Ziv Bar-Joseph - Publications

Affiliations: 
Carnegie Mellon University, Pittsburgh, PA 
Area:
Computer Science, Bioinformatics Biology, Statistics

73 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Navlakha S, Bar-Joseph Z, Barth AL. Network Design and the Brain. Trends in Cognitive Sciences. PMID 29054336 DOI: 10.1016/j.tics.2017.09.012  0.4
2017 Lin C, Jain S, Kim H, Bar-Joseph Z. Using neural networks for reducing the dimensions of single-cell RNA-Seq data. Nucleic Acids Research. 45: e156. PMID 28973464 DOI: 10.1093/nar/gkx681  0.44
2016 Venkatachari NJ, Jain S, Walker L, Bivalkar-Mehla S, Chattopadhyay A, Bar-Joseph Z, Rinaldo C, Ragin A, Seaberg E, Levine A, Becker J, Martin E, Sacktor N, Ayyavoo V. Transcriptome analyses identify key cellular factors associated with HIV-1 associated neuropathogenesis in infected men. Aids (London, England). PMID 28005686 DOI: 10.1097/QAD.0000000000001379  0.44
2016 Jain S, Arrais J, Venkatachari NJ, Ayyavoo V, Bar-Joseph Z. Reconstructing the temporal progression of HIV-1 immune response pathways. Bioinformatics (Oxford, England). 32: i253-i261. PMID 27307624 DOI: 10.1093/bioinformatics/btw254  0.44
2016 Gitter A, Bar-Joseph Z. The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease Progression. Methods in Molecular Biology (Clifton, N.J.). 1303: 493-506. PMID 26235087 DOI: 10.1007/978-1-4939-2627-5_30  1
2015 Chandrasekaran S, Navlakha S, Audette NJ, McCreary DD, Suhan J, Bar-Joseph Z, Barth AL. Unbiased, High-Throughput Electron Microscopy Analysis of Experience-Dependent Synaptic Changes in the Neocortex. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 35: 16450-62. PMID 26674870 DOI: 10.1523/JNEUROSCI.1573-15.2015  1
2015 Venkatachari NJ, Zerbato JM, Jain S, Mancini AE, Chattopadhyay A, Sluis-Cremer N, Bar-Joseph Z, Ayyavoo V. Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch. Retrovirology. 12: 85. PMID 26438393 DOI: 10.1186/s12977-015-0211-3  1
2015 He X, Cicek AE, Wang Y, Schulz MH, Le HS, Bar-Joseph Z. De novo ChIP-seq analysis. Genome Biology. 16: 205. PMID 26400819 DOI: 10.1186/s13059-015-0756-4  1
2015 Navlakha S, Barth AL, Bar-Joseph Z. Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks. Plos Computational Biology. 11: e1004347. PMID 26217933 DOI: 10.1371/journal.pcbi.1004347  0.4
2015 Zinman GE, Naiman S, O'Dee DM, Kumar N, Nau GJ, Cohen HY, Bar-Joseph Z. ModuleBlast: identifying activated sub-networks within and across species. Nucleic Acids Research. 43: e20. PMID 25428368 DOI: 10.1093/nar/gku1224  1
2014 Jain S, Gitter A, Bar-Joseph Z. Multitask learning of signaling and regulatory networks with application to studying human response to flu. Plos Computational Biology. 10: e1003943. PMID 25522349 DOI: 10.1371/journal.pcbi.1003943  1
2014 Modena BD, Tedrow JR, Milosevic J, Bleecker ER, Meyers DA, Wu W, Bar-Joseph Z, Erzurum SC, Gaston BM, Busse WW, Jarjour NN, Kaminski N, Wenzel SE. Gene expression in relation to exhaled nitric oxide identifies novel asthma phenotypes with unique biomolecular pathways. American Journal of Respiratory and Critical Care Medicine. 190: 1363-72. PMID 25338189 DOI: 10.1164/rccm.201406-1099OC  1
2014 Navlakha S, He X, Faloutsos C, Bar-Joseph Z. Topological properties of robust biological and computational networks. Journal of the Royal Society, Interface / the Royal Society. 11: 20140283. PMID 24789562 DOI: 10.1098/rsif.2014.0283  0.4
