Publications

This publication list was generated using PubCrawler. [Updated: August 2009]

2009

Figueroa ME, Skrabanek L, Li Y, Jiemjit A, Fandy TE, Paietta E, Fernandez H, Tallman MS, Greally JM, Carraway H, Licht JD, Gore SD, Melnick A. MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. Blood. 2009 Aug 3;. [PubMed]

Han Y, Moreira IS, Urizar E, Weinstein H, Javitch JA. Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation. Nature chemical biology. 2009 Aug 2;. [PubMed]

Pflueger D, Rickman DS, Sboner A, Perner S, LaFargue CJ, Svensson MA, Moss BJ, Kitabayashi N, Pan Y, de la Taille A, Kuefer R, Tewari AK, Demichelis F, Chee MS, Gerstein MB, Rubin MA. N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia (New York, N.Y.). 2009 Aug;11(8):804-11. [PubMed]

Christini DJ. Improving the utility of T-wave alternans by quantifying its relationship to underlying action-potential duration alternans. Heart rhythm : the official journal of the Heart Rhythm Society. 2009 Aug;6(8):1220-1. [PubMed]

Di Lorenzo PM, Platt D, Victor JD. Information processing in the parabrachial nucleus of the pons. Annals of the New York Academy of Sciences. 2009 Jul;1170:365-71. [PubMed]

Smith AC, Shah SA, Hudson AE, Purpura KP, Victor JD, Brown EN, Schiff ND. A Bayesian statistical analysis of behavioral facilitation associated with deep brain stimulation. Journal of neuroscience methods. 2009 Jul 1;. [PubMed]

Hudson AE, Schiff ND, Victor JD, Purpura KP. Attentional modulation of adaptation in V4. The European journal of neuroscience. 2009 Jun 25;. [PubMed]

Kentsis A, Lin YY, Kurek K, Calicchio M, Wang YY, Monigatti F, Campagne F, Lee R, Horwitz B, Steen H, Bachur R. Discovery and Validation of Urine Markers of Acute Pediatric Appendicitis Using High-Accuracy Mass Spectrometry. Annals of emergency medicine. 2009 Jun 24;. [PubMed]

Di Vizio D, Kim J, Hager MH, Morello M, Yang W, Lafargue CJ, True LD, Rubin MA, Adam RM, Beroukhim R, Demichelis F, Freeman MR. Oncosome Formation in Prostate Cancer: Association with a Region of Frequent Chromosomal Deletion in Metastatic Disease. Cancer research. 2009 Jun 23;. [PubMed]

Destexhe A, Victor JD. Editorial. Journal of computational neuroscience. 2009 Jun 16;. [PubMed]

Roudi Y, Nirenberg S, Latham PE. Pairwise maximum entropy models for studying large biological systems: when they can work and when they can't. PLoS computational biology. 2009 May;5(5):e1000380. [PubMed]

Quick M, Winther AM, Shi L, Nissen P, Weinstein H, Javitch JA. Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation. Proc Natl Acad Sci U S A. 2009 Mar 23;. [PubMed]

Ci W, Polo JM, Cerchietti L, Shaknovich R, Wang L, Yang SN, Ye K, Farinha P, Horsman DE, Gascoyne RD, Elemento O, Melnick A. The BCL6 transcriptional program features repression of multiple oncogenes in primary B-cells and is deregulated in DLBCL. Blood. 2009 Mar 23;. [PubMed]

Jacobs AL, Fridman G, Douglas RM, Alam NM, Latham PE, Prusky GT, Nirenberg S. Ruling out and ruling in neural codes. Proc Natl Acad Sci U S A. 2009 Mar 18;. [PubMed]

Rickman DS, Pflueger D, Moss B, Vandoren VE, Chen CX, de la Taille A, Kuefer R, Tewari AK, Setlur SR, Demichelis F, Rubin MA. SLC45A3-ELK4 Is a Novel and Frequent Erythroblast Transformation-Specific Fusion Transcript in Prostate Cancer. Cancer Res. 2009 Mar 17;. [PubMed]

Ahrens-Nicklas RC, Clancy CE, Christini DJ. Re-evaluating the efficacy of {beta}-adrenergic agonists and antagonists in long QT-3 syndrome through computational modeling. Cardiovasc Res. 2009 Mar 5;. [PubMed]

Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA. let-7 Overexpression Leads to an Increased Fraction of Cells in G2/M, Direct Down-regulation of Cdc34, and Stabilization of Wee1 Kinase in Primary Fibroblasts. J Biol Chem. 2009 Mar 13;284(11):6605-9. [PubMed]

Deng X, Xu J, Hui J, Wang C. Probability fold change: a robust computational approach for identifying differentially expressed gene lists. Comput Methods Programs Biomed. 2009 Feb;93(2):124-39. [PubMed]

Xu X, Kanda VA, Choi E, Panaghie G, Roepke TK, Gaeta SA, Christini DJ, Lerner DJ, Abbott GW. MinK-dependent internalization of the IKs potassium channel. Cardiovasc Res. 2009 Feb 7;. [PubMed]

Xin Z, Bucchi A, Oren RV, Kryukova Y, Dun W, Clancy CE, Robinson RB. In vitro characterization of HCN channel kinetics and frequency-dependence in myocytes predicts biological pacemaker functionality. J Physiol. 2009 Jan 26;. [PubMed]

Figueroa ME, Wouters BJ, Skrabanek L, Glass J, Li Y, Erpelinck-Verschueren CA, Langerak AW, Lowenberg B, Fazzari M, Greally JM, Valk PJ, Melnick A, Delwel R. Genome wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. Blood. 2009 Jan 23;. [PubMed]

Hofer MD, Kuefer R, Maier C, Herkommer K, Perner S, Demichelis F, Paiss T, Vogel W, Rubin MA, Hoegel J. Genome-wide linkage analysis of TMPRSS2-ERG fusion in familial prostate cancer. Cancer Res. 2009 Jan 15;69(2):640-6. [PubMed]

Guptaroy B, Zhang M, Bowton E, Binda F, Shi L, Weinstein H, Galli A, Javitch JA, Neubig RR, Gnegy ME. A juxtamembrane mutation in the N-terminus of the dopamine transporter induces preference for an inward-facing conformation. Mol Pharmacol. 2009 Jan 5;. [PubMed]

2008

Topisirovic I, Siddiqui N, Orolicki S, Skrabanek L, Tremblay M, Hoang T, Borden KL. The stability of eIF4E mRNA is regulated by HuR and this activity is dysregulated in cancer. Mol Cell Biol. 2008 Dec 29;. [PubMed]

Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins. 2008 Dec 23;. [PubMed]

Campagne F, Lambert JC, Dreses-Werringloer U, Vingtdeux V, Lendon C, Campion D, Amouyel P, Lee AT, Gregersen PK, Davies P, Marambaud P. Response: CALHM1 Association with Alzheimer's Disease Risk. Cell. 2008 Dec 12;135(6):994-6. [PubMed]

Salvarezza SB, Deborde S, Schreiner R, Campagne F, Kessels MM, Qualmann B, Caceres A, Kreitzer G, Rodriguez-Boulan E. LIM Kinase 1 and Cofilin Regulate Actin Filament Population Required for Dynamin-dependent Apical Carrier Fission from the TGN. Mol Biol Cell. 2008 Nov 5;. [PubMed]

