Tse D, Sideleva O, Deharvengt SJ, Luciano MR, Xu Y, McGarry CL, Chidlow J, Pilch PF, Sessa WC, Toomre DK, Stan RV. Caveolae, fenestrae and transendothelial channels retain PV1 on the surface of endothelial cells. PLoS ONE, 2012; 7(3):e32655. Epub 2012 Mar 5.
Chittenden TW, Howe EA, Taylor JM, Mar JC, Aryee MJ, Gómez H, Sultana R, Braisted J, Nair SJ, Quackenbush J, Holmes C. nEASE: a Method for Phenotype-specific Gene Ontology Classification of High-Throughput Gene Expression Data. Bioinformatics, 2012 Mar 1;28(5):726-728. Epub 2012 Jan 13.
Clark KB. Social biases determine spatiotemporal sparseness of ciliate mating heuristics. Commun Integr Biol, 2012 Jan 1; 5(1): 3-11.
Winkler DA, Burden FR. Robust, quantitative tools for modelling ex-vivo expansion of haematopoietic stem cells and progenitors. Mol. BioSyst, 2012 Mar;8(3):913-20.
Le TC, Epa VC, Burden FR, Winkler, DA. Quantitative Structure–Property Relationship Modeling of Diverse Materials Properties. Chem. Rev, 2012 May 9;112(5):2889-919.
Epa VC, Yang J, Mei Y, Hook AL, Langer R, Anderson DG, Davies M, Alexander MR, Winkler DA. Modelling human embryoid body cell adhesion to a combinatorial library of polymer surfaces. J Mat. Chem, 2012;(22):20902-20906.
Epa VC, Burden FR, Tassa C, Weissleder R, Shaw S, Winkler DA. Modelling biological activities of nanoparticles. Nano Lett, 2012;(12):5808−5812.
Dimitrov RA, Gouliamova DE. New Method for Sequence Alignment Based on Probabilities of Nucleotide Correspondences. Biotechnology & Biotechnological Equipment, 2012; 26(1):218-223.
Dimitrov RA, Gouliamova DE. Biological Sequence Comparison, Molecular Evolution And Phylogen?tics. Biotechnology & Biotechnological Equipment, 2012; 26(1):209-217.
Nakhjavani M, Morteza A, Jenab Y, Ghaneei A, Esteghamati A, Karimi M, Farokhian A. Gender difference in albuminuria and ischemic heart disease in type 2 diabetes. Clin Med Res, 2012;10:51-6.
Morteza A, Abdollahi A, Bandarian M. Serum nitric oxide syntheses and lipid profile of the mothers with IUGR pregnancies uncomplicated with preeclampsia. Does insulin resistance matter? Gynecol Endocrinol, 2012;28:139-42.
Esteghamati A, Morteza A., Zandieh A, Jafari S, Rezaee M, Nakhjavani M, Jamali A, Esteghamati AR, Khalilzadeh O.The value of visfatin in the prediction of metabolic syndrome: a multi-factorial analysis. J Cardiovasc Transl Res, 2012;5:541-6.
Ricard N, Ciais D, Levet S, Subileau M, Mallet C, Zimmers TA, et al. BMP9 and BMP10 are critical for postnatal retinal vascular remodeling. Blood, 2012;119(25):6162-71.
Bidart M, Ricard N, Levet S, Samson M, Mallet C, David L, et al. BMP9 is produced by hepatocytes and circulates mainly in an active mature form complexed to its prodomain. Cellular and molecular life sciences : CMLS, 2012;69(2):313-24.
Tirziu D, Jaba IM, Yu P, Larrivée B, Coon BG, Cristofaro B, Zhuang ZW, Lanahan AA, Schwartz MA, Eichmann A, Simons M. Endothelial NFκB -dependent regulation of arteriogenesis and branching. Circulation, 2012;126:2589-2600. PMID: 23091063
2011
Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The genetic landscape of the childhood cancer medulloblastoma. Science, 2011 Jan 28;331(6016):435-9.
Galligan JT, Marchetti SE, Kennell, JC. Reverse transcription of the pFOXC mitochondrial retroplasmids of Fusarium oxysporum is protein primed. Mobile DNA, 2011 Jan 21;2(1):1
Qin Y, Xu J, Aysola K, Begum N, Reddy V, Chai Y, Grizzle WE, Partridge EE, Reddy ES, Rao VN. Ubc9 mediates nuclear localization and growth suppression of BRCA1 and BRCA1a proteins. J Cell Physiol, 2011 Dec;226(12):3355-67.
Trakhtenberg EF and Goldberg JL. Neuroimmune Communication. Science, 2011 6052:47-48.
Taccioli C, Tegner J, Maselli V, Gomez-Cabrero D, Altobelli G, et al. ParkDB: a Parkinson's disease gene expression database. Database (Oxford) 2011: bar007.
Wilkins JF. Genomic imprinting and conflict-induced decanalization. Evolution, 2011 Feb;65(2):537-53.
Ùbeda F & Wilkins JF. The Red Queen theory of recombination hotspots. J. Evol. Biol, 2011 Mar;24(3):541-53.
Locasale JW, Cantley LC. Metabolic flux and the regulation of mammalian cell growth. Cell Metab, 2011 Oct 5;14(4):443-51.
Locasale JW, Grassian AR, Cantley LC and Vander Heiden MG, et al. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nature Genetics, 2011 Jul 31;43(9):869-74.
Nery FC, Armata IA, Farley JE, Cho JA, Yaqub U, Chen P, da Hora CC, Wang Q, Tagaya M, Klein C, Tannous B, Caldwell KA, Caldwell GA, Lencer WI, Ye Y, Breakefield XO. TorsinA participates in endoplasmic reticulum-associated degradation. Nat Commun, 2011 Jul 12;2:393.
Guo W, Greaser M, Li S, Schulz H, Saar K, Radke M, Hacker TA, Saupe KW, Vakeel P, Govindarajan T, et al. A novel Splicing Factor that Affects Titin Alternative Splicing. Biophys. J, 2011;100:287a.
Ball DA, Marchand J, Poulet M, Baumann WT, Chen KC, Tyson JJ, Peccoud J. Oscillatory Dynamics of Cell Cycle Proteins in Single Yeast Cells Analyzed by Imaging Cytometry. PLoS ONE, 2011;6(10): 12.
Chaki M, Hoefele J, Allen S, Ramaswami G et al. Genotype-phenotype correlation in 440 individuals with NPHP-related ciliopathies. Kidney Int, 2011;80(11):1239-45.
Hu Y, Scully R, Sobhian B, Xie A, Shestakova E, Livingston DM. RAP80-directed tuning of BRCA1 homologous recombination function at ionizing radiation-induced nuclear foci. Genes Dev, 2011;25(7): 685-700.
Heeringa S*, Chernin G*, Chaki M, Zhou W et al. COQ6 mutations cause nephrotic syndrome with sensorineural deafness in humans, concurrent with increased apoptosis. J Clin Invest, 2011;21(5):2013-24. *Equally contributed to the study.
Chaki M, Sengupta M, Mondal M, Bhattacharyya A et al. Molecular and functional studies on Tyrosinase variants: An implication towards Oculocutaneous Albinism type 1 (OCA1) among Indians. J Invest Dermatol, 2011;131(1):260-2
Hu T, Sinnott-Armstrong NA, Kiralis JW, Andrew AS, Karagas MR, Moore JH. Characterizing genetic interactions in human disease association studies using statistical epistasis networks. BMC Bioinformatics, 2011 Sep 12;12:364.
Preza GC, Ruchala P, Pinon R, Ramos E, Qiao B, Peralta MA, Sharma S, Waring AJ, Ganz T, Nemeth E. Minihepcidins are rationally designed small peptides that mimic hepcidin activity in mice and may be useful for the treatment of iron overload. J Clin Invest, 2011;121(12):4880-4888.
Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S.
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J, 2011 Aug 16;30(20):4198-210.
Tse D, Armstrong DA, Oppenheim A, Kuksin D, Norkin L, Stan RV. Plasmalemmal vesicle associated protein (PV1) modulates SV40 virus infectivity in CV-1 cells. Biochem Biophys Res Commun, 2011 Aug 26; 412(2):220-5.
Stitham J, Arehart E, Elderon L, Gleim SR, Douville K, Kasza Z, Fetalvero K, Mackenzie T, Robb J, Martin KA, and Hwa J.
Comprehensive biochemical analysis of rare prostacyclin receptor variants: Study of association of signaling with coronary artery obstruction. J Biol Chem, 2011;286(9): 7060-69.
Ung P, Winkler, DA. Tripeptide motifs in biology as drug targets. J. Med. Chem, 2011;(54): 1111–1125.
Andrecut M, Winkler DA, Huang S, Halley JD. A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity. PLoS ONE, 2011;6(5): e19358.
Wijffels G, Johnson WMP, Oakley A, Turner K, Epa VC, Briscoe S, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple B, Alewood P, Jennings P, Dixon NE, Winkler DA. Binding inhibitors of the bacterial sliding clamp by design. J. Med. Chem, 2011;54 (13): 4831-4838.
Tarasova A, Haylock D, Winkler DA. Principal signalling complexes in haematopoiesis: structural aspects and mimetic discovery. Cytokine Growth Factor Rev, 2011 Aug;22(4):231-53.
Wojtkowiak JW*, Sane KM*, Kleinman M, Sloane BF, Reiners, JJ, Jr., Mattingly RR. Aborted autophagy and non-apoptotic death induced by farnesyl transferase inhibitor and lovastatin. Journal of Pharmacology and Experimental Therapeutics, 2011 Apr;337(1);65-74 *Equally contributing authors.
Corti F, Olson KE, Marcus AJ, Levi R. The Expression Level of Ecto-NTP Diphosphohydrolase1/CD39 Modulates Exocytotic and Ischemic Release of Neurotransmitters in a Cellular Model of Sympathetic Neurons. J Pharmacol Exp Ther, 2011;337(2):524-32.