2014 Blackwell TS, Tager AM, Borok Z, Moore BB, Schwartz DA, Anstrom KJ, Bar-Joseph Z, Bitterman P, Blackburn MR, Bradford W, Brown KK, Chapman HA, Collard HR, Cosgrove GP, Deterding R, et al. Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report. American Journal of Respiratory and Critical Care Medicine. 189: 214-22. PMID 24160862 DOI: 10.1164/rccm.201306-1141WS  1
2013 Zhou Y, Vazquez A, Wise A, Warita T, Warita K, Bar-Joseph Z, Oltvai ZN. Carbon catabolite repression correlates with the maintenance of near invariant molecular crowding in proliferating E. coli cells. Bmc Systems Biology. 7: 138. PMID 24330501 DOI: 10.1186/1752-0509-7-138  0.32
2013 Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z. ExpressionBlast: mining large, unstructured expression databases. Nature Methods. 10: 925-6. PMID 24076985 DOI: 10.1038/nmeth.2630  1
2013 Navlakha S, Suhan J, Barth AL, Bar-Joseph Z. A high-throughput framework to detect synapses in electron microscopy images. Bioinformatics (Oxford, England). 29: i9-17. PMID 23813014 DOI: 10.1093/bioinformatics/btt222  1
2013 Gitter A, Bar-Joseph Z. Identifying proteins controlling key disease signaling pathways. Bioinformatics (Oxford, England). 29: i227-36. PMID 23812988 DOI: 10.1093/bioinformatics/btt241  1
2013 Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, ... ... Bar-Joseph Z, et al. Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis. Elife. 2: e00675. PMID 23795294 DOI: 10.7554/eLife.00675  1
2013 Duskova K, Nagilla P, Le HS, Iyer P, Thalamuthu A, Martinson J, Bar-Joseph Z, Buchanan W, Rinaldo C, Ayyavoo V. MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts. Bmc Infectious Diseases. 13: 250. PMID 23721325 DOI: 10.1186/1471-2334-13-250  1
2013 Gitter A, Carmi M, Barkai N, Bar-Joseph Z. Linking the signaling cascades and dynamic regulatory networks controlling stress responses. Genome Research. 23: 365-76. PMID 23064748 DOI: 10.1101/gr.138628.112  1
2012 Navlakha S, Gitter A, Bar-Joseph Z. A network-based approach for predicting missing pathway interactions. Plos Computational Biology. 8: e1002640. PMID 22916002 DOI: 10.1371/journal.pcbi.1002640  1
2012 Schulz MH, Devanny WE, Gitter A, Zhong S, Ernst J, Bar-Joseph Z. DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data. Bmc Systems Biology. 6: 104. PMID 22897824 DOI: 10.1186/1752-0509-6-104  1
2012 Bar-Joseph Z, Gitter A, Simon I. Studying and modelling dynamic biological processes using time-series gene expression data. Nature Reviews. Genetics. 13: 552-64. PMID 22805708 DOI: 10.1038/nrg3244  1
2012 Wise A, Oltvai ZN, Bar-Joseph Z. Matching experiments across species using expression values and textual information. Bioinformatics (Oxford, England). 28: i258-64. PMID 22689770 DOI: 10.1093/bioinformatics/bts205  0.32
2012 Kanfi Y, Naiman S, Amir G, Peshti V, Zinman G, Nahum L, Bar-Joseph Z, Cohen HY. The sirtuin SIRT6 regulates lifespan in male mice. Nature. 483: 218-21. PMID 22367546 DOI: 10.1038/nature10815  1
2011 Navlakha S, Bar-Joseph Z. Algorithms in nature: the convergence of systems biology and computational thinking. Molecular Systems Biology. 7: 546. PMID 22068329 DOI: 10.1038/msb.2011.78  0.4