Lambert JC, Campagne F, Marambaud P. [CALHM1, a novel gene to blame in Alzheimer disease.]. Med Sci (Paris). 2008 Nov;24(11):923-924. [PubMed]

Alamo L, Wriggers W, Pinto A, Bártoli F, Salazar L, Zhao FQ, Craig R, Padrón R. Three-Dimensional Reconstruction of Tarantula Myosin Filaments Suggests How Phosphorylation May Regulate Myosin Activity. J Mol Biol. 2008 Oct 14;. [PubMed]

Rudy Y, Ackerman MJ, Bers DM, Clancy CE, Houser SR, London B, McCulloch AD, Przywara DA, Rasmusson RL, Solaro RJ, Trayanova NA, Van Wagoner DR, Varró A, Weiss JN, Lathrop DA. Systems approach to understanding electromechanical activity in the human heart: a national heart, lung, and blood institute workshop summary. Circulation. 2008 Sep 9;118(11):1202-11. [PubMed]

Rusu M, Birmanns S, Wriggers W. Biomolecular Pleiomorphism Probed by Spatial Interpolation of Coarse Models. Bioinformatics. 2008 Aug 30;. [PubMed]

Chang CW, Poteet E, Schetz JA, Gumus ZH, Weinstein H. Towards a quantitative representation of the cell signaling mechanisms of hallucinogens: Measurement and mathematical modeling of 5-HT1A and 5-HT2A receptor-mediated ERK1/2 activation. Neuropharmacology. 2008 Aug 13;. [PubMed]

Beuming T, Kniazeff J, Bergmann ML, Shi L, Gracia L, Raniszewska K, Newman AH, Javitch JA, Weinstein H, Gether U, Loland CJ. The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci. 2008 Jul;11(7):780-9. [PubMed]

Beuming T, Kniazeff J, Bergmann ML, Shi L, Gracia L, Raniszewska K, Newman AH, Javitch JA, Weinstein H, Gether U, Loland CJ. The binding sites for cocaine and dopamine in the dopamine transporter overlap. Nat Neurosci. 2008 Jul;11(7):780-9. [PubMed]

Gumus ZH, Du B, Kacker A, Boyle JO, Bocker JM, Mukherjee P, Subbaramaiah K, Dannenberg AJ, Weinstein H. Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia. Cancer Prev Res (Phila Pa). 2008 Jul;1(2):100-11. [PubMed]

Gumus ZH, Du B, Kacker A, Boyle JO, Bocker JM, Mukherjee P, Subbaramaiah K, Dannenberg AJ, Weinstein H. Effects of tobacco smoke on gene expression and cellular pathways in a cellular model of oral leukoplakia. Cancer Prev Res (Phila Pa). 2008 Jul;1(2):100-11. [PubMed]

Mucci LA, Pawitan Y, Demichelis F, Fall K, Stark JR, Adami HO, Andersson SO, Andrén O, Eisenstein A, Holmberg L, Huang W, Kantoff PW, Kim R, Perner S, Stampfer MJ, Johansson JE, Rubin MA. Testing a Multigene Signature of Prostate Cancer Death in the Swedish Watchful Waiting Cohort. Cancer Epidemiol Biomarkers Prev. 2008 Jun 26;. [PubMed]

Shi L, Quick M, Zhao Y, Weinstein H, Javitch JA. The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell. 2008 Jun 20;30(6):667-77. [PubMed]

Conte MM, Victor JD. VEP indices of cortical lateral interactions in epilepsy treatment. Vision Res. 2008 Jun 20;. [PubMed]

Shi L, Quick M, Zhao Y, Weinstein H, Javitch JA. The mechanism of a neurotransmitter:sodium symporter--inward release of Na+ and substrate is triggered by substrate in a second binding site. Mol Cell. 2008 Jun 20;30(6):667-77. [PubMed]

Han DS, Wang SX, Weinstein H. Active State-like Conformational Elements in the beta2-AR and a Photoactivated Intermediate of Rhodopsin Identified by Dynamic Properties of GPCRs. Biochemistry. 2008 Jun 18;. [PubMed]

Aguilar D, Skrabanek L, Gross SS, Oliva B, Campagne F. Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. Nucleic Acids Res. 2008 May 15;. [PubMed]

Mertz KD, Demichelis F, Sboner A, Hirsch MS, Cin PD, Struckmann K, Storz M, Scherrer S, Schmid DM, Strebel RT, Probst-Hensch NM, Gerstein M, Moch H, Rubin MA. Association of cytokeratin 7 and 19 expression with genomic stability and favorable prognosis in clear cell renal cell cancer. Int J Cancer. 2008 May 13;. [PubMed]

Deng X, Xu J, Wang C. Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists. BMC Bioinformatics. 2008 May 28;9 Suppl 6:S14. [PubMed]

Di Vizio D, Demichelis F, Simonetti S, Pettinato G, Terracciano L, Tornillo L, Freeman M, Insabato L. Skp2 expression is associated with high risk and Elevated Ki67 expression in gastrointestinal stromal tumours. BMC Cancer. 2008 May 13;8(1):134. [PubMed]

Madsen KL, Eriksen J, Milan-Lobo L, Han DS, Niv MY, Ammendrup-Johnsen I, Henriksen U, Bhatia VK, Stamou D, Sitte HH, McMahon HT, Weinstein H, Gether U. Membrane localization is critical for activation of the PICK1 BAR (Bin/amphiphysin/Rvs) domain. Traffic. 2008 May 8;. [PubMed]

Xu J, Clancy CE. Ionic mechanisms of endogenous bursting in CA3 hippocampal pyramidal neurons: a model study. PLoS ONE. 2008 Apr 30;3(4):e2056. [PubMed]

Kniazeff J, Shi L, Loland CJ, Javitch JA, Weinstein H, Gether U. An intracellular interaction network regulates conformational transitions in the dopamine transporter. J Biol Chem. 2008 Apr 21;. [PubMed]

Schiff ND, Giacino JT, Kalmar K, Victor JD, Baker K, Gerber M, Fritz B, Eisenberg B, Biondi T, O'Connor J, Kobylarz EJ, Farris S, Machado A, McCagg C, Plum F, Fins JJ, Rezai AR. Behavioural improvements with thalamic stimulation after severe traumatic brain injury. Nature. 2008 Mar 6;452(7183):120. [PubMed]

Dedek K, Pandarinath C, Alam NM, Wellershaus K, Schubert T, Willecke K, Prusky GT, Weiler R, Nirenberg S. Ganglion cell adaptability: does the coupling of horizontal cells play a role?. PLoS ONE. 2008 Mar 5;3(3):e1714. [PubMed]

Skrabanek L, Niv MY. Scan2S: Increasing the precision of PROSITE pattern motifs using secondary structure constraints. Proteins. 2008 Mar 4;. [PubMed]

Vogels RL, Oosterman JM, Laman DM, Gouw AA, Schroeder-Tanka JM, Scheltens P, van der Flier WM, Weinstein HC. Transcranial Doppler Blood Flow Assessment in Patients With Mild Heart Failure: Correlates With Neuroimaging and Cognitive Performance. Congest Heart Fail. 2008 March/April;14(2):61-65. [PubMed]