2010
Chittenden TW, Pak J, Rubio R, Cheng H, Holton K, Prendergast N, Glinskii V, Cai Y, Culhane A, Bentink S, Schwede M, Mar JC, Howe EA, Aryee M, Sultana R, Lanahan AA, Taylor JM, Holmes C, Hahn WC, Zhao JJ, Iglehart JD, Quackenbush J. Therapeutic Implications of GIPC1 Silencing in Cancer. PLoS ONE, 2010 Dec;5(12):e15581.
Nonlinear stimulation and hormesis in human aging: practical examples and action mechanisms. Kyriazis M. Rejuvenation Res, 2010 Aug;13(4):445-52.
Kleene R*, Mzoughi M*, Joshi G, Kalus I, Bormann U, Schulze, Xiao M , Dityatev A, and Schachner M. NCAM-induced neurite outgrowth depends on binding of calmodulin to NCAM and on nuclear import of NCAM and fak fragments. Journal of Neuroscience, 2010;30(32):10784-98 (*Equal contribution).
Bartolovic K, Mongkoldhumrongkul N, Waddington SN, Jayasinghe SN, Howe SJ. The differentiation and engraftment potential of mouse hematopoietic stem cells is maintained after bio-electrospray. Analyst, 2010 Jan;135(1):157-64. Epub 2009 Nov 13.
*Fang F, *Balch C, Schilder J, Breen T, Zhang S, Shen C, Li L, Kulesavage C, Synder AJ, Nephew KP, Matei D (*co-first authors). A Phase I and pharmacodynamic study of decitabine in combination with carboplatin in patients with recurrent, platinum-resistant, epithelial ovarian cancer. Cancer, 2010 Sep 1;116(17):4043-53.
Arias-Pulido H, Yun G, Lomo L, Joste NE, Lee SJ, Lara J, Prossnitz E, Cristofanilli M, Royce M. GPR30 and estrogen receptor expression: New insights into hormone dependence of inflammatory breast cancer. Breast Cancer Res Treat, 2010;123:51-8.
Huang GS, Brouwer-Visser J, Hebert TM, Kim CH, Ramirez MJ, Arias-Pulido H, Qualls CR, Lin J, Goldberg GL, Smith HO, Horwitz SB. Insulin-like growth factor 2 (IGF2) expression modulates Taxol resistance and is a candidate biomarker for reduced disease-free survival in ovarian cancer. Clin Cancer Res, 2010;16:2999-3010.
Clark KB. Arrhenius-kinetics evidence for quantum tunneling in microbial “social” decision rates. Commun Integr Biol, 2010; Nov 3(6): 540-4.
Clark KB. On classical and quantum error-correction in ciliate mate selection. Commun Integr Biol, 2010 Jul 3(4): 374-8.
Clark KB. Origins of learned reciprocity in solitary ciliates searching grouped ‘courting’ assurances at quantum efficiencies. BioSystems, 2010 Jan 99(1): 27-41.
Otto E*, Hurd T*, Airik R, Chaki M et al. Candidate Exome Capture Reveals Mutation of SDCCAG8 as Causing a Retinal-Renal Ciliopathy. Nat Genet, 2010;42(10):840-50. *Equally contributed to the study.
Ursini-Siegel J, Cory S, Zuo D, Hardy WR, Rexhepaj E, Lam S, Schade B, Jirstrom K, Bjur E, Piccirillo CA, Denardo D, Coussens LM, Brennan DJ, Gallagher WM, Park M, Pawson T, Hallett M, Muller WJ. Receptor tyrosine kinase signaling favors a protumorigenic state in breast cancer cells by inhibiting the adaptive immune response. Cancer Res, 2010 Oct 15;70(20):7776-87. Epub 2010 Oct 5.
Clark KB. Bose-Einstein condensates form in heuristics learned by ciliates deciding to signal ‘social’ commitments. BioSystems, 2010 Mar; 99(3): 167-78.
Hawkins BJ, Irrinki KM, Mallilankaraman K, Lien YC, Wang Y, Bhanumathy CD, Subbiah R, Ritchie MF, Soboloff J, Baba Y, Kurosaki T, Joseph SK, Gill DL, Madesh M. S-glutathionylation activates STIM1 and alters mitochondrial homeostasis. J Cell Biol, 2010;190 (3), 391-405.
Hawkins BJ, Levin MD, Doonan PJ, Petrenko NB, Davis CW, Patel VV, Madesh M. Mitochondrial complex II prevents hypoxic but not calcium- and proapoptotic Bcl-2 protein-induced mitochondrial membrane potential loss. J Biol Chem, 2010;285 (34), 26494-505.
Davis C, Hawkins BJ, Ramasamy S, Irrinki KM, Cameron BA, Islam KM, Daswani VP, Doonan PJ, Manevich Y, Madesh M. Nitration of the mitochondrial complex I subunit NDUFB8 elicits RIP1 and 3-mediated necrosis. Free Radic Biol Med, 2010;48, 306-17.
Lanahan AA, Hermans K, Claes F, Hamilton J, Zhuang Z, Giordano F, Carmeliet P and Simons M. VEGF receptor 2 endocytic trafficking regulates arterial morphogenesis. Developmental Cell, 2010;18(5): 713-724.
Sane KM, Mynderse M, LaLonde DT, Dean IS, Wojtkowiak JW, Fouad F, Borch RF, Reiners, JJ, Jr., Gibbs RA, Mattingly RR. A novel geranylgeranyl transferase inhibitor in combination with lovastatin inhibits proliferation and induces autophagy in STS-26T MPNST cells. Journal of Pharmacology and Experimental Therapeutics, 2010 Apr;333(1);23-33.
Gowder SJ, Devaraj H. A review on the nephrotoxicity of food flavor Cinnamaldehyde. Curr Bio Comp, 2010;6:106-117.
Gowder SJ, McMartin KE. Development of a primary culture system of rat kidney proximal tubule cells for transport and toxicity studies. J Ep Biol Pharm, 2010;3:15-19.
Vogel CW and Fritzinger DC. Cobra venom factor: Structure, function, and humanization for therapeutic complement depletion. Toxicon, 2010;56:1198-1222.
Ricard N, Bidart M, Mallet C, Lesca G, Giraud S, Prudent R, et al. Functional analysis of the BMP9 response of ALK1 mutants from HHT2 patients: a diagnostic tool for novel ACVRL1 mutations. Blood, 2010;116(9):1604-12.
Tirziu D, Giordano FJ, Simons M. Cell communications in the heart. Circulation, 2010;122:928-37. PMID: 20805439
2009
Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Parmigiani G, Kern SE, Velculescu VE, Kinzler KW, Vogelstein B, Eshleman JR, Goggins M, Klein AP. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science, 2009 Apr 10;324(5924):217.
Joshi G, Pradhan S, Mittal B. Role of the Estrogen Receptor (ESR1 PvuII and ESR1 325 C>G) and Progesterone Receptor (PROGINS) polymorphisms in genetic susceptibility to Migraine in a North Indian Population. Cephalalgia, 2009;30(3):311-320.
Wilkins JF & Godfrey-Smith P. Adaptationism and the adaptive landscape. Biology and Philosophy, 2009;24:199-214.
Shen X, Kim W, Fujiwara Y, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates Polycomb activity and self-renewal versus differentiation of stem cells. Cell, 2009 Dec 24;139(7):1303-14.
Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min, 2009 Sep 22;2(1):5.
Halley JD, Burden FR, Winkler DA. Stem cell decision making and critical-like exploratory networks. Stem Cell Res, 2009 May;2(3):165-77. Epub 2009 Mar 17. Review.
Lapenna S, Giordano A. Cell cycle kinases as therapeutic targets for cancer. Nat Rev Drug Discov, 2009 Jul;8(7):547-66.
Askland K, Read C, Moore JH. Pathway-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission. Hum Genet, 2009 Feb;125(1):63-79. Epub 2008 Dec 4.
Cai Y, Lux MW, Adam L, Peccoud J. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Computational Biology, 2009;5(10): e1000529.
Tarasova A, Winkler DA. Modelling atypical small molecule mimics of an important stem cell cytokine, thrombopoietin. ChemMedChem, 2009 Dec;4(12):2002-2011.
Yang Y-T, *Balch C, Kulp S, Mand MR, Nephew KP, *Chen C-S. (*co-corresponding authors). A rationally designed histone deacetylase inhibitor with distinct antitumor activity against ovarian cancer. Neoplasia, 2009 Jun;11(6):552-63, 3 p following 563.
Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MiRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of miRNA expression. Nucleic Acids Res, 2009 Jul;37(Web Server issue):W356-62.
Burden FR, Winkler DA. An optimal self-pruning neural network that performs nonlinear descriptor selection for QSAR. QSAR Comb. Sci, 2009;(28):1092–1097.
Swanson B, Fuerstenau-Sharp M, Stankewicz C, Meyer N, Ma J, Fiene S, Anson BD, Reil D, Wang W. Industrialized Production of Human iPS Cell-derived Cardiomyocytes. Soc. Biomol Sciences, 2009; Stem Cell Symposium.
Bryant S, Wyllie C, Palmer R, Heal R, Demmon J, Nicol S, Anson B, Rudy-Reil D, Ma J. Effects of isoprenaline on human stem cell derived cardiomyocytes. J Pharm Tox, 2009;60(2):219-220.
Gowder SJ, McMartin KE. Methods to evaluate the effect of ethanol on the folate analogue, fluorescein methotrexate uptake in human proximal tubular cells. Advan Pharmacol Sci, 2009;2009:291349.
Fritzinger DC, Hew BE, Thorne M, Pangburn M., Janssen BJ, Gros P, and Vogel CW. Functional characterization of human C3/cobra venom factor hybrid proteins for therapeutic complement depletion. Dev. Comp. Immunol, 2009;33:105-116.
2008
Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science, 2008 Sep 26;321(5897):1801-6.