2011 Lin TH, Bar-Joseph Z, Murphy RF. Learning cellular sorting pathways using protein interactions and sequence motifs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1709-22. PMID 21999284 DOI: 10.1089/cmb.2011.0193  1
2011 Zinman GE, Zhong S, Bar-Joseph Z. Biological interaction networks are conserved at the module level. Bmc Systems Biology. 5: 134. PMID 21861884 DOI: 10.1186/1752-0509-5-134  1
2011 Gupta A, Nagilla P, Le HS, Bunney C, Zych C, Thalamuthu A, Bar-Joseph Z, Mathavan S, Ayyavoo V. Comparative expression profile of miRNA and mRNA in primary peripheral blood mononuclear cells infected with human immunodeficiency virus (HIV-1). Plos One. 6: e22730. PMID 21829495 DOI: 10.1371/journal.pone.0022730  0.36
2011 Huggins P, Zhong S, Shiff I, Beckerman R, Laptenko O, Prives C, Schulz MH, Simon I, Bar-Joseph Z. DECOD: fast and accurate discriminative DNA motif finding. Bioinformatics (Oxford, England). 27: 2361-7. PMID 21752801 DOI: 10.1093/bioinformatics/btr412  1
2011 Kellis M, Califano A, Bar-Joseph Z. Preface: RECOMB Conference on Systems Biology, Regulatory Genomics, and DREAM Challenges 2010 special issue. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 131. PMID 21314452 DOI: 10.1089/cmb.2010.005p  0.36
2011 Lin TH, Murphy RF, Bar-Joseph Z. Discriminative motif finding for predicting protein subcellular localization. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 441-51. PMID 21233524 DOI: 10.1109/TCBB.2009.82  1
2011 Afek Y, Alon N, Barad O, Hornstein E, Barkai N, Bar-Joseph Z. A biological solution to a fundamental distributed computing problem. Science (New York, N.Y.). 331: 183-5. PMID 21233379 DOI: 10.1126/science.1193210  1
2011 Gitter A, Klein-Seetharaman J, Gupta A, Bar-Joseph Z. Discovering pathways by orienting edges in protein interaction networks. Nucleic Acids Research. 39: e22. PMID 21109539 DOI: 10.1093/nar/gkq1207  1
2010 Gitter A, Lu Y, Bar-Joseph Z. Computational methods for analyzing dynamic regulatory networks. Methods in Molecular Biology (Clifton, N.J.). 674: 419-41. PMID 20827605 DOI: 10.1007/978-1-60761-854-6_24  1
2010 Klutstein M, Siegfried Z, Gispan A, Farkash-Amar S, Zinman G, Bar-Joseph Z, Simchen G, Simon I. Combination of genomic approaches with functional genetic experiments reveals two modes of repression of yeast middle-phase meiosis genes. Bmc Genomics. 11: 478. PMID 20716365 DOI: 10.1186/1471-2164-11-478  1
2010 Le HS, Oltvai ZN, Bar-Joseph Z. Cross-species queries of large gene expression databases. Bioinformatics (Oxford, England). 26: 2416-23. PMID 20702396 DOI: 10.1093/bioinformatics/btq451  0.32
2010 Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biology. 11: R77. PMID 20653936 DOI: 10.1186/gb-2010-11-7-r77  1
2010 Lu Y, Rosenfeld R, Nau GJ, Bar-Joseph Z. Cross species expression analysis of innate immune response. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 253-68. PMID 20377444 DOI: 10.1089/cmb.2009.0147  0.44
2010 Ernst J, Plasterer HL, Simon I, Bar-Joseph Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Research. 20: 526-36. PMID 20219943 DOI: 10.1101/gr.096305.109  0.4
2009 Ernst J, Ghanem L, Bar-Joseph Z, McNamara M, Brown J, Steinman RA. IL-3 and oncogenic Abl regulate the myeloblast transcriptome by altering mRNA stability. Plos One. 4: e7469. PMID 19829692 DOI: 10.1371/journal.pone.0007469  0.32