Perner S, Wagner PL, Demichelis F, Mehra R, Lafargue CJ, Moss BJ, Arbogast S, Soltermann A, Weder W, Giordano TJ, Beer DG, Rickman DS, Chinnaiyan AM, Moch H, Rubin MA. EML4-ALK fusion lung cancer: a rare acquired event. Neoplasia. 2008 Mar;10(3):298-302. [PubMed]

Campagne F. Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols. BMC Bioinformatics. 2008 Feb 29;9(1):132. [PubMed]

Demichelis F, Greulich H, Macoska JA, Beroukhim R, Sellers WR, Garraway L, Rubin MA. SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res. 2008 Feb 27;. [PubMed]

Victor JD, Schiff ND. Meeting rigorous statistical standards in case reports. Ann Neurol. 2008 Feb 25;. [PubMed]

Aksay E. Reply to cardiac troponin and risk stratification in pulmonary embolism. Am J Emerg Med. 2008 Feb;26(2):236-237. [PubMed]

Xu J, Deng X, Demetriou AA, Farkas DL, Hui T, Wang C. Factors released from cholestatic rat livers possibly involved in inducing bone marrow hepatic stem cell priming. Stem Cells Dev. 2008 Feb;17(1):143-55. [PubMed]

Geng H, Deng X, Ali HH. Message Passing Clustering (MPC): a knowledge-based framework for clustering under biological constraints. Int J Data Min Bioinform. 2008;2(2):95-120. [PubMed]

Deng X, Geng H, Ali HH. A Hidden Markov Model approach to predicting yeast gene function from sequential gene expression data. Int J Bioinform Res Appl. 2008;4(3):263-73. [PubMed]

Krogh-Madsen T, Christini DJ. Resetting and termination of reentry in a loop-and-tail cardiac model. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jan;77(1 Pt 1):011916. [PubMed]

Gordon E, Panaghie G, Deng L, Bee KJ, Roepke TK, Krogh-Madsen T, Christini DJ, Ostrer H, Basson CT, Chung W, Abbott GW. A KCNE2 mutation in a patient with cardiac arrhythmia induced by auditory stimuli and serum electrolyte imbalance. Cardiovasc Res. 2008 Jan;77(1):98-106. [PubMed]

Mukherjee P, Thomas S, Pasinetti GM. Complement anaphylatoxin C5a neuroprotects through regulation of glutamate receptor subunit 2 in vitro and in vivo. J Neuroinflammation. 2008 Jan 29;5:5. [PubMed]

Taylor MS, Fung HK, Rajgaria R, Filizola M, Weinstein H, Floudas CA. Mutations Affecting the Oligomerization Interface of G-Protein Coupled Receptors Revealed by a Novel De-novo Protein Design Framework. Biophys J. 2008 Jan 4;. [PubMed]

Mucci LA, Pawitan Y, Demichelis F, Fall K, Stark JR, Adami HO, Andersson SO, Andrén O, Eisenstein AS, Holmberg L, Huang W, Kantoff PW, Perner S, Stampfer MJ, Johansson JE, Rubin MA. Nine-gene molecular signature is not associated with prostate cancer death in a watchful waiting cohort. Cancer Epidemiol Biomarkers Prev. 2008 Jan;17(1):249-51. [PubMed]

Skrabanek L, Saini HK, Bader GD, Enright AJ. Computational prediction of protein-protein interactions. Mol Biotechnol. 2008 Jan;38(1):1-17. [PubMed]

2007

Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, Sellers WR. Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma. Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12. [PubMed]

Khelashvili G, Weinstein H, Harries D. Protein diffusion on charged membranes: A dynamic mean-field model describes time evolution and lipid reorganization. Biophys J. 2007 Dec 7;. [PubMed]

Nakamura H, Kurokawa J, Bai CX, Asada K, Xu J, Oren RV, Zhu ZI, Clancy CE, Isobe M, Furukawa T. Progesterone Regulates Cardiac Repolarization Through a Nongenomic Pathway. An In Vitro Patch-Clamp and Computational Modeling Study. Circulation. 2007 Dec 3;. [PubMed]

Lehnart SE, Ackerman MJ, Benson DW Jr, Brugada R, Clancy CE, Donahue JK, George AL Jr, Grant AO, Groft SC, January CT, Lathrop DA, Lederer WJ, Makielski JC, Mohler PJ, Moss A, Nerbonne JM, Olson TM, Przywara DA, Towbin JA, Wang LH, Marks AR. Inherited Arrhythmias: A National Heart, Lung, and Blood Institute and Office of Rare Diseases Workshop Consensus Report About the Diagnosis, Phenotyping, Molecular Mechanisms, and Therapeutic Approaches for Primary Cardiomyopathies of Gene Mutations Affecting Ion Channel Function. Circulation. 2007 Nov 13;116(20):2325-2345. [PubMed]

Zhu ZI, Clancy CE. Genetic mutations and arrhythmia: simulation from DNA to electrocardiogram. J Electrocardiol. 2007 Nov-Dec;40(6 Suppl):S47-50. [PubMed]

Setlur SR, Royce TE, Sboner A, Mosquera JM, Demichelis F, Hofer MD, Mertz KD, Gerstein M, Rubin MA. Integrative Microarray Analysis of Pathways Dysregulated in Metastatic Prostate Cancer. Cancer Res. 2007 Nov 1;67(21):10296-10303. [PubMed]

Demichelis F, Rubin MA. TMPRSS2-ETS fusion prostate cancer: biological and clinical implications. J Clin Pathol. 2007 Nov;60(11):1185-1186. [PubMed]

Gordon E, Panaghie G, Deng L, Bee KJ, Roepke TK, Krogh-Madsen T, Christini DJ, Ostrer H, Basson CT, Chung W, Abbott GW. A KCNE2 mutation in a patient with cardiac arrhythmia induced by auditory stimuli and serum electrolyte imbalance. Cardiovasc Res. 2007 Oct 31;. [PubMed]

Niv MY, Skrabanek L, Roberts RJ, Scheraga HA, Weinstein H. Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S-A novel motif scan algorithm with optional secondary structure constraints. Proteins. 2007 Oct 30;. [PubMed]

Sun J, Weinstein H. Toward realistic modeling of dynamic processes in cell signaling: Quantification of macromolecular crowding effects. J Chem Phys. 2007 Oct 21;127(15):155105. [PubMed]

Zhu ZI, Clancy CE. L-type Ca2+ channel mutations and T-wave alternans: A model study. Am J Physiol Heart Circ Physiol. 2007 Oct 12;. [PubMed]

Roussin AT, Victor JD, Chen JY, Di Lorenzo PM. Variability in responses and temporal coding of tastants of similar quality in the nucleus of the solitary tract of the rat. J Neurophysiol. 2007 Oct 3;. [PubMed]

Barry M, Perner S, Demichelis F, Rubin MA. TMPRSS2-ERG Fusion Heterogeneity in Multifocal Prostate Cancer: Clinical and Biologic Implications. Urology. 2007 Oct;70(4):630-633. [PubMed]

Mertz KD, Demichelis F, Kim R, Schraml P, Storz M, Diener PA, Moch H, Rubin MA. Automated immunofluorescence analysis defines microvessel area as a prognostic parameter in clear cell renal cell cancer. Hum Pathol. 2007 Oct;38(10):1454-62. [PubMed]