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2007
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2006
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2005
Halley JD, Warden AC, Sadedin S, Li W. Rapid self-organized criticality: Fractal evolution in extreme environments. Phys Rev E Stat Nonlin Soft Matter Phys, 2004 Sep;70(3 Pt 2):036118. Epub 2004 Sep 28. Erratum in: Phys Rev E Stat Nonlin Soft Matter Phys, 2005 Feb;71(2 Pt 2):029901.
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2004
Zhang Y, Chittenden T, Simons M. Characterization of synectin expression and promoter activity. Gene, 2004 Nov 10;342(1):29-34.
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2003
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2002
Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA, 2002 Aug 6;99(16):10494-9.
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2001
Steppan CM, Bailey ST, Bhat S, Wright CM, Brown EJ, Banerjee RR, Patel HR, Ahima RS, and Lazar MA. The hormone resistin links obesity to diabetes. Nature, 2001;409:307-312.
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2000
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1999
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1998
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1997
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1995
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1994
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1993
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1992
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1991
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1989
Giordano A, Whyte P, Harlow E, Franza BR Jr, Beach D, Draetta G. A 60 kd cdc2-associated polypeptide complexes with the E1A proteins in adenovirus-infected cells. Cell, 1989 Sep 8;58(5):981-90.
Pei-Yu Chen, Lingfeng Qin, Guangxin Li, Jose Malagon-Lopez, Zheng Wang, Sonia Bergaya, Sharvari Gujja, Alexander W. Caulk, Sae-Il Murtada, Xinbo Zhang, Zhen W. Zhuang, Deepak A. Rao, Guilin Wang, Zuzana Tobiasova, Bo Jiang, Ruth R Montgomery, Lele Sun, Hongye Sun, Edward A. Fisher, Jeffrey R. Gulcher, Carlos Fernandez-Hernando, Jay D. Humphrey, George Tellides, Thomas W. Chittenden, Michael Simons. Smooth muscle cell reprogramming in aortic aneurysms. Cell Stem Cell, 2020 Apr 2;26(4):542-557.e11. doi: 10.1016/j.stem.2020.02.013 (featured article at NHLBI of NIH).
Michael Simons, Pei-Yu Chen, Thomas W. Chittenden. Resilience, disease and the age of single cell science. Aging, 2020 Feb 10;12(3):2028-2029. DOI: 10.18632/aging.
Guangxin Li, Mo Wang, Alexander W. Caulk, Nicholas A. Cilfone, Sharvari Gujja, Lingfeng Qin, Pei-Yu Chen, Zehua Chen, Sameh Yousef, Yang Jiao, Changshun He, Bo Jiang, Arina Korneva, Matthew R. Bersi, Guilin Wang, Xinran Liu, Sameet Mehta, Arnar Geirsson, Jeffrey R. Gulcher, Thomas W. Chittenden, Michael Simons, Jay D. Humphrey, George Tellides. Chronic mTOR activation induces a degradative smooth muscle cell phenotype. Journal of Clinical Investigation, 2020 Feb 10 DOI: 10.1172/JCI131048 (accompanying commissioned editorial).
2019
Pei-Yu Chen, Lingfeng Qin, Guangxin Li, Zheng Wang, James E. Dahlman, Jose Malagon-Lopez, Sharvari Gujja, Kevin J. Kauffman, Lele Sun, Hongye Sun, Xinbo Zhang, Binod Aryal, Alberto Canfran-Duque, Rebecca Liu, Pascal Kusters, Alfica Sehgal, Yang Jiao, Daniel G. Anderson, Jeffrey Gulcher, Carlos Fernandez-Hernando, Esther Lutgens, Martin A. Schwartz, Jordan S. Pober, Thomas W. Chittenden, George Tellides, and Michael Simons. Endothelial TGF-beta signaling drives vascular inflammation and atherosclerosis. Nature Metabolism, 2019 Aug 26 DOI: 10.1038/s42255-019-0102-3 (accompanying commissioned editorial).
Nicolas Ricard, Rizaldy Scott, Carmen Booth, Heino Velazquez, Nicholas Cilfone, Javier Baylon, Jeffrey Gulcher, Susan Quaggin, Thomas W. Chittenden, and Michael Simons. Endothelial ERK1/2 signaling maintains integrity of the quiescent endothelium. Journal of Experimental Medicine, 2019 Jun 13 DOI: 10.1084/jem.20182151 (accompanying commissioned editorial).
Javier Baylon, Nicholas Cilfone, Jeffrey Gulcher, Thomas W. Chittenden. Enhancing Retrosynthetic Reaction Prediction with Deep Learning using Multiscale Reaction Classification. Journal of Chemical Information and Modeling, 2019 Jan 14 DOI: 10.1021/acs.jcim.8b00801 (featured on cover).
2018
Kristin L. Ayers, Benjamin S. Glicksberg, Alastair S. Garfield3, Simonne Longerich4, Joseph A. White, Pengwei Yang, Lei Du, Thomas W. Chittenden, Jeffery R. Gulcher, Sophie Roy, Fred Fiedorek, Keith Gottesdiener, Sarah Cohen, Kari E. North, Eric E. Schadt, Shuyu D. Li1, Rong Chen, Lex H.T. Van der Ploeg. Melanocortin-4 receptor pathway dysfunction in obesity: Patient stratification aimed at MC4R agonist treatment. Journal of Clinical Endocrinology & Metabolism, 2018 May 2. doi: 10.1210/ jc.2018-00258.
Michael A. Lodato, Rachel E. Rodin, Craig L. Bohrson, Michael E. Coulter, Alison R. Barton, Minseok Kwon, Maxwell A. Sherman, Carl M. Vitzthum, Lovelace J. Luquette, Chandri Yandava, Pengwei Yang, Thomas W. Chittenden, Nicole E. Hatem, Steven C. Ryu, Mollie B. Woodworth, Peter J. Park, Christopher A. Walsh. Aging and neurodegeneration are associated with increased mutations in single human Neurons. Science, 2018 Feb 2;359(6375):555-559. doi: 10.1126/science.aao4426.
2017
Jennifer S. Fang, Brian G. Coon, Noelle Gillis, Zehua Chen, Jingyao Qiu, Thomas W. Chittenden, Janis M. Burt, Martin A. Schwartz, Karen K. Hirschi. Shear-induced Notch-Cx37-p27 axis arrests endothelial cell cycle to enable arterial specification. Nature Communications, 2017 Dec 15;8(1):2149.
Pengchun Yu, Joe K. Tung, Kerstin Wilhelm, Alexandra Dubrac, Tiago C. Alves, Jennifer S. Fang; Yi Xie, Jie Zhu, Zehua Chen, Frederik De Smet, Jiasheng Zhang, Suk-Won Jin, Lele Sun, Hongye Sun, Richard Kibbey, Karen K. Hirschi, Nissim Hay, Peter Carmeliet, Thomas W. Chittenden, Anne Eichmann, Michael Potente, Michael Simons. FGF-dependent metabolic control of vascular development. Nature, 2017 May 11;545(7653): 224-228.
2016
Banerjee, S. A biologically inspired model of distributed online communication supporting efficient search and diffusion of innovation. Interdisciplinary Description of Complex Systems, 2016;14(1):10-22.
Zehua Chen, Ryan P. Abo, Shannon T. Bailey, Jike Cui, Curt Balch, Jeffrey R. Gulcher, Thomas W. Chittenden. RNA Sequencing and Genetic Disease. Current Genetic Medicine Reports, 2016 Sep;4(3): 49-56.
Ephraim F. Trakhtenberg, Nam Pho, Kristina M. Holton, Thomas W. Chittenden, Jeffrey L. Goldberg, Lingsheng Dong. Cell types differ in global coordination of splicing and proportion of highly expressed genes. Scientific Reports, 2016 Aug 31;6:32249.
2015
Lodato MA, Woodworth MB, Lee S, Evrony GD, Mehta BK, Karger A, Lee S, Chittenden TW, D'Gama AM, Cai X, Luquette LJ, Lee E, Park PJ, Walsh CA. Somatic mutation in single human neurons tracks developmental and transcriptional history. Science, 2015 Oct 2;350(6256):94-8.
Corder EH, Khalsa KP. Rejuvenation by inhibiting TGF-β1/pSmad signaling. Oncotarget 2015 Jul 10;6(19):16790-1.
Galligan JT, Martinez-Noël G, Arndt V, Hayes S, Chittenden TW, Harper JW, Howley PM. Proteomic analysis and identification of cellular interactors of the giant ubiquitin ligase HERC2. Journal of Proteome Research, 2015 Feb 6;14(2):953-66. Epub 2014 Dec 15.
Balch C, Arias-Pulido H, Banerjee S, Lancaster AK, Clark KB, Perilstein M, Hawkins B, Rhodes J, Sliz P, Wilkins J, Chittenden TW. Science and technology consortia in US biomedical research: A paradigm shift in response to unsustainable academic growth. BioEssays, 2015 Feb;37(2):119-22. Epub 2014 Nov 12.
Bailey ST, Westerling T, and Brown M. Loss estrogen-regulated microRNA expression increases HER2 signaling and is predictive of poor outcome in luminal breast cancer. Cancer Research, 2015 Jan 11;75(2):436-45.
Bailey ST, Shin H, Westerling T, Liu XS, Brown M. Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proceedings of the National Academy of Sciences, 2015;109 (44): 18060-18065.
Vogel CW, Fritzinger DC, Gorsuch WB, Stahl GL. Complement Depletion with Humanized Cobra Venom Factor: Efficacy in Preclinical Models of Vascular Diseases. Thrombosis and Haemostasis, 2015;113:548-552.
Systems neuroscience in focus: from the human brain to the global brain? Kyriazis M. Front Syst Neurosci, 2015 Feb 6;9:7.
Trakhtenberg EF, Morkin MI, Patel KH, Fernandez SG, Sang A, Shaw P, Liu X, Wang Y, Mlacker GM, Gao H, Velmeshev D, Dombrowski SM, Vitek MP, Goldberg JL. N-terminal Set-ß protein isoform induces neuronal death. J Biol Chem, (In Press).