2009 Qi Y, Dhiman HK, Bhola N, Budyak I, Kar S, Man D, Dutta A, Tirupula K, Carr BI, Grandis J, Bar-Joseph Z, Klein-Seetharaman J. Systematic prediction of human membrane receptor interactions. Proteomics. 9: 5243-55. PMID 19798668 DOI: 10.1002/pmic.200900259  0.6
2009 Shi Y, Klutstein M, Simon I, Mitchell T, Bar-Joseph Z. A combined expression-interaction model for inferring the temporal activity of transcription factors Journal of Computational Biology. 16: 1035-1049. PMID 19630541 DOI: 10.1089/cmb.2009.0024  1
2009 Li L, Lu Y, Qin LX, Bar-Joseph Z, Werner-Washburne M, Breeden LL. Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells. Molecular Biology of the Cell. 20: 3851-64. PMID 19570907 DOI: 10.1091/mbc.E09-04-0347  0.44
2009 Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, Bar-Joseph Z. Backup in gene regulatory networks explains differences between binding and knockout results. Molecular Systems Biology. 5: 276. PMID 19536199 DOI: 10.1038/msb.2009.33  1
2009 Lu Y, Huggins P, Bar-Joseph Z. Cross species analysis of microarray expression data. Bioinformatics (Oxford, England). 25: 1476-83. PMID 19357096 DOI: 10.1093/bioinformatics/btp247  1
2008 Lu Y, Rosenfeld R, Simon I, Nau GJ, Bar-Joseph Z. A probabilistic generative model for GO enrichment analysis. Nucleic Acids Research. 36: e109. PMID 18676451 DOI: 10.1093/nar/gkn434  0.44
2008 Peña-Castillo L, Tasan M, Myers CL, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim WK, Krumpelman C, Tian W, Obozinski G, Qi Y, Mostafavi S, ... ... Bar-Joseph Z, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology. 9: S2. PMID 18613946 DOI: 10.1186/gb-2008-9-s1-s2  1
2008 Qi Y, Balem F, Faloutsos C, Klein-Seetharaman J, Bar-Joseph Z. Protein complex identification by supervised graph local clustering. Bioinformatics (Oxford, England). 24: i250-8. PMID 18586722 DOI: 10.1093/bioinformatics/btn164  0.6
2008 Lin TH, Kaminski N, Bar-Joseph Z. Alignment and classification of time series gene expression in clinical studies. Bioinformatics (Oxford, England). 24: i147-55. PMID 18586707 DOI: 10.1093/bioinformatics/btn152  1
2008 Gupta A, Bar-Joseph Z. Extracting dynamics from static cancer expression data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 5: 172-82. PMID 18451427 DOI: 10.1109/TCBB.2007.70233  0.36
2008 Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z. A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. Plos Computational Biology. 4: e1000044. PMID 18369434 DOI: 10.1371/journal.pcbi.1000044  0.32
2008 Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, Barabási AL, Boros LG, Oltvai ZN. Impact of the solvent capacity constraint on E. coli metabolism. Bmc Systems Biology. 2: 7. PMID 18215292 DOI: 10.1186/1752-0509-2-7  0.32
2008 Bar-Joseph Z, Siegfried Z, Brandeis M, Brors B, Lu Y, Eils R, Dynlacht BD, Simon I. Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proceedings of the National Academy of Sciences of the United States of America. 105: 955-60. PMID 18195366 DOI: 10.1073/pnas.0704723105  1
2007 Qi Y, Klein-Seetharaman J, Bar-Joseph Z. A mixture of feature experts approach for protein-protein interaction prediction. Bmc Bioinformatics. 8: S6. PMID 18269700 DOI: 10.1186/1471-2105-8-S10-S6  0.6
2007 Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z. Combined analysis reveals a core set of cycling genes. Genome Biology. 8: R146. PMID 17650318 DOI: 10.1186/gb-2007-8-7-r146  0.44
