| Year |
Citation |
Score |
| 2023 |
Hislop J, Song Q, Keshavarz F K, Alavi A, Schoenberger R, LeGraw R, Velazquez J, Mokhtari T, Taheri MN, Rytel M, Chuva de Sousa Lopes SM, Watkins S, Stolz D, Kiani S, Sozen B, ... Bar-Joseph Z, et al. Modeling post-implantation human development to yolk sac blood emergence. Nature. PMID 38092041 DOI: 10.1038/s41586-023-06914-8 |
0.386 |
|
| 2023 |
Hislop J, Alavi A, Song Q, Schoenberger R, Keshavarz F K, LeGraw R, Velazquez J, Mokhtari T, Taheri MN, Rytel M, de Sousa Lopes SMC, Watkins S, Stolz D, Kiani S, Sozen B, ... Bar-Joseph Z, et al. Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. Biorxiv : the Preprint Server For Biology. PMID 37398391 DOI: 10.1101/2023.06.15.545118 |
0.381 |
|
| 2023 |
Song Q, Ruffalo M, Bar-Joseph Z. Using single cell atlas data to reconstruct regulatory networks. Nucleic Acids Research. PMID 36762475 DOI: 10.1093/nar/gkad053 |
0.537 |
|
| 2022 |
Berger B, Tian D, Li WV, El-Kebir M, Tomescu AI, Singh R, Beerenwinkel N, Li Y, Boucher C, Bar-Joseph Z. What are the keys to succeeding as a computational biologist in today's research climate? Cell Systems. 13: 781-785. PMID 36265464 DOI: 10.1016/j.cels.2022.09.005 |
0.65 |
|
| 2022 |
Li D, Ding J, Bar-Joseph Z. UNIFAN: A Tool for Unsupervised Single-Cell Clustering and Annotation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 36036832 DOI: 10.1089/cmb.2022.0251 |
0.407 |
|
| 2022 |
Song Q, Wang J, Bar-Joseph Z. scSTEM: clustering pseudotime ordered single-cell data. Genome Biology. 23: 150. PMID 35799304 DOI: 10.1186/s13059-022-02716-9 |
0.484 |
|
| 2022 |
Li D, Ding J, Bar-Joseph Z. Unsupervised cell functional annotation for single-cell RNA-seq. Genome Research. PMID 35764397 DOI: 10.1101/gr.276609.122 |
0.451 |
|
| 2022 |
Hasanaj E, Wang J, Sarathi A, Ding J, Bar-Joseph Z. Interactive single-cell data analysis using Cellar. Nature Communications. 13: 1998. PMID 35422041 DOI: 10.1038/s41467-022-29744-0 |
0.433 |
|
| 2022 |
Li D, Velazquez JJ, Ding J, Hislop J, Ebrahimkhani MR, Bar-Joseph Z. TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. Genome Biology. 23: 73. PMID 35255944 DOI: 10.1186/s13059-022-02629-7 |
0.45 |
|
| 2022 |
Ding J, Sharon N, Bar-Joseph Z. Temporal modelling using single-cell transcriptomics. Nature Reviews. Genetics. PMID 35102309 DOI: 10.1038/s41576-021-00444-7 |
0.495 |
|
| 2021 |
Ding J, Alavi A, Ebrahimkhani MR, Bar-Joseph Z. Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. Cell Reports Methods. 1: 100087. PMID 35474899 DOI: 10.1016/j.crmeth.2021.100087 |
0.412 |
|
| 2021 |
Yuan Y, Bar-Joseph Z. Deep learning of gene relationships from single cell time-course expression data. Briefings in Bioinformatics. PMID 33876191 DOI: 10.1093/bib/bbab142 |
0.327 |
|
| 2021 |
Ruiz-Perez D, Lugo-Martinez J, Bourguignon N, Mathee K, Lerner B, Bar-Joseph Z, Narasimhan G. Dynamic Bayesian Networks for Integrating Multi-omics Time Series Microbiome Data. Msystems. 6. PMID 33785573 DOI: 10.1128/mSystems.01105-20 |
0.338 |
|
| 2020 |
Ding J, Lugo-Martinez J, Yuan Y, Kotton DN, Bar-Joseph Z. Reconstructing SARS-CoV-2 response signaling and regulatory networks. Biorxiv : the Preprint Server For Biology. PMID 33083801 DOI: 10.1101/2020.06.01.127589 |
0.481 |
|
| 2020 |
Li D, Ding J, Bar-Joseph Z. Identifying signaling genes in spatial single cell expression data. Bioinformatics (Oxford, England). PMID 32886099 DOI: 10.1093/Bioinformatics/Btaa769 |
0.533 |
|
| 2020 |
Zafar H, Lin C, Bar-Joseph Z. Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data. Nature Communications. 11: 3055. PMID 32546686 DOI: 10.1038/S41467-020-16821-5 |
0.342 |
|
| 2020 |
Zander M, Lewsey MG, Clark NM, Yin L, Bartlett A, Saldierna Guzmán JP, Hann E, Langford AE, Jow B, Wise A, Nery JR, Chen H, Bar-Joseph Z, Walley JW, Solano R, et al. Integrated multi-omics framework of the plant response to jasmonic acid. Nature Plants. 6: 290-302. PMID 32170290 DOI: 10.1038/S41477-020-0605-7 |
0.37 |
|
| 2020 |
Lin C, Ding J, Bar-Joseph Z. Inferring TF activation order in time series scRNA-Seq studies. Plos Computational Biology. 16: e1007644. PMID 32069291 DOI: 10.1371/Journal.Pcbi.1007644 |
0.544 |