Andereggen L, Trakhtenberg EF, Yin Y, and Benowitz LI. Neuroinflammation: New Insights into Beneficial and Detrimental Functions. Editor: Samuel David. Inflammation and Optic Nerve Regeneration, 2015; (12):189-204.
Venkatesan RC and Plastino A. Hellmann-Feynman connection for the relative Fisher information. Annals of Physics, (In Press).
2014
Venkatesan RC and Plastino A. Legendre transform structure and extremal properties of the relative Fisher information. Physics Letters A, 2014 April 4;378(20):1341–1345.
Sinadinos C, Valles-Ortega J, Boulan L, Solsona E, Tevy MF, Marquez M, Duran J, Lopez-Iglesias C, Calbó J, Blasco E, Pumarola M, Milán M, Guinovart JJ. Neuronal glycogen synthesis contributes to physiological aging. Aging Cell, 2014 Oct;13(5):935-45.
Technological integration and hyperconnectivity: Tools for promoting extreme human lifespans. Kyriazis M. Complexity, 2014 doi: 10.1002/cplx.21626.
The impracticality of biomedical rejuvenation therapies: translational and pharmacological barriers. Kyriazis M. Rejuvenation Res, 2014 Aug;17(4):390-6.
Reversal of informational entropy and the acquisition of germ-like immortality by somatic cells. Kyriazis M. Curr Aging Sci, 2014;7(1):9-16. Review.
Saez I, Duran J, Sinadinos C, Beltran A, Yanes O, Tevy MF, Martínez-Pons C, Milán M, Guinovart JJ. Neurons have an active glycogen metabolism that contributes to tolerance to hypoxia. J Cereb Blood Flow Metab, 2014 Jun;34(6):945-55.
Joshi G, Chi Y, Huang Z, Wang Y. Aβ-induced Golgi fragmentation in Alzheimer's disease enhances Aβ production. Proc Natl Acad Sci USA, 2014;111(13):E1230-9.
Trakhtenberg EF, Wang Y, Morkin MI, Fernandez SG, Mlacker GM, Shechter JM, Liu X, Patel KH, Lapins A, Yang S, Dombrowski SM, and Goldberg JL. Regulating Set-β’s subcellular localization toggles its function between inhibiting and promoting axon growth and regeneration. Journal of Neuroscience, 2014;34:7361–7374.
Joe MK, Kwon HS, Cojocaru R, Tomarev SI. Myocilin regulates cell proliferation and survival. J Biol Chem, 2014 Feb 22.
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Vogel CW and Fritzinger DC. Cobra Venom Factor: The Unique Component of Cobra Venom that Activates the Complement System. Toxinology, Snake Venoms, (Gopalakrishnakone, P. ed) 2014 Springer.
Vogel CW, Finnegan PW, Fritzinger DC. Humanized Cobra Venom Factor: Structure, Activity, and Therapeutic Efficacy in Preclinical Disease Models. Mol. Immunol, 2014;61: 191-203.
Baeyens N, Mulligan-Kehoe MJ, Corti F, Simon DD, Ross TD, Rhodes JM, et al. Syndecan 4 is required for endothelial alignment in flow and atheroprotective signaling. Proc Natl Acad Sci USA, 2014; 111(48):17308-13.
Ricard N, Tu L, Le Hiress M, Huertas A, Phan C, Thuillet R, et al. Increased pericyte coverage mediated by endothelial-derived fibroblast growth factor-2 and interleukin-6 is a source of smooth muscle-like cells in pulmonary hypertension. Circulation, 2014;129(15):1586-97.
Stacy MR, Yu DY, Maxfield MW, Jaba IM, Jozwik BP, Zhuang ZW, Lin BA, Hawley CL, Caracciolo CM, Pal P, Tirziu D, Sampath S, Sinusas AJ. A multimodality imaging approach for serial assessment of regional changes in lower extremity arteriogenesis and tissue perfusion in a porcine model of peripheral arterial disease. Circ Cardiovasc Imaging, 2014;7:92-99.
Nallaseth FS. Is There a Role for an Evolutionary Genetics Based Rational Health Policy In Global Biomedical, Health and Economic Policies? Mol Biol, 2014 3:1000e118.
2013
Ma W, Cojocaru R, Gotoh N, Gieser L, Villasmil R, Cogliati T, Swaroop A, Wong WT. Gene expression changes in aging retinal microglia: relationship to microglial support functions and regulation of activation. Neurobiol Aging, 2013 Oct;34(10):2310-21.
King IF, Yandava CN, Mabb AM, Hsiao JS, Huang HS, Pearson BL, Calabrese JM, Starmer J, Parker JS, Magnuson T, Chamberlain SJ, Philpot BD, Zylka MJ. Topoisomerases facilitate transcription of long genes linked to autism. Nature, 2013 Sep 5;501(7465):58-62.
Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP Jr, Buitendijk GH, Sim X, Weeks DE, Guymer RH, Merriam JE, Francis PJ, Hannum G, Agarwal A, Armbrecht AM, Audo I, Aung T, Barile GR, Benchaboune M, Bird AC, Bishop PN, Branham KE, Brooks M, Brucker AJ, Cade WH, Cain MS, Campochiaro PA, Chan CC, Cheng CY, Chew EY, Chin KA, Chowers I, Clayton DG, Cojocaru R, Conley YP, Cornes BK, Daly MJ, Dhillon B, Edwards AO, Evangelou E, Fagerness J, Ferreyra HA, Friedman JS, Geirsdottir A, George RJ, Gieger C, Gupta N, Hagstrom SA, Harding SP, Haritoglou C, Heckenlively JR, Holz FG, Hughes G, Ioannidis JP, Ishibashi T, Joseph P, Jun G, Kamatani Y, Katsanis N, N Keilhauer C, Khan JC, Kim IK, Kiyohara Y, Klein BE, Klein R, Kovach JL, Kozak I, Lee CJ, Lee KE, Lichtner P, Lotery AJ, Meitinger T, Mitchell P, Mohand-Saïd S, Moore AT, Morgan DJ, Morrison MA, Myers CE, Naj AC, Nakamura Y, Okada Y, Orlin A, Ortube MC, Othman MI, Pappas C, Park KH, Pauer GJ, Peachey NS, Poch O, Priya RR, Reynolds R, Richardson AJ, Ripp R, Rudolph G, Ryu E, Sahel JA, Schaumberg DA, Scholl HP, Schwartz SG, Scott WK, Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson H, Sturgill-Short GM, Takahashi A, Tosakulwong N, Truitt BJ, Tsironi EE, Uitterlinden AG, van Duijn CM, Vijaya L, Vingerling JR, Vithana EN, Webster AR, Wichmann HE, Winkler TW, Wong TY, Wright AF, Zelenika D, Zhang M, Zhao L, Zhang K, Klein ML, Hageman GS, Lathrop GM, Stefansson K, Allikmets R, Baird PN, Gorin MB, Wang JJ, Klaver CC, Seddon JM, Pericak-Vance MA, Iyengar SK, Yates JR, Swaroop A, Weber BH, Kubo M, Deangelis MM, Léveillard T, Thorsteinsdottir U, Haines JL, Farrer LA, Heid IM, Abecasis GR; AMD Gene Consortium. Seven new loci associated with age-related macular degeneration. Nat Genet, 2013 Apr;45(4):433-9, 439e1-2.
Tevy MF, Giebultowicz J, Pincus Z, Mazzoccoli G, Vinciguerra M. Aging signaling pathways and circadian clock-dependent metabolic derangements. Trends Endocrinol Metab, 2013 May;24(5):229-37.
Gupta K, Madan E, Sayyid M, Arias-Pulido H, Moreno E, Kuppusamy P, Gogna R. Oxygen regulates Molecular mechanisms of Cancer. Cancer Metastasis Rev, 2013 Dec 15. [Epub ahead of print].
Altobelli G*¶, Bogdarina IG*, Stupka E, Clark AJ, Langley-Evans S. Genome-Wide Methylation and Gene Expression Changes in Newborn Rats following Maternal Protein Restriction and Reversal by Folic Acid. PLoS One, 2013 Dec 23; 8: e82989. *Equal contributors, ¶corresponding author.
Lepoivre C*, Belhocine M*, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau JC, Puthier D, Spicuglia S. Divergent transcription is associated with promoters of transcriptional regulators. BMC Genomics, 2013 Dec 23;14(1):914.*Equal contributors.
Clark KB, Hassert DL. Undecidability and opacity of metacognition in animals and humans. Front Psychol, 2013;4:171.
Clark KB. Ciliates learn to diagnose and correct classical error syndromes in mating strategies. Front Microbiol, 2013;4:229.
Clark KB, Eisenstein EM. Targeting host store-operated Ca2+ release to attenuate viral infections. Curr Top Med Chem, 2013;13(16):1916-1932.
Clark KB. New therapeutic bearings for repositioned drugs. Curr Top Med Chem, 2013;13(18):2281-2282.
Clark KB, Eisenstein EM, Krahl SE. Calcium antagonists: a ready prescription for treating infectious diseases? Curr Top Med Chem, 2013;13(18):2291-2305.
Clark KB. Biotic activity of Ca2+-modulating nontraditional antimicrobial and -viral agents. Front Microbiol, 2013;4:381.
Balch C, Nephew KP. Epigenetic targeting therapies to overcome chemotherapy resistance. Adv Exp Med Biol, 2013;754:285-311.
Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS ONE, 2013 May 31;8(5): e64832.
Jayasinghe SN. Cell electrospinning: a novel tool for functionalising fibres, scaffolds and membranes with living cells and other advanced materials for regenerative biology and medicine. Analyst, 2013 Mar 18;138(8):2215-23.
Morteza A, Nakhjavani M, Asgarani F, Carvalho FL, Karimi R, Esteghamati A.Inconsistency in albuminuria predictors in type 2 diabetes: a comparison between neural network and conditional logistic regression. Transl Res, 2013;161:397-405.