Schiff ND, Giacino JT, Kalmar K, Victor JD, Baker K, Gerber M, Fritz B, Eisenberg B, O'Connor J, Kobylarz EJ, Farris S, Machado A, McCagg C, Plum F, Fins JJ, Rezai AR. Behavioural improvements with thalamic stimulation after severe traumatic brain injury. Nature. 2007 Aug 2;448(7153):600-3. [PubMed]

Demichelis F, Fall K, Perner S, Andren O, Schmidt F, Setlur SR, Hoshida Y, Mosquera JM, Pawitan Y, Lee C, Adami HO, Mucci LA, Kantoff PW, Andersson SO, Chinnaiyan AM, Johansson JE, Rubin MA. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene. 2007 Jul 5;26(31):4596-9. [PubMed]

Oka S, Victor JD, Conte MM, Yanagida T. VEPs elicited by local correlations and global symmetry: characteristics and interactions. Vision Res. 2007 Jul;47(16):2212-22. [PubMed]

Perner S, Mosquera JM, Demichelis F, Hofer MD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, De Marzo AM, Rubin MA. TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Am J Surg Pathol. 2007 Jun;31(6):882-8. [PubMed]

Mosquera JM, Perner S, Demichelis F, Kim R, Hofer MD, Mertz KD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, Rubin MA. Morphological features of TMPRSS2-ERG gene fusion prostate cancer. J Pathol. 2007 May;212(1):91-101. [PubMed]

Clancy CE, Wehrens XH. Mutation-specific effects of lidocaine in Brugada syndrome. International journal of cardiology. 2007 Oct 18;121(3):249-52. [PubMed]

Roussin AT, Victor JD, Chen JY, Di Lorenzo PM. Variability in responses and temporal coding of tastants of similar quality in the nucleus of the solitary tract of the rat. Journal of neurophysiology. 2007 Oct 3;. [PubMed]

Mertz KD, Demichelis F, Kim R, Schraml P, Storz M, Diener PA, Moch H, Rubin MA. Automated immunofluorescence analysis defines microvessel area as a prognostic parameter in clear cell renal cell cancer. Human pathology. 2007 Oct;38(10):1454-62. [PubMed]

Iravanian S, Christini DJ. Optical mapping system with real-time control capability. American journal of physiology. Heart and circulatory physiology. 2007 Oct;293(4):H2605-11. [PubMed]

Jordan PN, Christini DJ. Characterizing the contribution of voltage- and calcium-dependent coupling to action potential stability: implications for repolarization alternans. American journal of physiology. Heart and circulatory physiology. 2007 Oct;293(4):H2109-18. [PubMed]

Schiff ND, Giacino JT, Kalmar K, Victor JD, Baker K, Gerber M, Fritz B, Eisenberg B, O'Connor J, Kobylarz EJ, Farris S, Machado A, McCagg C, Plum F, Fins JJ, Rezai AR. Behavioural improvements with thalamic stimulation after severe traumatic brain injury. Nature. 2007 Aug 2;448(7153):600-3. [PubMed]

Nirenberg SH, Victor JD. Analyzing the activity of large populations of neurons: how tractable is the problem?. Current opinion in neurobiology. 2007 Aug;17(4):397-400. [PubMed]

Demichelis F, Fall K, Perner S, Andren O, Schmidt F, Setlur SR, Hoshida Y, Mosquera JM, Pawitan Y, Lee C, Adami HO, Mucci LA, Kantoff PW, Andersson SO, Chinnaiyan AM, Johansson JE, Rubin MA. TMPRSS2:ERG gene fusion associated with lethal prostate cancer in a watchful waiting cohort. Oncogene. 2007 Jul 5;26(31):4596-9. [PubMed]

Oka S, Victor JD, Conte MM, Yanagida T. VEPs elicited by local correlations and global symmetry: characteristics and interactions. Vision research. 2007 Jul;47(16):2212-22. [PubMed]

Weinstein H, Bates AT, Spaltro BE, Thaler HT, Steingart RM. Influence of preoperative exercise capacity on length of stay after thoracic cancer surgery. The Annals of thoracic surgery. 2007 Jul;84(1):197-202. [PubMed]

Perner S, Mosquera JM, Demichelis F, Hofer MD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, De Marzo AM, Rubin MA. TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. The American journal of surgical pathology. 2007 Jun;31(6):882-8. [PubMed]

Skrabanek L, Murcia M, Bouvier M, Devi L, George SR, Lohse MJ, Milligan G, Neubig R, Palczewski K, Parmentier M, Pin JP, Vriend G, Javitch JA, Campagne F, Filizola M. Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base. BMC bioinformatics. 2007 May 30;8:177. [PubMed]

Mosquera JM, Perner S, Demichelis F, Kim R, Hofer MD, Mertz KD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, Rubin MA. Morphological features of TMPRSS2-ERG gene fusion prostate cancer. The Journal of pathology. 2007 May;212(1):91-101. [PubMed]

Gong Y, Xie F, Stein KM, Garfinkel A, Culianu CA, Lerman BB, Christini DJ. Mechanism underlying initiation of paroxysmal atrial flutter/atrial fibrillation by ectopic foci: a simulation study. Circulation. 2007 Apr 24;115(16):2094-102. [PubMed]

Li X, Wang XJ, Tannenhauser J, Podell S, Mukherjee P, Hertel M, Biane J, Masuda S, Nottebohm F, Gaasterland T. Genomic resources for songbird research and their use in characterizing gene expression during brain development. Proceedings of the National Academy of Sciences of the United States of America. 2007 Apr 17;104(16):6834-9. [PubMed]

Victor JD, Goldberg DH, Gardner D. Dynamic programming algorithms for comparing multineuronal spike trains via cost-based metrics and alignments. Journal of neuroscience methods. 2007 Apr 15;161(2):351-60. [PubMed]

Aksay E, Olasagasti I, Mensh BD, Baker R, Goldman MS, Tank DW. Functional dissection of circuitry in a neural integrator. Nature neuroscience. 2007 Apr;10(4):494-504. [PubMed]

Oosterman J, van Harten B, Vogels R, Gouw A, Weinstein H, Scheltens P, Scherder E. Distortions in rest-activity rhythm in aging relate to white matter hyperintensities. Neurobiology of aging. 2007 Mar 16;. [PubMed]

Martin AG, Depoix F, Stohr M, Meissner U, Hagner-Holler S, Hammouti K, Burmester T, Heyd J, Wriggers W, Markl J. Limulus polyphemus hemocyanin: 10 A cryo-EM structure, sequence analysis, molecular modelling and rigid-body fitting reveal the interfaces between the eight hexamers. Journal of molecular biology. 2007 Mar 2;366(4):1332-50. [PubMed]

Mertz KD, Setlur SR, Dhanasekaran SM, Demichelis F, Perner S, Tomlins S, Tchinda J, Laxman B, Vessella RL, Beroukhim R, Lee C, Chinnaiyan AM, Rubin MA. Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model. Neoplasia (New York, N.Y.). 2007 Mar;9(3):200-6. [PubMed]

Mechler F, Ohiorhenuan IE, Victor JD. Speed dependence of tuning to one-dimensional features in V1. Journal of neurophysiology. 2007 Mar;97(3):2423-38. [PubMed]