|
| 2020 |
Hurley K, Ding J, Villacorta-Martin C, Herriges MJ, Jacob A, Vedaie M, Alysandratos KD, Sun YL, Lin C, Werder RB, Huang J, Wilson AA, Mithal A, Mostoslavsky G, Oglesby I, ... ... Bar-Joseph Z, et al. Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. Cell Stem Cell. PMID 32004478 DOI: 10.1016/J.Stem.2019.12.009 |
0.451 |
|
| 2020 |
Ding J, Bar-Joseph Z. Analysis of time-series regulatory networks Current Opinion in Systems Biology. 21: 16-24. DOI: 10.1016/J.Coisb.2020.07.005 |
0.386 |
|
| 2019 |
Yuan Y, Bar-Joseph Z. Deep learning for inferring gene relationships from single-cell expression data. Proceedings of the National Academy of Sciences of the United States of America. PMID 31822622 DOI: 10.1073/Pnas.1911536116 |
0.453 |
|
| 2019 |
McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, ... ... Bar-Joseph Z, et al. Transcriptional regulatory model of fibrosis progression in the human lung. Jci Insight. PMID 31600171 DOI: 10.1172/Jci.Insight.131597 |
0.493 |
|
| 2019 |
Liu H, Zhang CH, Ammanamanchi N, Suresh S, Lewarchik C, Rao K, Uys GM, Han L, Abrial M, Yimlamai D, Ganapathy B, Guillermier C, Chen N, Khaladkar M, Spaethling J, ... ... Bar-Joseph Z, et al. Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. Science Translational Medicine. 11. PMID 31597755 DOI: 10.1126/Scitranslmed.Aaw6419 |
0.419 |
|
| 2019 |
Ding J, Ahangari F, Espinoza CR, Chhabra D, Nicola T, Yan X, Lal CV, Hagood JS, Kaminski N, Bar-Joseph Z, Ambalavanan N. Integrating multi-omics longitudinal data to reconstruct networks underlying lung development. American Journal of Physiology. Lung Cellular and Molecular Physiology. PMID 31432713 DOI: 10.1152/Ajplung.00554.2018 |
0.525 |
|
| 2019 |
Rashid S, Long Z, Singh S, Kohram M, Vashistha H, Navlakha S, Salman H, Oltvai ZN, Bar-Joseph Z. Adjustment in tumbling rates improves bacterial chemotaxis on obstacle-laden terrains. Proceedings of the National Academy of Sciences of the United States of America. PMID 31127043 DOI: 10.1073/Pnas.1816315116 |
0.662 |
|
| 2019 |
Lin C, Bar-Joseph Z. Continuous State HMMs for Modeling Time Series Single Cell RNA-Seq Data. Bioinformatics (Oxford, England). PMID 31038684 DOI: 10.1093/Bioinformatics/Btz296 |
0.326 |
|
| 2019 |
Ruffalo M, Bar-Joseph Z. Protein interaction disruption in cancer. Bmc Cancer. 19: 370. PMID 31014259 DOI: 10.1186/S12885-019-5532-5 |
0.359 |
|
| 2019 |
Lugo-Martinez J, Ruiz-Perez D, Narasimhan G, Bar-Joseph Z. Dynamic interaction network inference from longitudinal microbiome data. Microbiome. 7: 54. PMID 30940197 DOI: 10.1186/S40168-019-0660-3 |
0.363 |
|
| 2019 |
Ding J, Lin C, Bar-Joseph Z. Cell lineage inference from SNP and scRNA-Seq data. Nucleic Acids Research. PMID 30820578 DOI: 10.1093/Nar/Gkz146 |
0.486 |
|
| 2019 |
Ruffalo M, Thomas R, Chen J, Lee AV, Oesterreich S, Bar-Joseph Z. Network-guided prediction of aromatase inhibitor response in breast cancer. Plos Computational Biology. 15: e1006730. PMID 30742607 DOI: 10.1371/Journal.Pcbi.1006730 |
0.322 |
|
| 2019 |
Rashid S, Singh S, Navlakha S, Bar-Joseph Z. A bacterial based distributed gradient descent model for mass scale evacuations Swarm and Evolutionary Computation. 46: 97-103. DOI: 10.1016/J.Swevo.2019.01.011 |
0.671 |
|
| 2018 |
Pabon NA, Xia Y, Estabrooks SK, Ye Z, Herbrand AK, Süß E, Biondi RM, Assimon VA, Gestwicki JE, Brodsky JL, Camacho CJ, Bar-Joseph Z. Predicting protein targets for drug-like compounds using transcriptomics. Plos Computational Biology. 14: e1006651. PMID 30532261 DOI: 10.1371/Journal.Pcbi.1006651 |
0.311 |
|
| 2018 |
Alavi A, Ruffalo M, Parvangada A, Huang Z, Bar-Joseph Z. A web server for comparative analysis of single-cell RNA-seq data. Nature Communications. 9: 4768. PMID 30425249 DOI: 10.1038/S41467-018-07165-2 |
0.387 |
|
| 2018 |
Friedman CE, Nguyen Q, Lukowski SW, Helfer A, Chiu HS, Miklas J, Levy S, Suo S, Han JJ, Osteil P, Peng G, Jing N, Baillie GJ, Senabouth A, Christ AN, ... ... Bar-Joseph Z, et al. Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation. Cell Stem Cell. 23: 586-598.e8. PMID 30290179 DOI: 10.1016/J.Stem.2018.09.009 |
0.505 |
|
| 2018 |
Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. Plos Computational Biology. 14: e1006019. PMID 29538379 DOI: 10.1371/Journal.Pcbi.1006019 |
0.562 |
|
| 2018 |
Ding J, Aronow B, Kaminski N, Kitzmiller J, Whitsett J, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single cell expression data. Genome Research. PMID 29317474 DOI: 10.1101/Gr.225979.117 |
0.559 |
|
| 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 |
0.677 |
|
| 2017 |
Ding J, Bar-Joseph Z. MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. Bioinformatics (Oxford, England). PMID 29036558 DOI: 10.1093/Bioinformatics/Btx449 |
0.436 |
|
| 2017 |
Ruffalo M, Stojanov P, Pillutla VK, Varma R, Bar-Joseph Z. Reconstructing cancer drug response networks using multitask learning. Bmc Systems Biology. 11: 96. PMID 29017547 DOI: 10.1186/S12918-017-0471-8 |
0.309 |
|
| 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 |
0.392 |
|
| 2017 |
Rashid S, Kotton DN, Bar-Joseph Z. TASIC: Determining branching models from time series single cell data. Bioinformatics (Oxford, England). PMID 28379537 DOI: 10.1093/Bioinformatics/Btx173 |
0.351 |
|
| 2017 |
Kleyman M, Sefer E, Nicola T, Espinoza C, Chhabra D, Hagood JS, Kaminski N, Ambalavanan N, Bar-Joseph Z. Selecting the most appropriate time points to profile in high-throughput studies. Elife. 6. PMID 28124972 DOI: 10.7554/Elife.18541 |
0.363 |
|
| 2016 |
Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR. A transcription factor hierarchy defines an environmental stress response network. Science (New York, N.Y.). 354. PMID 27811239 DOI: 10.1126/Science.Aag1550 |
0.366 |
|
| 2016 |
Ruffalo M, Bar-Joseph Z. Genome wide predictions of miRNA regulation by transcription factors. Bioinformatics (Oxford, England). 32: i746-i754. PMID 27587697 DOI: 10.1093/Bioinformatics/Btw452 |
0.346 |
|
| 2016 |
Sefer E, Kleyman M, Bar-Joseph Z. Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments. Cell Systems. 3: 35-42. PMID 27453445 DOI: 10.1016/J.Cels.2016.06.007 |
0.321 |
|
| 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 |
0.611 |
|
| 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 |
0.634 |
|
| 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 |
0.313 |
|
| 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 |
0.681 |
|
| 2015 |
Wise A, Bar-Joseph Z. cDREM: inferring dynamic combinatorial gene regulation. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 324-33. PMID 25844671 DOI: 10.1089/Cmb.2015.0010 |
0.444 |
|
| 2015 |
Wise A, Bar-Joseph Z. SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data. Bioinformatics (Oxford, England). 31: 1250-7. PMID 25480376 DOI: 10.1093/Bioinformatics/Btu800 |
0.415 |
|
| 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 |
0.409 |
|
| 2015 |
Navlakha S, Bar-Joseph Z. Distributed information processing in biological and computational systems Communications of the Acm. 58: 94-102. DOI: 10.1145/2678280 |
0.645 |
|
| 2015 |
Navlakha S, Faloutsos C, Bar-Joseph Z. MassExodus: modeling evolving networks in harsh environments Data Mining and Knowledge Discovery. 29: 1211-1232. DOI: 10.1007/S10618-014-0399-1 |
0.681 |
|
| 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 |
0.603 |
|
| 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 |
0.695 |
|
| 2013 |
Zhong S, He X, Bar-Joseph Z. Predicting tissue specific transcription factor binding sites. Bmc Genomics. 14: 796. PMID 24238150 DOI: 10.1186/1471-2164-14-796 |
0.359 |
|
| 2013 |
Schulz MH, Pandit KV, Lino Cardenas CL, Ambalavanan N, Kaminski N, Bar-Joseph Z. Reconstructing dynamic microRNA-regulated interaction networks. Proceedings of the National Academy of Sciences of the United States of America. 110: 15686-91. PMID 23986498 DOI: 10.1073/Pnas.1303236110 |
0.3 |
|
| 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 |
0.652 |
|
| 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 |
0.596 |
|
| 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 |
0.311 |
|
| 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 |
0.638 |
|
| 2012 |
Gupta A, Nagilla P, Le H, Bunney C, Zych C, Thalamuthu A, Bar-Joseph Z, Mathavan S, Ayyavoo V. Retraction: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) Plos One. 7. PMID 22952567 DOI: 10.1371/Annotation/D28D38B2-41A3-42A6-B421-68F9460A676D |