Morteza A, Nakhjavani M, Asgarani F, Ghaneei A, Esteghamati A, Mirmiranpour H. The lost correlation between leptin and CRP in type 2 diabetes. Eur Cytokine Netw, 2013;24:53-9.
Morteza A, Nakhjavani M, Larry M, Nargesi AA, Esteghamati A. Heat shock protein 70 and albuminuria in patients with type 2 diabetes: a matched case control study. Cell Stress Chaperones, 2013 May 17.
Nallaseth FS, Anderson S. A screen for over-secretion of proteins by yeast based on a dual component cellular phosphatase and immuno-chromogenic stain for exported bacterial alkaline phosphatase reporter. Microb Cell Fact, 2013 Apr 19;12:36.
Corti F, Finetti F, Ziche M, Simons M. The syndecan-4/protein kinase Calpha pathway mediates prostaglandin E2-induced extracellular regulated kinase (ERK) activation in endothelial cells and angiogenesis in vivo. J Biol Chem, 2013; 288(18):12712-21.
Solito R, Corti F, Chen CH, Mochly-Rosen D, Giachetti A, Ziche M, et al. Mitochondrial aldehyde dehydrogenase-2 activation prevents beta-amyloid-induced endothelial cell dysfunction and restores angiogenesis. J Cell Sci, 2013;126(Pt 9):1952-61.
Jaba IM, Zhuang ZW, Li N, Jiang Y, Martin K, Sinusas AJ, Papademetris X, Simons M, Sessa W, Young L, Tirziu D. NO triggers RGS4 degradation to coordinate angiogenesis and cardiomyocyte growth. J Clin Invest, 2013;123:1718-1731.
2012
Scannell JW, Blanckley A, Boldon H, Warrington B. Diagnosing the decline in pharmaceutical R&D efficiency. Nat Rev Drug Discov, 2012 Mar 1;11(3):191-200.
Human Microbiome Project Consortium. A framework for human microbiome research. Nature, 2012 Jun 13;486(7402):215-21.
Mathew MJ, Subramanian G, Nguyen TT, Robert C, Mediannikov O, Fournier PE, Raoult D. J Bacteriol. Genome Sequence of Diplorickettsia massiliensis, an Emerging Ixodes ricinus-Associated Human Pathogen. 2012 Jun 194(12):3287.
Martinez-Noël G, Galligan JT, Sowa ME, Arndt V, Overton TM, Harper JW, Howley PM. Identification and proteomic analysis of distinct UBE3A/E6AP protein complexes. Molecular Cell Biology, 2012;32(15):3095-3106.
Duran J*, Tevy MF*, Garcia-Rocha M, Calbó J, Milán M, Guinovart JJ. Deleterious effects of neuronal accumulation of glycogen in flies and mice. EMBO Mol Med, 2012 Aug;4(8):719-29.
Qin Y, Xu J, Aysola K, Oprea G, Reddy A, Matthews R, Okoli J, Cantor A, Grizzle WE, Partridge EE, Reddy ES, Landen C, Rao VN. BRCA1 proteins regulate growth of ovarian cancer cells by tethering Ubc9. Am J Cancer Res, 2012;2(5):540-8.
Lutz D*, Wolters-Eisfeld G*, Joshi G*, Djogo N, Jakovcevski I, Schachner M, Kleene R. Generation and nuclear translocation of sumoylated transmembrane fragment of cell adhesion molecule L1. Journal of Biological Chemistry, 2012;287(21):17161-75 (*Equal contribution).
Trakhtenberg EF and Goldberg JL. The role of serotonin in axon and dendrite growth. International Review of Neurobiology: Axon Growth and Regeneration, 2012;106 (4):105-126.
Goldberg JL and Trakhtenberg EF. International Review of Neurobiology: Axon Growth and Regeneration, 2012 Volumes 106-1077: Academic Press.
Corredor RG, Trakhtenberg EF, Pita-Thomas W, Jin X, Hu Y, and Goldberg JL. Soluble adenylyl cyclase activity is necessary for retinal ganglion cell survival and axon growth. Journal of Neuroscience, 2012;32:7734-7744.
Trakhtenberg EF and Goldberg JL. Epigenetic regulation of axon and dendrite growth. Frontiers in Neuroscience, 2012; 5:1-8.
Sharma YV, Cojocaru RI, Ritter LM, Khattree N, Brooks M, Scott A, Swaroop A, Goldberg AF. Protective gene expression changes elicited by an inherited defect in photoreceptor structure. PLoS One, 2012;7(2):e31371.
Roger JE, Ranganath K, Zhao L, Cojocaru RI, Brooks M, Gotoh N, Veleri S, Hiriyanna A, Rachel RA, Campos MM, Fariss RN, Wong WT, Swaroop A.Preservation of cone photoreceptors after a rapid yet transient degeneration and remodeling in cone-only Nrl-/- mouse retina. J Neurosci, 2012 Jan 11;32(2):528-41.
Saravanamuthu SS, Le TT, Gao CY, Cojocaru RI, Pandiyan P, Liu C, Zhang J, Zelenka PS, Brown NL. Conditional ablation of the Notch2 receptor in the ocular lens. Dev Biol, 2012 Feb 15;362(2):219-29.
Fanchiang SS, Cojocaru R, Othman M, Khanna R, Brooks MJ, Smith T, Tang X, Maricic I, Swaroop A, Kumar V. Global expression profiling of peripheral Qa-1-restricted CD8αα+TCRαβ+ regulatory T cells reveals innate-like features: implications for immune-regulatory repertoire. Hum Immunol, 2012 Mar;73(3):214-22.
Clark KB. Bioreaction quantum computing without quantum diffusion. NeuroQuantol, 2012;10(4): 646-54.
Guo W, Schafer S, Greaser ML, Radke MH, Liss M, Govindarajan T, Maatz H, Schulz H, Li S, Parrish AM, et al. RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nature Medicine, 2012;18:766–773.
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Atai NA, Ryan SD, Kothary R, Breakefield XO, Nery FC. Untethering the nuclear envelope and cytoskeleton - biologically distinct dystonias arising from a common cellular dysfunction. Int J Cell Biol, 2012;2012:634214.
Xu J, Shao Z, Glass K, Bauer DE, Pinello L, van Handel B, Hou S, Stamatoyannopoulos JA, Mikkola HKA, Yuan GC, Orkin SH. Combinatorial Assembly of Developmental Stage Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis. Developmental Cell, 2012 Oct 16;23(4):796-811.
Andreu N, Thomas D, Saraiva L, Ward N, Gustafsson K, Jayasinghe SN, Robertson BD. In vitro and in vivo interrogation of bio-sprayed cells. Small, 2012 Aug 20;8(16):2495-500. Epub 2012 May 31.
Teng M, Wang Y, Kim S, Li L, Shen C, Wang G, Liu Y, Huang T H-M, Nephew KP, Balch C. Empirical Bayes model comparisons for differential methylation analysis. Compt Funct Genomics, 2012;376706.
Yo Y-T, Lin Y-W, Wang Y-C, Balch C, Huang R-L, Lee H-Y, Chang MWY, Sytwu H-K, Cheng C-K, Chang C-C, Nephew KP, Huang T, Yu M-H, Lai H-C. Growth inhibition of ovarian tumor-initiating cells by niclosamide. Mol Cancer Ther, 2012 Aug;11(8):1703-12.
Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH. The Cancer Genome Atlas Research Network. Integrated Analyses of microRNAs Demonstrate Their Widespread Influence on Gene Expression in High-Grade Serous Ovarian Carcinoma. PLoS ONE, 2012;7(3):e34546. Epub 2012 Mar 29.
*Balch C, Naegeli K, Nam S, Ballard B, Hyslop A, Melki C, Reilly E, Hur M-W, *Nephew KP (*co-corresponding authors). A unique histone deacetylase inhibitor alters microRNA expression and signal transduction in chemoresistant ovarian cancer cells. Cancer Biol Ther, 2012 Jun;13(8):681-93.
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Krahl SE, Clark KB. Vagus nerve stimulation for epilepsy: A review of central mechanisms. Surg Neurol Int, 2012;3(4): S255-9.
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Locasale JW. Metabolic rewiring drives resistance to targeted cancer therapy. Mol Syst Biol, 2012 Jul 17;8:597.
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Chaher N, Arias-Pulido H, Terki N, Qualls C, Bouzid K, Verschraegen C, Wallace AN, Royce M. Molecular and epidemiological characteristics of inflammatory breast cancer in Algerian patients. Breast Cancer Res Treat, 2012;131:437-44.
Arias-Pulido H, Chaher N, Gong Y, Qualls C, Vargas J, Lomo L, Terki N, Bouzid K, Royce M. Stromal VEGF-A preditcs worse breast cancer-specific and disease-free survival in inflammatory breast cancer. BMC Cancer, 2012;12:298.
Ramos E, Ruchala P, Goodnough JB, Kautz L, Preza GC, Nemeth E, Ganz T. Minihepcidins prevent iron overload in a hepcidin-deficient mouse model of severe hemochromatosis. Blood, 2012 [Epub ahead of print].
Xu J, Ruchala YP, Ebenstein, Li JJ, Weiss S. Stable, compact, bright biofunctional quantum dots with improved peptide coating. J Phys Chem B, 2012;116(36): 11370–11378.
Khachatoorian R, Arumugaswami V, Ruchala P, Raychaudhuri S, Maloney EM, Miao E, Dasgupta A, French SW. A cell-permeable hairpin peptide inhibits hepatitis C viral nonstructural protein 5A mediated translation and virus production. Hepatology, 2012; 55(6):1662-72.
Doss M, Ruchala P, Tecle T, Gantz D, Hartshorn A, Crouch EC, Luong H, Micewicz ED, Lehrer RI, Hartshorn KL. Hapivirins and diprovirins: novel Θ-defensin analogs with potent activity against influenza A virus. J Immunol, 2012;188(6):2759-2768.