Victor JD, Goldberg DH, Gardner D. Dynamic programming algorithms for comparing multineuronal spike trains via cost-based metrics and alignments. J Neurosci Methods. 2007 Apr 15;161(2):351-60. [PubMed]

Martin AG, Depoix F, Stohr M, Meissner U, Hagner-Holler S, Hammouti K, Burmester T, Heyd J, Wriggers W, Markl J. Limulus polyphemus hemocyanin: 10 A cryo-EM structure, sequence analysis, molecular modelling and rigid-body fitting reveal the interfaces between the eight hexamers. J Mol Biol. 2007 Mar 2;366(4):1332-50. [PubMed]

Mechler F, Ohiorhenuan IE, Victor JD. Speed dependence of tuning to one-dimensional features in V1. J Neurophysiol. 2007 Mar;97(3):2423-38. [PubMed]

Mertz KD, Setlur SR, Dhanasekaran SM, Demichelis F, Perner S, Tomlins S, Tchinda J, Laxman B, Vessella RL, Beroukhim R, Lee C, Chinnaiyan AM, Rubin MA. Molecular characterization of TMPRSS2-ERG gene fusion in the NCI-H660 prostate cancer cell line: a new perspective for an old model. Neoplasia. 2007 Mar;9(3):200-6. [PubMed]

Victor JD, Blessing EM, Forte JD, Buzas P, Martin PR. Response variability of marmoset parvocellular neurons. J Physiol. 2007 Feb 15;579(Pt 1):29-51. [PubMed]

Maddess T, Nagai Y, Victor JD, Taylor RR. Multilevel isotrigon textures. J Opt Soc Am A Opt Image Sci Vis. 2007 Feb;24(2):278-93. [PubMed]

Di Lorenzo PM, Victor JD. Neural coding mechanisms for flow rate in taste-responsive cells in the nucleus of the solitary tract of the rat. J Neurophysiol. 2007 Feb;97(2):1857-61. [PubMed]

Birmanns S, Wriggers W. Multi-resolution anchor-point registration of biomolecular assemblies and their components. J Struct Biol. 2007 Jan;157(1):271-80. [PubMed]

Victor JD, Blessing EM, Forte JD, Buzas P, Martin PR. Response variability of marmoset parvocellular neurons. The Journal of physiology. 2007 Feb 15;579(Pt 1):29-51. [PubMed]

Krogh-Madsen T, Christini DJ. Action potential duration dispersion and alternans in simulated heterogeneous cardiac tissue with a structural barrier. Biophysical journal. 2007 Feb 15;92(4):1138-49. [PubMed]

Maddess T, Nagai Y, Victor JD, Taylor RR. Multilevel isotrigon textures. Journal of the Optical Society of America. A, Optics, image science, and vision. 2007 Feb;24(2):278-93. [PubMed]

Di Lorenzo PM, Victor JD. Neural coding mechanisms for flow rate in taste-responsive cells in the nucleus of the solitary tract of the rat. Journal of neurophysiology. 2007 Feb;97(2):1857-61. [PubMed]

Birmanns S, Wriggers W. Multi-resolution anchor-point registration of biomolecular assemblies and their components. Journal of structural biology. 2007 Jan;157(1):271-80. [PubMed]

Urban JD, Clarke WP, von Zastrow M, Nichols DE, Kobilka B, Weinstein H, Javitch JA, Roth BL, Christopoulos A, Sexton PM, Miller KJ, Spedding M, Mailman RB. Functional selectivity and classical concepts of quantitative pharmacology. The Journal of pharmacology and experimental therapeutics. 2007 Jan;320(1):1-13. [PubMed]

Peyser H, Altesman R, Anfang S, Berger J, Rogoff J, Vickar G, Peele R, Weinstein H, Koss M, Weker J, Seligman R. Boycott of Israeli academics and the position of the American Psychiatric Association. The Israel journal of psychiatry and related sciences. 2007;44(1):74. [PubMed]

Niv MY, Ripoll DR, Vila JA, Liwo A, Vanamee ES, Aggarwal AK, Weinstein H, Scheraga HA. Topology of Type II REases revisited; structural classes and the common conserved core. Nucleic acids research. 2007;35(7):2227-37. [PubMed]

Clancy CE, Zhu ZI, Rudy Y. Pharmacogenetics and anti-arrhythmic drug therapy: a theoretical investigation. American journal of physiology. Heart and circulatory physiology. 2007 Jan;292(1):H66-75. [PubMed]

Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell. 2007 Oct 26;28(2):337-50. [PubMed]

De Renzis S, Elemento O, Tavazoie S, Wieschaus EF. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol. 2007 May;5(5):e117. [PubMed]

Deng X, Geng H, Matache MT. Dynamics of asynchronous random Boolean networks with asynchrony generated by stochastic processes. Biosystems. 2007 Mar;88(1-2):16-34. [PubMed]

Krogh-Madsen T, Christini DJ. Action potential duration dispersion and alternans in simulated heterogeneous cardiac tissue with a structural barrier. Biophys J. 2007 Feb 15;92(4):1138-49. [PubMed]

Elemento O, Tavazoie S. Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation. Methods Mol Biol. 2007;395:349-66. [PubMed]

Elemento O. Developing a systems-level understanding of gene expression. Genome Biol. 2007;8(4):304. [PubMed]

2006

Zhang Z, Boyle PC, Lu BY, Chang JY, Wriggers W. Entropic Folding Pathway of Human Epidermal Growth Factor Explored by Disulfide Scrambling and Amplified Collective Motion Simulations(,). Biochemistry. 2006 Dec 26;45(51):15269-15278. [PubMed]

Rohan S, Tu JJ, Kao J, Mukherjee P, Campagne F, Zhou XK, Hyjek E, Alonso MA, Chen YT. Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes. Clinical cancer research : an official journal of the American Association for Cancer Research. 2006 Dec 1;12(23):6937-45. [PubMed]

Demichelis F, Magni P, Piergiorgi P, Rubin MA, Bellazzi R. A hierarchical Naive Bayes Model for handling sample heterogeneity in classification problems: an application to tissue microarrays. BMC bioinformatics. 2006 Nov 24;7:514. [PubMed]

Culjkovic B, Topisirovic I, Skrabanek L, Ruiz-Gutierrez M, Borden KL. eIF4E is a central node of an RNA regulon that governs cellular proliferation. The Journal of cell biology. 2006 Nov 6;175(3):415-26. [PubMed]

Victor JD, Conte MM. Encoding and stability of image statistics in working memory. Vision research. 2006 Nov;46(24):4152-62. [PubMed]

Shoyeb A, Weinstein H, Roistacher N, Spaltro B, Bates A, Yusim G, Steingart R. Preoperative exercise echocardiography and perioperative cardiovascular outcomes in elderly patients undergoing cancer surgery. The American journal of geriatric cardiology. 2006 Nov-Dec;15(6):338-44. [PubMed]

Campagne F, Skrabanek L. Mining expressed sequence tags identifies cancer markers of clinical interest. BMC bioinformatics. 2006 Nov 1;7:481. [PubMed]

Beuming T, Shi L, Javitch JA, Weinstein H. A comprehensive structure-based alignment of prokaryotic and eukaryotic neurotransmitter/Na+ symporters (NSS) aids in the use of the LeuT structure to probe NSS structure and function. Molecular pharmacology. 2006 Nov;70(5):1630-42. [PubMed]