2007 Shi Y, Klustein M, Simon I, Mitchell T, Bar-Joseph Z. Continuous hidden process model for time series expression experiments Bioinformatics. 23: i459-i467. PMID 17646331 DOI: 10.1093/bioinformatics/btm218  1
2007 Kaminski N, Bar-Joseph Z. A patient-gene model for temporal expression profiles in clinical studies. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 324-38. PMID 17563314 DOI: 10.1089/cmb.2007.0001  1
2007 Shi Y, Mitchell T, Bar-Joseph Z. Inferring pairwise regulatory relationships from multiple time series datasets Bioinformatics. 23: 755-763. PMID 17237067 DOI: 10.1093/bioinformatics/btl676  1
2007 Ernst J, Vainas O, Harbison CT, Simon I, Bar-Joseph Z. Reconstructing dynamic regulatory maps. Molecular Systems Biology. 3: 74. PMID 17224918 DOI: 10.1038/msb4100115  0.4
2006 Lu Y, Rosenfeld R, Bar-Joseph Z. Identifying cycling genes by combining sequence homology and expression data. Bioinformatics (Oxford, England). 22: e314-22. PMID 16873488 DOI: 10.1093/bioinformatics/btl229  0.44
2006 Ernst J, Bar-Joseph Z. STEM: a tool for the analysis of short time series gene expression data. Bmc Bioinformatics. 7: 191. PMID 16597342 DOI: 10.1186/1471-2105-7-191  0.32
2006 Qi Y, Bar-Joseph Z, Klein-Seetharaman J. Evaluation of different biological data and computational classification methods for use in protein interaction prediction. Proteins. 63: 490-500. PMID 16450363 DOI: 10.1002/prot.20865  0.6
2005 Simon I, Siegfried Z, Ernst J, Bar-Joseph Z. Combined static and dynamic analysis for determining the quality of time-series expression profiles. Nature Biotechnology. 23: 1503-8. PMID 16333294 DOI: 10.1038/nbt1164  0.4
2005 Ernst J, Nau GJ, Bar-Joseph Z. Clustering short time series gene expression data. Bioinformatics (Oxford, England). 21: i159-68. PMID 15961453 DOI: 10.1093/bioinformatics/bti1022  0.32
2005 Qi Y, Klein-Seetharaman J, Bar-Joseph Z. Random forest similarity for protein-protein interaction prediction from multiple sources. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 531-42. PMID 15759657  0.6
2004 Bar-Joseph Z, Farkash S, Gifford DK, Simon I, Rosenfeld R. Deconvolving cell cycle expression data with complementary information. Bioinformatics (Oxford, England). 20: i23-30. PMID 15262777 DOI: 10.1093/bioinformatics/bth915  0.4
2003 Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nature Biotechnology. 21: 1337-42. PMID 14555958 DOI: 10.1038/nbt890  1
2003 Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous representations of time-series gene expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 341-56. PMID 12935332 DOI: 10.1089/10665270360688057  1
2003 Bar-Joseph Z, Gerber G, Simon I, Gifford DK, Jaakkola TS. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proceedings of the National Academy of Sciences of the United States of America. 100: 10146-51. PMID 12934016 DOI: 10.1073/pnas.1732547100  1
2003 Bar-Joseph Z, Demaine ED, Gifford DK, Srebro N, Hamel AM, Jaakkola TS. K-ary clustering with optimal leaf ordering for gene expression data. Bioinformatics (Oxford, England). 19: 1070-8. PMID 12801867 DOI: 10.1093/bioinformatics/btg030  1
2002 Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (New York, N.Y.). 298: 799-804. PMID 12399584 DOI: 10.1126/science.1075090  1
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