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Deharvengt SJ, Tse D, Sideleva O, McGarry C, Gunn JR, Longnecker DS, Carriere C, Stan RV. PV1 downregulation via shRNA inhibits the growth of pancreatic adenocarcinoma xenografts. J Cell Mol Med, 2012 May 9.
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Elfenbein A, Lanahan A, Zhou TX, Yamasaki A, Tkachenko E, Matsuda M and Simons M. Syndecan 4 regulates FGFR1 signaling in endothelial cells by directing macropinocytosis. Sci Signal, 2012 May 8;5(223):ra36.
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Tirziu D, Jaba IM, Yu P, Larrivée B, Coon BG, Cristofaro B, Zhuang ZW, Lanahan AA, Schwartz MA, Eichmann A, Simons M. Endothelial NFκB -dependent regulation of arteriogenesis and branching. Circulation, 2012;126:2589-2600. PMID: 23091063
2011
Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The genetic landscape of the childhood cancer medulloblastoma. Science, 2011 Jan 28;331(6016):435-9.
Galligan JT, Marchetti SE, Kennell, JC. Reverse transcription of the pFOXC mitochondrial retroplasmids of Fusarium oxysporum is protein primed. Mobile DNA, 2011 Jan 21;2(1):1
Qin Y, Xu J, Aysola K, Begum N, Reddy V, Chai Y, Grizzle WE, Partridge EE, Reddy ES, Rao VN. Ubc9 mediates nuclear localization and growth suppression of BRCA1 and BRCA1a proteins. J Cell Physiol, 2011 Dec;226(12):3355-67.
Trakhtenberg EF and Goldberg JL. Neuroimmune Communication. Science, 2011 6052:47-48.
Taccioli C, Tegner J, Maselli V, Gomez-Cabrero D, Altobelli G, et al. ParkDB: a Parkinson's disease gene expression database. Database (Oxford) 2011: bar007.
Wilkins JF. Genomic imprinting and conflict-induced decanalization. Evolution, 2011 Feb;65(2):537-53.
Ùbeda F & Wilkins JF. The Red Queen theory of recombination hotspots. J. Evol. Biol, 2011 Mar;24(3):541-53.
Locasale JW, Cantley LC. Metabolic flux and the regulation of mammalian cell growth. Cell Metab, 2011 Oct 5;14(4):443-51.
Locasale JW, Grassian AR, Cantley LC and Vander Heiden MG, et al. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis. Nature Genetics, 2011 Jul 31;43(9):869-74.
Nery FC, Armata IA, Farley JE, Cho JA, Yaqub U, Chen P, da Hora CC, Wang Q, Tagaya M, Klein C, Tannous B, Caldwell KA, Caldwell GA, Lencer WI, Ye Y, Breakefield XO. TorsinA participates in endoplasmic reticulum-associated degradation. Nat Commun, 2011 Jul 12;2:393.
Guo W, Greaser M, Li S, Schulz H, Saar K, Radke M, Hacker TA, Saupe KW, Vakeel P, Govindarajan T, et al. A novel Splicing Factor that Affects Titin Alternative Splicing. Biophys. J, 2011;100:287a.
Ball DA, Marchand J, Poulet M, Baumann WT, Chen KC, Tyson JJ, Peccoud J. Oscillatory Dynamics of Cell Cycle Proteins in Single Yeast Cells Analyzed by Imaging Cytometry. PLoS ONE, 2011;6(10): 12.
Chaki M, Hoefele J, Allen S, Ramaswami G et al. Genotype-phenotype correlation in 440 individuals with NPHP-related ciliopathies. Kidney Int, 2011;80(11):1239-45.
Hu Y, Scully R, Sobhian B, Xie A, Shestakova E, Livingston DM. RAP80-directed tuning of BRCA1 homologous recombination function at ionizing radiation-induced nuclear foci. Genes Dev, 2011;25(7): 685-700.
Heeringa S*, Chernin G*, Chaki M, Zhou W et al. COQ6 mutations cause nephrotic syndrome with sensorineural deafness in humans, concurrent with increased apoptosis. J Clin Invest, 2011;21(5):2013-24. *Equally contributed to the study.
Chaki M, Sengupta M, Mondal M, Bhattacharyya A et al. Molecular and functional studies on Tyrosinase variants: An implication towards Oculocutaneous Albinism type 1 (OCA1) among Indians. J Invest Dermatol, 2011;131(1):260-2
Hu T, Sinnott-Armstrong NA, Kiralis JW, Andrew AS, Karagas MR, Moore JH. Characterizing genetic interactions in human disease association studies using statistical epistasis networks. BMC Bioinformatics, 2011 Sep 12;12:364.
Preza GC, Ruchala P, Pinon R, Ramos E, Qiao B, Peralta MA, Sharma S, Waring AJ, Ganz T, Nemeth E. Minihepcidins are rationally designed small peptides that mimic hepcidin activity in mice and may be useful for the treatment of iron overload. J Clin Invest, 2011;121(12):4880-4888.
Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau JC, Ferrier P, Spicuglia S.
H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J, 2011 Aug 16;30(20):4198-210.
Tse D, Armstrong DA, Oppenheim A, Kuksin D, Norkin L, Stan RV. Plasmalemmal vesicle associated protein (PV1) modulates SV40 virus infectivity in CV-1 cells. Biochem Biophys Res Commun, 2011 Aug 26; 412(2):220-5.
Stitham J, Arehart E, Elderon L, Gleim SR, Douville K, Kasza Z, Fetalvero K, Mackenzie T, Robb J, Martin KA, and Hwa J.
Comprehensive biochemical analysis of rare prostacyclin receptor variants: Study of association of signaling with coronary artery obstruction. J Biol Chem, 2011;286(9): 7060-69.
Ung P, Winkler, DA. Tripeptide motifs in biology as drug targets. J. Med. Chem, 2011;(54): 1111–1125.
Andrecut M, Winkler DA, Huang S, Halley JD. A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity. PLoS ONE, 2011;6(5): e19358.
Wijffels G, Johnson WMP, Oakley A, Turner K, Epa VC, Briscoe S, Polley M, Liepa AJ, Hofmann A, Buchardt J, Christensen C, Prosselkov P, Dalrymple B, Alewood P, Jennings P, Dixon NE, Winkler DA. Binding inhibitors of the bacterial sliding clamp by design. J. Med. Chem, 2011;54 (13): 4831-4838.
Tarasova A, Haylock D, Winkler DA. Principal signalling complexes in haematopoiesis: structural aspects and mimetic discovery. Cytokine Growth Factor Rev, 2011 Aug;22(4):231-53.
Wojtkowiak JW*, Sane KM*, Kleinman M, Sloane BF, Reiners, JJ, Jr., Mattingly RR. Aborted autophagy and non-apoptotic death induced by farnesyl transferase inhibitor and lovastatin. Journal of Pharmacology and Experimental Therapeutics, 2011 Apr;337(1);65-74 *Equally contributing authors.
Corti F, Olson KE, Marcus AJ, Levi R. The Expression Level of Ecto-NTP Diphosphohydrolase1/CD39 Modulates Exocytotic and Ischemic Release of Neurotransmitters in a Cellular Model of Sympathetic Neurons. J Pharmacol Exp Ther, 2011;337(2):524-32.
2010
Chittenden TW, Pak J, Rubio R, Cheng H, Holton K, Prendergast N, Glinskii V, Cai Y, Culhane A, Bentink S, Schwede M, Mar JC, Howe EA, Aryee M, Sultana R, Lanahan AA, Taylor JM, Holmes C, Hahn WC, Zhao JJ, Iglehart JD, Quackenbush J. Therapeutic Implications of GIPC1 Silencing in Cancer. PLoS ONE, 2010 Dec;5(12):e15581.
Nonlinear stimulation and hormesis in human aging: practical examples and action mechanisms. Kyriazis M. Rejuvenation Res, 2010 Aug;13(4):445-52.
Kleene R*, Mzoughi M*, Joshi G, Kalus I, Bormann U, Schulze, Xiao M , Dityatev A, and Schachner M. NCAM-induced neurite outgrowth depends on binding of calmodulin to NCAM and on nuclear import of NCAM and fak fragments. Journal of Neuroscience, 2010;30(32):10784-98 (*Equal contribution).
Bartolovic K, Mongkoldhumrongkul N, Waddington SN, Jayasinghe SN, Howe SJ. The differentiation and engraftment potential of mouse hematopoietic stem cells is maintained after bio-electrospray. Analyst, 2010 Jan;135(1):157-64. Epub 2009 Nov 13.
*Fang F, *Balch C, Schilder J, Breen T, Zhang S, Shen C, Li L, Kulesavage C, Synder AJ, Nephew KP, Matei D (*co-first authors). A Phase I and pharmacodynamic study of decitabine in combination with carboplatin in patients with recurrent, platinum-resistant, epithelial ovarian cancer. Cancer, 2010 Sep 1;116(17):4043-53.
Arias-Pulido H, Yun G, Lomo L, Joste NE, Lee SJ, Lara J, Prossnitz E, Cristofanilli M, Royce M. GPR30 and estrogen receptor expression: New insights into hormone dependence of inflammatory breast cancer. Breast Cancer Res Treat, 2010;123:51-8.
Huang GS, Brouwer-Visser J, Hebert TM, Kim CH, Ramirez MJ, Arias-Pulido H, Qualls CR, Lin J, Goldberg GL, Smith HO, Horwitz SB. Insulin-like growth factor 2 (IGF2) expression modulates Taxol resistance and is a candidate biomarker for reduced disease-free survival in ovarian cancer. Clin Cancer Res, 2010;16:2999-3010.
Clark KB. Arrhenius-kinetics evidence for quantum tunneling in microbial “social” decision rates. Commun Integr Biol, 2010; Nov 3(6): 540-4.
Clark KB. On classical and quantum error-correction in ciliate mate selection. Commun Integr Biol, 2010 Jul 3(4): 374-8.