Aldovini D, Demichelis F, Doglioni C, Di Vizio D, Galligioni E, Brugnara S, Zeni B, Griso C, Pegoraro C, Zannoni M, Gariboldi M, Balladore E, Mezzanzanica D, Canevari S, Barbareschi M. M-CAM expression as marker of poor prognosis in epithelial ovarian cancer. International journal of cancer. Journal international du cancer. 2006 Oct 15;119(8):1920-6. [PubMed]

Deng X, Geng H, Bastola DR, Ali HH. Link test--A statistical method for finding prostate cancer biomarkers. Comput Biol Chem. 2006 Dec;30(6):425-33. [PubMed]

Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, Zhang L, Mei N, Chen T, Herman D, Goodsaid FM, Hurban P, Phillips KL, Xu J, Deng X, Sun YA, Tong W, Dragan YP, Shi L. Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol. 2006 Sep;24(9):1162-9. [PubMed]

Basdevant N, Weinstein H, Ceruso M. Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. Journal of the American Chemical Society. 2006 Oct 4;128(39):12766-77. [PubMed]

Savasan S, Buck S, Raimondi SC, Becton DL, Weinstein H, Chang M, Ravindranath Y. CD36 (thrombospondin receptor) expression in childhood acute megakaryoblastic leukemia: in vitro drug sensitivity and outcome. Leukemia & lymphoma. 2006 Oct;47(10):2076-83. [PubMed]

Choe CU, Schulze-Bahr E, Neu A, Xu J, Zhu ZI, Sauter K, Bahring R, Priori S, Guicheney P, Monnig G, Neapolitano C, Heidemann J, Clancy CE, Pongs O, Isbrandt D. C-terminal HERG (LQT2) mutations disrupt IKr channel regulation through 14-3-3epsilon. Human molecular genetics. 2006 Oct 1;15(19):2888-902. [PubMed]

Quick M, Yano H, Goldberg NR, Duan L, Beuming T, Shi L, Weinstein H, Javitch JA. State-dependent conformations of the translocation pathway in the tyrosine transporter Tyt1, a novel neurotransmitter:sodium symporter from Fusobacterium nucleatum. The Journal of biological chemistry. 2006 Sep 8;281(36):26444-54. [PubMed]

Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JC, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Amur S, Bao W, Barbacioru CC, Lucas AB, Bertholet V, Boysen C, Bromley B, Brown D, Brunner A, Canales R, Cao XM, Cebula TA, Chen JJ, Cheng J, Chu TM, Chudin E, Corson J, Corton JC, Croner LJ, Davies C, Davison TS, Delenstarr G, Deng X, Dorris D, Eklund AC, Fan XH, Fang H, Fulmer-Smentek S, Fuscoe JC, Gallagher K, Ge W, Guo L, Guo X, Hager J, Haje PK, Han J, Han T, Harbottle HC, Harris SC, Hatchwell E, Hauser CA, Hester S, Hong H, Hurban P, Jackson SA, Ji H, Knight CR, Kuo WP, LeClerc JE, Levy S, Li QZ, Liu C, Liu Y, Lombardi MJ, Ma Y, Magnuson SR, Maqsodi B, McDaniel T, Mei N, Myklebost O, Ning B, Novoradovskaya N, Orr MS, Osborn TW, Papallo A, Patterson TA, Perkins RG, Peters EH, Peterson R, Philips KL, Pine PS, Pusztai L, Qian F, Ren H, Rosen M, Rosenzweig BA, Samaha RR, Schena M, Schroth GP, Shchegrova S, Smith DD, Staedtler F, Su Z, Sun H, Szallasi Z, Tezak Z, Thierry-Mieg D, Thompson KL, Tikhonova I, Turpaz Y, Vallanat B, Van C, Walker SJ, Wang SJ, Wang Y, Wolfinger R, Wong A, Wu J, Xiao C, Xie Q, Xu J, Yang W, Zhang L, Zhong S, Zong Y, Slikker W Jr. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006 Sep;24(9):1151-61. [PubMed]

Perner S, Demichelis F, Beroukhim R, Schmidt FH, Mosquera JM, Setlur S, Tchinda J, Tomlins SA, Hofer MD, Pienta KG, Kuefer R, Vessella R, Sun XW, Meyerson M, Lee C, Sellers WR, Chinnaiyan AM, Rubin MA. TMPRSS2:ERG Fusion-Associated Deletions Provide Insight into the Heterogeneity of Prostate Cancer. Cancer research. 2006 Sep 1;66(17):8337-41. [PubMed]

Mehler EL, Hassan SA, Kortagere S, Weinstein H. Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin. Proteins. 2006 Aug 15;64(3):673-90. [PubMed]

Zhang Z, Wriggers W. Local feature analysis: a statistical theory for reproducible essential dynamics of large macromolecules. Proteins. 2006 Aug 1;64(2):391-403. [PubMed]

Christini DJ, Lerman BB. Implantable cardioverter-defibrillator detection of repolarization alternans: uncovering a marker of electrical instability. Heart rhythm : the official journal of the Heart Rhythm Society. 2006 Jul;3(7):798-9. [PubMed]

Niv MY, Skrabanek L, Filizola M, Weinstein H. Modeling activated states of GPCRs: the rhodopsin template. Journal of computer-aided molecular design. 2006 Jul-Aug;20(7-8):437-48. [PubMed]

Filizola M, Wang SX, Weinstein H. Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. Journal of computer-aided molecular design. 2006 Jul-Aug;20(7-8):405-16. [PubMed]

Speidel JA, Banfelder JR, and Mezei M. Automatic Control of Solvent Density in Grand Canonical Ensemble Monte Carlo Simulations, J. Chem. Theory and Comp. 2006. Jul 2(5): 1429-1434 [Abstract]

Della Mea V, Demichelis F, Viel F, Dalla Palma P, Beltrami CA. User attitudes in analyzing digital slides in a quality control test bed: a preliminary study. Computer methods and programs in biomedicine. 2006 May;82(2):177-86. [PubMed]

Yio X, Diamond M, Zhang JY, Weinstein H, Wang LH, Werther L, Itzkowitz S. Trefoil factor family-1 mutations enhance gastric cancer cell invasion through distinct signaling pathways. Gastroenterology. 2006 May;130(6):1696-706. [PubMed]

Deng X, Geng H, Ali HH. Joint learning of gene functions--a Bayesian network model approach. J Bioinform Comput Biol. 2006 Apr;4(2):217-39. [PubMed]

Slonim N, Elemento O, Tavazoie S. Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks. Mol Syst Biol. 2006;2:2006.0005. [PubMed]

Christini DJ, Riccio ML, Culianu CA, Fox JJ, Karma A, Gilmour RF Jr. Control of electrical alternans in canine cardiac purkinje fibers. Physical review letters. 2006 Mar 17;96(10):104101. [PubMed]

Lu S, Gong Y, Iwai S, Stein KM, Lerman BB, Christini DJ. Structural Barrier Increases QT-peak Dispersion in Swine Left Ventricle in Vivo. Conf Proc IEEE Eng Med Biol Soc. 2006;1:4039-4042. [PubMed]