0.55 |
|
| 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 |
0.757 |
|
| 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 |
0.754 |
|
| 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 |
0.624 |
|
| 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 |
0.34 |
|
| 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 |
0.671 |
|
| 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 |
0.307 |
|
| 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 |
0.363 |
|
| 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 |
0.496 |
|
| 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 |
0.311 |
|
| 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 |
0.336 |
|
| 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 |
0.603 |
|
| 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 |
0.649 |
|
| 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 |
0.334 |
|
| 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 |
0.338 |
|
| 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 |
0.348 |
|
| 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 |
0.339 |
|
| 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 |
0.6 |
|
| 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 |
0.576 |
|
| 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 |
0.53 |
|
| 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 |
0.404 |
|
| 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 |
0.313 |
|
| 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 |
0.636 |
|
| 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 |
0.349 |
|
| 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 |
0.387 |
|
| 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 |
0.651 |
|
| 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 |
0.492 |
|
| 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 |
0.384 |
|
| 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 |
0.669 |
|
| 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 |
0.579 |
|
| 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 |
0.382 |
|
| 2008 |
Ernst J, Bar-Joseph Z, Ghanem L, Steinman RA. IL-3 Coordination of the Myeloblast Transcriptome by Modulating mRNA Stability Blood. 112: 3863-3863. DOI: 10.1182/Blood.V112.11.3863.3863 |
0.575 |
|
| 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 |
0.559 |
|
| 2007 |
Beg QK, Vazquez A, Ernst J, Menezes MAd, Bar-Joseph Z, Barabási A-, Oltvai ZN. Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity Proceedings of the National Academy of Sciences of the United States of America. 104: 12663-12668. PMID 17652176 DOI: 10.1073/Pnas.0609845104 |
0.599 |
|
| 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 |
0.338 |
|
| 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 |
0.354 |
|
| 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 |
0.37 |
|
| 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 |
0.64 |
|
| 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 |
0.383 |
|
| 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 |
0.649 |
|
| 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 |
0.554 |
|
| 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 |
0.663 |
|
| 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 |
0.648 |
|
| 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 |
0.522 |
|
| 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 |
0.522 |
|
| 2004 |
Bar-Joseph Z. Analyzing time series gene expression data. Bioinformatics (Oxford, England). 20: 2493-503. PMID 15130923 DOI: 10.1093/Bioinformatics/Bth283 |
0.388 |
|
| 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 |
0.804 |
|
| 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 |
0.795 |
|
| 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 |
0.804 |
|
| 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 |
0.749 |
|
| 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 |
0.76 |
|
| 2001 |
Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics (Oxford, England). 17: S22-9. PMID 11472989 DOI: 10.1093/Bioinformatics/17.Suppl_1.S22 |
0.696 |
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