Clark KB. Origins of learned reciprocity in solitary ciliates searching grouped ‘courting’ assurances at quantum efficiencies. BioSystems, 2010 Jan 99(1): 27-41.
Otto E*, Hurd T*, Airik R, Chaki M et al. Candidate Exome Capture Reveals Mutation of SDCCAG8 as Causing a Retinal-Renal Ciliopathy. Nat Genet, 2010;42(10):840-50. *Equally contributed to the study.
Ursini-Siegel J, Cory S, Zuo D, Hardy WR, Rexhepaj E, Lam S, Schade B, Jirstrom K, Bjur E, Piccirillo CA, Denardo D, Coussens LM, Brennan DJ, Gallagher WM, Park M, Pawson T, Hallett M, Muller WJ. Receptor tyrosine kinase signaling favors a protumorigenic state in breast cancer cells by inhibiting the adaptive immune response. Cancer Res, 2010 Oct 15;70(20):7776-87. Epub 2010 Oct 5.
Clark KB. Bose-Einstein condensates form in heuristics learned by ciliates deciding to signal ‘social’ commitments. BioSystems, 2010 Mar; 99(3): 167-78.
Hawkins BJ, Irrinki KM, Mallilankaraman K, Lien YC, Wang Y, Bhanumathy CD, Subbiah R, Ritchie MF, Soboloff J, Baba Y, Kurosaki T, Joseph SK, Gill DL, Madesh M. S-glutathionylation activates STIM1 and alters mitochondrial homeostasis. J Cell Biol, 2010;190 (3), 391-405.
Hawkins BJ, Levin MD, Doonan PJ, Petrenko NB, Davis CW, Patel VV, Madesh M. Mitochondrial complex II prevents hypoxic but not calcium- and proapoptotic Bcl-2 protein-induced mitochondrial membrane potential loss. J Biol Chem, 2010;285 (34), 26494-505.
Davis C, Hawkins BJ, Ramasamy S, Irrinki KM, Cameron BA, Islam KM, Daswani VP, Doonan PJ, Manevich Y, Madesh M. Nitration of the mitochondrial complex I subunit NDUFB8 elicits RIP1 and 3-mediated necrosis. Free Radic Biol Med, 2010;48, 306-17.
Lanahan AA, Hermans K, Claes F, Hamilton J, Zhuang Z, Giordano F, Carmeliet P and Simons M. VEGF receptor 2 endocytic trafficking regulates arterial morphogenesis. Developmental Cell, 2010;18(5): 713-724.
Sane KM, Mynderse M, LaLonde DT, Dean IS, Wojtkowiak JW, Fouad F, Borch RF, Reiners, JJ, Jr., Gibbs RA, Mattingly RR. A novel geranylgeranyl transferase inhibitor in combination with lovastatin inhibits proliferation and induces autophagy in STS-26T MPNST cells. Journal of Pharmacology and Experimental Therapeutics, 2010 Apr;333(1);23-33.
Gowder SJ, Devaraj H. A review on the nephrotoxicity of food flavor Cinnamaldehyde. Curr Bio Comp, 2010;6:106-117.
Gowder SJ, McMartin KE. Development of a primary culture system of rat kidney proximal tubule cells for transport and toxicity studies. J Ep Biol Pharm, 2010;3:15-19.
Vogel CW and Fritzinger DC. Cobra venom factor: Structure, function, and humanization for therapeutic complement depletion. Toxicon, 2010;56:1198-1222.
Ricard N, Bidart M, Mallet C, Lesca G, Giraud S, Prudent R, et al. Functional analysis of the BMP9 response of ALK1 mutants from HHT2 patients: a diagnostic tool for novel ACVRL1 mutations. Blood, 2010;116(9):1604-12.
Tirziu D, Giordano FJ, Simons M. Cell communications in the heart. Circulation, 2010;122:928-37. PMID: 20805439
2009
Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Parmigiani G, Kern SE, Velculescu VE, Kinzler KW, Vogelstein B, Eshleman JR, Goggins M, Klein AP. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science, 2009 Apr 10;324(5924):217.
Joshi G, Pradhan S, Mittal B. Role of the Estrogen Receptor (ESR1 PvuII and ESR1 325 C>G) and Progesterone Receptor (PROGINS) polymorphisms in genetic susceptibility to Migraine in a North Indian Population. Cephalalgia, 2009;30(3):311-320.
Wilkins JF & Godfrey-Smith P. Adaptationism and the adaptive landscape. Biology and Philosophy, 2009;24:199-214.
Shen X, Kim W, Fujiwara Y, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates Polycomb activity and self-renewal versus differentiation of stem cells. Cell, 2009 Dec 24;139(7):1303-14.
Greene CS, Penrod NM, Kiralis J, Moore JH. Spatially uniform ReliefF (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min, 2009 Sep 22;2(1):5.
Halley JD, Burden FR, Winkler DA. Stem cell decision making and critical-like exploratory networks. Stem Cell Res, 2009 May;2(3):165-77. Epub 2009 Mar 17. Review.
Lapenna S, Giordano A. Cell cycle kinases as therapeutic targets for cancer. Nat Rev Drug Discov, 2009 Jul;8(7):547-66.
Askland K, Read C, Moore JH. Pathway-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission. Hum Genet, 2009 Feb;125(1):63-79. Epub 2008 Dec 4.
Cai Y, Lux MW, Adam L, Peccoud J. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Computational Biology, 2009;5(10): e1000529.
Tarasova A, Winkler DA. Modelling atypical small molecule mimics of an important stem cell cytokine, thrombopoietin. ChemMedChem, 2009 Dec;4(12):2002-2011.
Yang Y-T, *Balch C, Kulp S, Mand MR, Nephew KP, *Chen C-S. (*co-corresponding authors). A rationally designed histone deacetylase inhibitor with distinct antitumor activity against ovarian cancer. Neoplasia, 2009 Jun;11(6):552-63, 3 p following 563.
Nam S, Li M, Choi K, Balch C, Kim S, Nephew KP. MiRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of miRNA expression. Nucleic Acids Res, 2009 Jul;37(Web Server issue):W356-62.
Burden FR, Winkler DA. An optimal self-pruning neural network that performs nonlinear descriptor selection for QSAR. QSAR Comb. Sci, 2009;(28):1092–1097.
Swanson B, Fuerstenau-Sharp M, Stankewicz C, Meyer N, Ma J, Fiene S, Anson BD, Reil D, Wang W. Industrialized Production of Human iPS Cell-derived Cardiomyocytes. Soc. Biomol Sciences, 2009; Stem Cell Symposium.
Bryant S, Wyllie C, Palmer R, Heal R, Demmon J, Nicol S, Anson B, Rudy-Reil D, Ma J. Effects of isoprenaline on human stem cell derived cardiomyocytes. J Pharm Tox, 2009;60(2):219-220.
Gowder SJ, McMartin KE. Methods to evaluate the effect of ethanol on the folate analogue, fluorescein methotrexate uptake in human proximal tubular cells. Advan Pharmacol Sci, 2009;2009:291349.
Fritzinger DC, Hew BE, Thorne M, Pangburn M., Janssen BJ, Gros P, and Vogel CW. Functional characterization of human C3/cobra venom factor hybrid proteins for therapeutic complement depletion. Dev. Comp. Immunol, 2009;33:105-116.
2008
Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science, 2008 Sep 26;321(5897):1801-6.
Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. An integrated genomic analysis of human glioblastoma multiforme. Science, 2008 Sep 26;321(5897):1807-12.
Chittenden TW, Howe EA, Culhane AC, Sultana R, Taylor JM, Holmes C, Quackenbush J. Functional Classification Analysis of Somatically Mutated Genes in Human Breast and Colorectal Cancers. Genomics, 2008 Jun;91(6):508-11. Epub 2008 Apr 22.
Nery FC, Zeng J, Niland BP, Hewett JW, Farley J, Irimia D, Li Y, Wiche G, Sonnenberg A and Breakefield XO. TorsinA participates in linkage between nuclear envelope and cytoskeleton. J Cell Sci, 2008 Oct 15;121(Pt 20):3476-86.
Hewett JW, Nery FC, Niland BP, Ge, P,Tan P, Philipp Hadwiger, Tannous B, Sah DWY and Breakefield XO. siRNA knock-down of mutant torsinA restores processing through secretory pathway in DYT1 dystonia cells. Hum Mol Genet, 2008;17: 1436-45.
Yuan GC, Liu JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Computational Biology, 2008 Jan;4(1):e13.
Halley JD, Winkler DA, Burden FR. Toward a Rosetta stone for the stem cell genome: stochastic gene expression, network architecture, and external influences. Stem Cell Res, 2008 Sep;1(3):157-68. Epub 2008 Apr 8. Review.
Halley JD, Winkler DA. Critical-like self-organization and natural selection: two facets of a single evolutionary process? Biosystems, 2008 May;92(2):148-58. Epub 2008 Feb 2.
Halley JD, Winkler DA. Consistent Concepts of Self-organization and Self-Assembly. Complexity, 2008;14(2):10-17.
Halley JD, Winkler DA. Classification of emergence and its relation to self-organization. Complexity, 2008;(13):10-15.
Cory SM, Perkins TJ. Implementing arithmetic and other analytic operations by transcriptional regulation. PLoS Compututaional Biology, 2008 May 9;4(4):e1000064.
Zhang S, Balch C, Chan MW, Lai HC, Matei D, Schilder J, Yan PS, Huang THM, Nephew KP.Identification and characterization of ovarian cancer-initiating cells from primary human tumors. Cancer Res, 2008 Jun 1;68(11):4311-20.
Salikhova A, Wang L, Lanahan AA, Liu M, Simons M, Leenders WP, Mukhopadhay D and Horowitz A. Vascular endothelial growth factor and semaphorin induce neuropilin-1 endocytosis via separate pathways. Circ Res, 2008;103(6): 71-79.