Becton D, Dahl GV, Ravindranath Y, Chang MN, Behm FG, Raimondi SC, Head DR, Stine KC, Lacayo NJ, Sikic BI, Arceci RJ, Weinstein H. Randomized use of cyclosporin A (CsA) to modulate P-glycoprotein in children with AML in remission: Pediatric Oncology Group Study 9421. Blood. 2006 Feb 15;107(4):1315-24. [PubMed]

Hao G, Derakhshan B, Shi L, Campagne F, Gross SS. SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures. Proceedings of the National Academy of Sciences of the United States of America. 2006 Jan 24;103(4):1012-7. [PubMed]

Jordan PN, Christini DJ. Action potential morphology influences intracellular calcium handling stability and the occurrence of alternans. Biophysical journal. 2006 Jan 15;90(2):672-80. [PubMed]

Weinstein H. Hallucinogen actions on 5-HT receptors reveal distinct mechanisms of activation and signaling by G protein-coupled receptors. The AAPS journal. 2006 Jan 6;7(4):E871-84. [PubMed]

Bismar TA, Demichelis F, Riva A, Kim R, Varambally S, He L, Kutok J, Aster JC, Tang J, Kuefer R, Hofer MD, Febbo PG, Chinnaiyan AM, Rubin MA. Defining aggressive prostate cancer using a 12-gene model. Neoplasia (New York, N.Y.). 2006 Jan;8(1):59-68. [PubMed]

Demichelis F, Sboner A, Barbareschi M, Dell'Anna R. TMABoost: an integrated system for comprehensive management of tissue microarray data. IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society. 2006 Jan;10(1):19-27. [PubMed]

Victor JD, Mechler F, Repucci MA, Purpura KP, Sharpee T. Responses of V1 neurons to two-dimensional hermite functions. Journal of neurophysiology. 2006 Jan;95(1):379-400. [PubMed]

Victor, JD. Approaches to information-theoretic analysis of neural activity. Biological Theory. 2006. 1:302-316.

Glaaser IW, Clancy CE. Cardiac Na+ channels as therapeutic targets for antiarrhythmic agents. Handbook of experimental pharmacology. 2006;(171):99-121. [PubMed]

Shi L, Javitch JA. A role for information collection, management, and integration in structure-function studies of G-protein coupled receptors. Current pharmaceutical design. 2006;12(14):1771-83. [PubMed]

2005

Kim R, Demichelis F, Tang J, Riva A, Shen R, Gibbs DF, Mahavishno V, Chinnaiyan AM, Rubin MA. Internet-based Profiler system as integrative framework to support translational research. BMC bioinformatics. 2005 Dec 19;6:304. [PubMed]

Victor JD. Analyzing receptive fields, classification images and functional images: challenges with opportunities for synergy. Nature neuroscience. 2005 Dec;8(12):1651-6. [PubMed]

Chan CS, Elemento O, Tavazoie S. Revealing posttranscriptional regulatory elements through network-level conservation. PLoS Comput Biol. 2005 Dec;1(7):e69. [PubMed]

Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature biotechnology. 2005 Dec;23(12):1509-15. [PubMed]

Guo W, Shi L, Filizola M, Weinstein H, Javitch JA. Crosstalk in G protein-coupled receptors: changes at the transmembrane homodimer interface determine activation. Proceedings of the National Academy of Sciences of the United States of America. 2005 Nov 29;102(48):17495-500. [PubMed]

Cong Y, Jiang W, Birmanns S, Zhou ZH, Chiu W, Wriggers W. Fast rotational matching of single-particle images. Journal of structural biology. 2005 Nov;152(2):104-12. [PubMed]

Sen N, Shi L, Beuming T, Weinstein H, Javitch JA. A pincer-like configuration of TM2 in the human dopamine transporter is responsible for indirect effects on cocaine binding. Neuropharmacology. 2005 Nov;49(6):780-90. [PubMed]

Niv MY, Weinstein H. A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains. Journal of the American Chemical Society. 2005 Oct 12;127(40):14072-9. [PubMed]

Victor JD. Spike train metrics. Current opinion in neurobiology. 2005 Oct;15(5):585-92. [PubMed]

Carter M, Chen X, Slowinska B, Minnerath S, Glickstein S, Shi L, Campagne F, Weinstein H, Ross ME. Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6. Proceedings of the National Academy of Sciences of the United States of America. 2005 Sep 6;102(36):12843-8. [PubMed]

Dell'Anna R, Demichelis F, Barbareschi M, Sboner A. An automated procedure to properly handle digital images in large scale tissue microarray experiments. Computer methods and programs in biomedicine. 2005 Sep;79(3):197-208. [PubMed]

Filizola M, Weinstein H. The structure and dynamics of GPCR oligomers: a new focus in models of cell-signaling mechanisms and drug design. Current opinion in drug discovery & development. 2005 Sep;8(5):577-84. [PubMed]

Deng X, Geng H, Ali H. EXAMINE: a computational approach to reconstructing gene regulatory networks. Biosystems. 2005 Aug;81(2):125-36. [PubMed]

Maybhate A, Hao SC, Iwai S, Lee JU, Guttigoli AB, Stein KM, Lerman BB, Christini DJ. Detection of repolarization alternans with an implantable cardioverter defibrillator lead in a porcine model. IEEE transactions on bio-medical engineering. 2005 Jul;52(7):1188-94. [PubMed]

Krogh-Madsen T, Schaffer P, Skriver AD, Taylor LK, Pelzmann B, Koidl B, Guevara MR. An ionic model for rhythmic activity in small clusters of embryonic chick ventricular cells. Am J Physiol Heart Circ Physiol. 2005 Jul;289(1):H398-413. [PubMed]

Filizola M, Weinstein H. The study of G-protein coupled receptor oligomerization with computational modeling and bioinformatics. The FEBS journal. 2005 Jun;272(12):2926-38. [PubMed]

Zhu ZI, Clancy CE. From mutation to clinical presentation: mechanisms in the black box. Journal of molecular and cellular cardiology. 2005 Jun;38(6):965-8. [PubMed]

Madsen KL, Beuming T, Niv MY, Chang CW, Dev KK, Weinstein H, Gether U. Molecular determinants for the complex binding specificity of the PDZ domain in PICK1. The Journal of biological chemistry. 2005 May 27;280(21):20539-48. [PubMed]

Latham PE, Nirenberg S. Synergy, redundancy, and independence in population codes, revisited. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2005 May 25;25(21):5195-206. [PubMed]

Palma M, Zurita J, Ferreras JA, Worgall S, Larone DH, Shi L, Campagne F, Quadri LE. Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response. Infection and immunity. 2005 May;73(5):2958-66. [PubMed]

Culjkovic B, Topisirovic I, Skrabanek L, Ruiz-Gutierrez M, Borden KL. eIF4E promotes nuclear export of cyclin D1 mRNAs via an element in the 3'UTR. The Journal of cell biology. 2005 Apr 25;169(2):245-56. [PubMed]

Hassan SA, Gracia L, Vasudevan G, Steinbach PJ. Computer simulation of protein-ligand interactions: challenges and applications. Methods Mol Biol. 2005;305:451-92. [PubMed]

Shi L, Campagne F. Building a protein name dictionary from full text: a machine learning term extraction approach. BMC bioinformatics. 2005 Apr 7;6:88. [PubMed]

Angelini TE, Liang H, Wriggers W, Wong GC. Direct observation of counterion organization in F-actin polyelectrolyte bundles. Eur Phys J E Soft Matter. 2005 Apr;16(4):389-400. [PubMed]