Prahst C, Heroult M, Lanahan AA, Uziel N, Kessler O, Shraga-Heled N, Simons M, Neufeld G and Augustin HG. Neuropilin-1-VEGFR-2 complexing requires the PDZ-binding domain of neuropilin-1. J Biol Chem, 2008;283(37): 25110-25114.
Arehart EJ, Stitham J, Asselbergs FW, Douville K, MacKenzie T, Fetalvero K, Gleim SR, Kasza Z, Rao Y, Martel L, Segal S, Robb J, Kaplan A, Simons M, Powell R, Moore J, Rimm EB, Martin KA, and Hwa J. Acceleration of cardiovascular disease by a dysfunctional prostacyclin receptor mutation: potential implications for cyclooxygenase-2 inhibition. Circulation Research, 2008;102(8): 986-93.
Gowder SJ, Devaraj H. Food flavor cinnamaldehyde – induced biochemical and histological changes in the kidney of male albino wistar rat. Environ Toxicol Pharmacol, 2008;26:68-74.
2007
Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science, 2007 Nov 16;318(5853):1108-13.
Galligan JT and Kennell JC. Retroplasmids: linear and circular DNAs that replicate via reverse transcription. In: Microbiology Monographs, volume 7; Microbial Linear Plasmids, F. Meinhardt and A. Steinbüchel (eds.), 2007 Springer. pp 163-185.
Sofola OA, Jin P, Qin Y, Duan R, Liu H, de Haro M, Nelson DL, Botas J. RNA-binding proteins hnRNP A2/B1 and CUGBP1 suppress fragile X CGG premutation repeat-induced neurodegeneration in a Drosophila model of FXTAS. Neuron, 2007 Aug 16;55(4):565-71.
Jin P, Duan R, Qurashi A, Qin Y, Tian D, Rosser TC, Liu H, Feng Y, Warren ST. Pur alpha binds to rCGG repeats and modulates repeat-mediated neurodegeneration in a Drosophila model of fragile X tremor/ataxia syndrome. Neuron, 2007 Aug 16;55(4):556-64.
Silver DP, Dimitrov SD, Feunteun J, Gelman R, Drapkin R, Lu SD, Shestakova E, Soundarapandian V, DeNunzio N, Dragomir S, Mar J, Liu X, Rottenberg S, Jonkers J, Ganesan S, Livingston DM. Further evidence for BRCA1 communication with the inactive X chromosome. Cell, 2007;128(5): 991-1002.
Dedkov EI, Thomas MT, Sonka M, Yang F, Chittenden TW, Rhodes JM, Simons M, Ritman EL, Tomanek RJ. Synectin/Syndecan-4 Regulates Coronary Arteriolar Growth During Development. Dev Dyn, 2007 July;236(7):2004-10.
Bagella L, Sun A, Tonini T, Abbadessa G, Cottone G, Paggi MG, De Luca A, Claudio PP, Giordano A. A small molecule based on the pRb2/p130 spacer domain leads to inhibition of cdk2 activity, cell cycle arrest and tumor growth reduction in vivo.
Oncogene, 2007 Mar 22;26(13):1829-39. Epub 2006 Oct 16.
Kaleth AS, Chittenden TW, Hawkins BJ, Hargens TA, Guill SG, Zedalis D, Gregg JM, Herbert WG. Unique cardiopulmonary exercise test responses in overweight middle-aged adults with obstructive sleep apnea. Sleep Med, 2007 Mar;8(2):160-168.
Hawkins BJ, Solt LA, Chowdhury I, Kazi AS, Abid MR, Aird WC, May MJ, Foskett JK, Madesh M. G-protein coupled receptor Ca2+-linked mitochondrial reactive oxygen species are essential for endothelial/leukocyte adherence. Mol Cell Biol, 2007;27 (21):7582-93.
Hawkins BJ, Madesh M, Kirkpatrick CJ, Fisher AB. Superoxide flux in endothelial cells via the chloride channel-3 mediates intracellular signaling. Mol Biol Cell, 2007;18(6):2002-12.
Tirziu D, Chorianopoulos E, Moodie KL, Palac RT, Zhuang ZW, Tjwa M, Roncal C, Eriksson U, Fu Q, Elfenbein A, Hall AE, Carmeliet P, Moons L, Simons M. Myocardial hypertrophy in the absence of external stimuli is induced by angiogenesis in mice. J Clin Invest, 2007;117:3188-97.
2006
Townsend-Nicholson A, Jayasinghe SN. Cell electrospinning: a unique biotechnique for encapsulating living organisms for generating active biological microthreads/scaffolds. Biomacromolecules, 2006 Dec;7(12):3364-9.
Lanahan AA, Chittenden TW, Mulvihill E, Smith K, Schwartz S, Simons M. Synectin-dependent gene expression in endothelial cells. Physiol Genomics, 2006 Nov 27;27(3):380-90.
Chittenden TW, Sherman JA, Xiong F, Hall AE, Lanahan AA, Taylor JM, Duan H, Pearlman JD, Moore JH, Schwartz SM,
Simons M. Transcriptional Regulation in Coronary Artery Disease: Indications for Novel Markers of Coronary Collateralization. Circulation, 2006 Oct 24;114(17):1811-20.
Chittenden TW, Claes F, Lanahan AA, Autiero M, Palac RT, Tkachenko EV, Elfenbein A, Ruiz de Almodovar C, Dedkov E, Tomanek R, Li W, Westmore M, Singh JP, Horowitz A, Mulligan-Kehoe MJ, Moodie KL, Zhuang ZW, Carmeliet P, Simons M. Selective regulation of arterial branching morphogenesis by synectin. Developmental Cell, 2006 Jun;10(6):783-95.
Chaki M, Sengupta M, Mukhopadhyay A, Subba Rao I et al. OCA1 in different ethnic groups of India is primarily due to founder mutations in the Tyrosinase gene. Ann Hum Genet, 2006;70(Pt 5):623-30.
Moore JH, Gilbert JC, Tsai CT, Chiang FT, Holden W, Barney N, White BC. A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol., 2006 Jul 21;241(2):252-61. Epub 2006 Feb 2.
Jayasinghe SN, Qureshi AN, Eagles PA. Electrohydrodynamic jet processing: an advanced electric-field-driven jetting phenomenon for processing living cells. Small, 2006 Feb;2(2):216-9.
Xiao WM, Liu WB, Li ZJ, Liang DC, Li LN, White LD, Fox DA, Overbeek PA, Chen Q. Gene expression profiling in embryonic mouse lenses. Molecular vision, 2006;12:1692-1698.
Nelson TJ, Ge ZD, VanOrman J, Barron M, Rudy-Reil D, Hacker TA, Misra R, Duncan SA, Auchampach JA, Lough JW. Improved cardiac function in infarcted mice after treatment with pluripotent embryonic stem cells. Anat Rec, 2006;288(11):1216-1224.
Gowder SJ, Devaraj H. Effect of food flavour cinnamaldehyde on the antioxidant status of rat kidney. Basic Clin Pharmacol Toxicol, 2006;99:379-382.
2005
Halley JD, Warden AC, Sadedin S, Li W. Rapid self-organized criticality: Fractal evolution in extreme environments. Phys Rev E Stat Nonlin Soft Matter Phys, 2004 Sep;70(3 Pt 2):036118. Epub 2004 Sep 28. Erratum in: Phys Rev E Stat Nonlin Soft Matter Phys, 2005 Feb;71(2 Pt 2):029901.
Qin Y, Liu J, Li X, Wei Q. Preparation and characterization of a single-chain calcineurin-calmodulin complex. Biochim Biophys Acta, 2005 Mar 14;1747(2):171-8.
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. Cerevisiae. Science, 2005;309(5734):626-630.
Jiang B, Xiao W, Shi Y, Liu M, Xiao X. Role of Smac/DIABLO in hydrogen peroxide-induced apoptosis in C2C12 myogenic cells. Free Radic Biol Med, 2005;39(5):658-667.
Qin J, Chittenden TW, Gao L, Pearlman JD. Automated migration analysis based on cell texture: method & reliability.
BMC Cell Biol, 2005 Mar 3;6(1):9.
Dimitrov RA. A New Formalism for Calculation of the Partition Function of Single Stranded Nucleic Acids. Bulg. J. Phys., 2005; 32:220-235.
Jiang B, Xiao W, Shi Y, Liu M, Xiao X. Heat shock pretreatment inhibited the release of Smac/DIABLO from mitochondria and apoptosis induced by hydrogen peroxide in cardiomyocytes and C2C12 myogenic cells. Cell Stress Chaperones, 2005;10(3):252-262.
2004
Zhang Y, Chittenden T, Simons M. Characterization of synectin expression and promoter activity. Gene, 2004 Nov 10;342(1):29-34.
Nery FC, Passos DO, Garcia VS, Kobarg J. Ki-1/57 interacts with RACK1 and is a substrate for the phosphorylation by Phorbol 12-myristate 13-acetate-activated protein kinase C. J Biol Chem, 2004 Mar 19;279(12):11444-55.
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2001
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Clark KB, Naritoku DK, Smith DC, Browning RA, Jensen RA. Enhanced recognition memory following vagus nerve stimulation in human subjects. Nat Neurosci, 1999 Jan;2(1):94-8.
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1998
Shao D, Rangwala S, Bailey ST, Krakow SL, Reginato MJ, Lazar MA. Interdomain communication regulating ligand binding by PPARg. Nature, 1998;396:377-380.
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1997
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1995
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1994
Nasr F, Bécam AM, Slonimski PP and Herbert CJ. YBR1012 an essential gene from Saccharomyces cerevisiae: construction of an RNA antisense conditional allele and isolation of a multicopy suppressor. C. R. Acad. Sci. Paris, 1994;317:607-613.
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1993
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1992
Ryan LJ, Clark KB. Alteration of neuronal responses in the subthalamic nucleus following globus pallidus and neostriatal lesions in rats. Brain Res Bull, 1992 Sept-Oct;29(3-4):319-27.
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1991
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1989
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