Victor JD, Conte MM. Local processes and spatial pooling in texture and symmetry detection. Vision research. 2005 Apr;45(8):1063-73. [PubMed]

Terrenoire C, Clancy CE, Cormier JW, Sampson KJ, Kass RS. Autonomic control of cardiac action potentials: role of potassium channel kinetics in response to sympathetic stimulation. Circulation research. 2005 Mar 18;96(5):e25-34. [PubMed]

Tsai JJ, Victor JD. Binocular depth perception from unpaired image points need not depend on scene organization. Vision research. 2005 Mar;45(5):527-32. [PubMed]

Beuming T, Weinstein H. Modeling membrane proteins based on low-resolution electron microscopy maps: a template for the TM domains of the oxalate transporter OxlT. Protein engineering, design & selection : PEDS. 2005 Mar;18(3):119-25. [PubMed]

Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H. PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics (Oxford, England). 2005 Mar;21(6):827-8. [PubMed]

Victor JD, Chubb C, Conte MM. Interaction of luminance and higher-order statistics in texture discrimination. Vision research. 2005 Feb;45(3):311-28. [PubMed]

Srdanovic M, Schenk U, Schwieger M, Campagne F. Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. BMC bioinformatics. 2005 Jan 10;6:5. [PubMed]

Wriggers W, Chakravarty S, Jennings PA. Control of protein functional dynamics by peptide linkers. Biopolymers. 2005;80(6):736-46. [PubMed]

Jordan PN, Christini DJ. Therapies for ventricular cardiac arrhythmias. Critical reviews in biomedical engineering. 2005;33(6):557-604. [PubMed]

Royer A, Demolombe S, El Harchi A, Le Quang K, Piron J, Toumaniantz G, Mazurais D, Bellocq C, Lande G, Terrenoire C, Motoike HK, Chevallier JC, Loussouarn G, Clancy CE, Escande D, Charpentier F. Expression of human ERG K+ channels in the mouse heart exerts anti-arrhythmic activity. Cardiovascular research. 2005 Jan 1;65(1):128-37. [PubMed]

Clancy CE, Kass RS. Inherited and acquired vulnerability to ventricular arrhythmias: cardiac Na+ and K+ channels. Physiological reviews. 2005 Jan;85(1):33-47. [PubMed]

Zhong Q, Roychowdhury V, Boykin P, Nirenberg S. Non-Poisson Fluctuation Statistics In Neuronal Inter-Spike Intervals (ISI): Hurst parameter Estimates of Mouse Retinal Ganglion Signals. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2005;2:2095-8. [PubMed]

Zhong Q, Roychowdhury V, Boykin P, Jacobs A, Nirenberg S. A filter based encoding model for mouse retinal ganglion cells. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2005;2:2087-90. [PubMed]

Xu L, Hui AY, Albanis E, Arthur MJ, O'Byrne SM, Blaner WS, Mukherjee P, Friedman SL, Eng FJ. Human hepatic stellate cell lines, LX-1 and LX-2: new tools for analysis of hepatic fibrosis. Gut. 2005 Jan;54(1):142-51. [PubMed]

Elemento O, Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol. 2005;6(2):R18. [PubMed]

Deng X, Geng H, Ali H. Learning yeast gene functions from heterogeneous sources of data using hybrid weighted Bayesian networks. Proc IEEE Comput Syst Bioinform Conf. 2005;:25-34. [PubMed]

2004

Arai R, Wriggers W, Nishikawa Y, Nagamune T, Fujisawa T. Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering. Proteins. 2004 Dec 1;57(4):829-38. [PubMed]

McCarthy PL Jr, Paltiel O, Maslova E, Kulikov S, Hahn T, Kopecky KJ, Drozdova V, Shmatina N, Tichonova L, Van Hoff J, Gavrilova I, Weinstein H. Histopathologic verification of acute leukemia (AL) in a cohort of 463 post-Chernobyl patients from Belarus, Russia and Ukraine. Leukemia research. 2004 Dec;28(12):1273-80. [PubMed]

Kortagere S, Gmeiner P, Weinstein H, Schetz JA. Certain 1,4-disubstituted aromatic piperidines and piperazines with extreme selectivity for the dopamine D4 receptor interact with a common receptor microdomain. Molecular pharmacology. 2004 Dec;66(6):1491-9. [PubMed]

Markowitz SM, Christini DJ, Stein KM, Mittal S, Iwai S, Slotwiner DJ, Lerman BB. Time course and predictors of autonomic dysfunction after ablation of the slow atrioventricular nodal pathway. Pacing and clinical electrophysiology : PACE. 2004 Dec;27(12):1638-43. [PubMed]

Lacayo NJ, Meshinchi S, Kinnunen P, Yu R, Wang Y, Stuber CM, Douglas L, Wahab R, Becton DL, Weinstein H, Chang MN, Willman CL, Radich JP, Tibshirani R, Ravindranath Y, Sikic BI, Dahl GV. Gene expression profiles at diagnosis in de novo childhood AML patients identify FLT3 mutations with good clinical outcomes. Blood. 2004 Nov 1;104(9):2646-54. [PubMed]

Jung JC, Mehta AD, Aksay E, Stepnoski R, Schnitzer MJ. In vivo mammalian brain imaging using one- and two-photon fluorescence microendoscopy. Journal of neurophysiology. 2004 Nov;92(5):3121-33. [PubMed]

Santagata S, Demichelis F, Riva A, Varambally S, Hofer MD, Kutok JL, Kim R, Tang J, Montie JE, Chinnaiyan AM, Rubin MA, Aster JC. JAGGED1 expression is associated with prostate cancer metastasis and recurrence. Cancer research. 2004 Oct 1;64(19):6854-7. [PubMed]

Jordan PN, Christini DJ. Adaptive diastolic interval control of cardiac action potential duration alternans. Journal of cardiovascular electrophysiology. 2004 Oct;15(10):1177-85. [PubMed]

Krogh-Madsen T, Glass L, Doedel EJ, Guevara MR. Apparent discontinuities in the phase-resetting response of cardiac pacemakers. J Theor Biol. 2004 Oct 21;230(4):499-519. [PubMed]

Campagne F, Neves S, Chang CW, Skrabanek L, Ram PT, Iyengar R, Weinstein H. Quantitative information management for the biochemical computation of cellular networks. Science's STKE : signal transduction knowledge environment. 2004 Aug 24;2004(248):pl11. [PubMed]

Beuming T, Weinstein H. A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins. Bioinformatics (Oxford, England). 2004 Aug 12;20(12):1822-35. [PubMed]

Jordan PN, Christini DJ. Determining the effects of memory and action potential duration alternans on cardiac restitution using a constant-memory restitution protocol. Physiological measurement. 2004 Aug;25(4):1013-24. [PubMed]

Dutheil N, Yoon-Robarts M, Ward P, Henckaerts E, Skrabanek L, Berns KI, Campagne F, Linden RM. Characterization of the mouse adeno-associated virus AAVS1 ortholog. Journal of virology. 2004 Aug;78(16):8917-21. [PubMed]

Latham PE, Nirenberg S. Computing and stability in cortical networks. Neural computation. 2004 Jul;16(7):1385-412. [PubMed]

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