| Year |
Citation |
Score |
| 2020 |
de Boer CG, Vaishnav ED, Sadeh R, Abeyta EL, Friedman N, Regev A. Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. Nature Biotechnology. PMID 32792646 DOI: 10.1038/S41587-020-0665-2 |
0.332 |
|
| 2019 |
de Boer CG, Vaishnav ED, Sadeh R, Abeyta EL, Friedman N, Regev A. Deciphering eukaryotic gene-regulatory logic with 100 million random promoters. Nature Biotechnology. PMID 31792407 DOI: 10.1038/S41587-019-0315-8 |
0.39 |
|
| 2019 |
Nitzan M, Karaiskos N, Friedman N, Rajewsky N. Gene expression cartography. Nature. PMID 31748748 DOI: 10.1038/S41586-019-1773-3 |
0.341 |
|
| 2019 |
Gutin J, Joseph-Strauss D, Sadeh A, Shalom E, Friedman N. Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases. Molecular Systems Biology. 15: e8939. PMID 31464369 DOI: 10.15252/Msb.20198939 |
0.344 |
|
| 2019 |
Klein-Brill A, Joseph-Strauss D, Appleboim A, Friedman N. Dynamics of Chromatin and Transcription during Transient Depletion of the RSC Chromatin Remodeling Complex. Cell Reports. 26: 279-292.e5. PMID 30605682 DOI: 10.1016/J.Celrep.2018.12.020 |
0.363 |
|
| 2018 |
Gutin J, Sadeh R, Bodenheimer N, Joseph-Strauss D, Klein-Brill A, Alajem A, Ram O, Friedman N. Fine-Resolution Mapping of TF Binding and Chromatin Interactions. Cell Reports. 22: 2797-2807. PMID 29514105 DOI: 10.1016/J.Celrep.2018.02.052 |
0.324 |
|
| 2016 |
Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, Marjanovic ND, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman TM, Lander ES, Weissman JS, Friedman N, et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 167: 1853-1866.e17. PMID 27984732 DOI: 10.1016/J.Cell.2016.11.038 |
0.367 |
|
| 2016 |
Sadeh R, Launer-Wachs R, Wandel H, Rahat A, Friedman N. Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution. Molecular Cell. PMID 27496019 DOI: 10.1016/J.Molcel.2016.07.023 |
0.343 |
|
| 2016 |
Setty M, Tadmor MD, Reich-Zeliger S, Angel O, Salame TM, Kathail P, Choi K, Bendall S, Friedman N, Pe'er D. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nature Biotechnology. PMID 27136076 DOI: 10.1038/Nbt.3569 |
0.525 |
|
| 2015 |
Gutin J, Sadeh A, Rahat A, Aharoni A, Friedman N. Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. Molecular Systems Biology. 11: 829. PMID 26446933 DOI: 10.15252/Msb.20156451 |
0.339 |
|
| 2015 |
Hsieh TH, Weiner A, Lajoie B, Dekker J, Friedman N, Rando OJ. Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C. Cell. 162: 108-19. PMID 26119342 DOI: 10.1016/J.Cell.2015.05.048 |
0.312 |
|
| 2015 |
Lerner I, Bartok O, Wolfson V, Menet JS, Weissbein U, Afik S, Haimovich D, Gafni C, Friedman N, Rosbash M, Kadener S. Clk post-transcriptional control denoises circadian transcription both temporally and spatially. Nature Communications. 6: 7056. PMID 25952406 DOI: 10.1038/Ncomms8056 |
0.323 |
|
| 2015 |
Weiner A, Hsieh TH, Appleboim A, Chen HV, Rahat A, Amit I, Rando OJ, Friedman N. High-resolution chromatin dynamics during a yeast stress response. Molecular Cell. 58: 371-86. PMID 25801168 DOI: 10.1016/J.Molcel.2015.02.002 |
0.331 |
|
| 2014 |
Rabani M, Raychowdhury R, Jovanovic M, Rooney M, Stumpo DJ, Pauli A, Hacohen N, Schier AF, Blackshear PJ, Friedman N, Amit I, Regev A. High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell. 159: 1698-710. PMID 25497548 DOI: 10.1016/J.Cell.2014.11.015 |
0.356 |
|
| 2014 |
Lara-Astiaso D, Weiner A, Lorenzo-Vivas E, Zaretsky I, Jaitin DA, David E, Keren-Shaul H, Mildner A, Winter D, Jung S, Friedman N, Amit I. Immunogenetics. Chromatin state dynamics during blood formation. Science (New York, N.Y.). 345: 943-9. PMID 25103404 DOI: 10.1126/Science.1256271 |
0.346 |
|
| 2014 |
Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, ... ... Friedman N, et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature. 510: 363-9. PMID 24919153 DOI: 10.1038/Nature13437 |
0.352 |
|
| 2013 |
Antebi YE, Reich-Zeliger S, Hart Y, Mayo A, Eizenberg I, Rimer J, Putheti P, Pe'er D, Friedman N. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates. Plos Biology. 11: e1001616. PMID 23935451 DOI: 10.1371/Journal.Pbio.1001616 |
0.555 |
|
| 2013 |
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, Macmanes MD, Ott M, Orvis J, Pochet N, Strozzi F, ... ... Friedman N, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8: 1494-512. PMID 23845962 DOI: 10.1038/Nprot.2013.084 |
0.367 |
|
| 2012 |
Habib N, Wapinski I, Margalit H, Regev A, Friedman N. A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. Molecular Systems Biology. 8: 619. PMID 23089682 DOI: 10.1038/Msb.2012.50 |
0.374 |
|
| 2012 |
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, ... ... Friedman N, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular Cell. 47: 810-22. PMID 22940246 DOI: 10.1016/J.Molcel.2012.07.030 |
0.392 |
|
| 2012 |
Weiner A, Chen HV, Liu CL, Rahat A, Klien A, Soares L, Gudipati M, Pfeffner J, Regev A, Buratowski S, Pleiss JA, Friedman N, Rando OJ. Systematic dissection of roles for chromatin regulators in a yeast stress response. Plos Biology. 10: e1001369. PMID 22912562 DOI: 10.1371/Journal.Pbio.1001369 |
0.411 |
|
| 2012 |
Kaplan T, Friedman N. Gene expression: Running to stand still. Nature. 484: 171-2. PMID 22498619 DOI: 10.1038/484171A |
0.356 |
|
| 2012 |
Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (New York, N.Y.). 335: 552-7. PMID 22194413 DOI: 10.1126/Science.1215110 |
0.339 |
|
| 2011 |
Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, et al. Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. Plos Biology. 9: e1001086. PMID 21738444 DOI: 10.1371/Journal.Pbio.1001086 |
0.343 |
|
| 2011 |
Radman-Livaja M, Verzijlbergen KF, Weiner A, van Welsem T, Friedman N, Rando OJ, van Leeuwen F. Patterns and mechanisms of ancestral histone protein inheritance in budding yeast. Plos Biology. 9: e1001075. PMID 21666805 DOI: 10.1371/Journal.Pbio.1001075 |
0.314 |
|
| 2011 |
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, ... ... Friedman N, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. 29: 644-52. PMID 21572440 DOI: 10.1038/Nbt.1883 |
0.352 |
|
| 2011 |
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, ... ... Friedman N, et al. Comparative functional genomics of the fission yeasts. Science (New York, N.Y.). 332: 930-6. PMID 21511999 DOI: 10.1126/Science.1203357 |
0.4 |
|
| 2011 |
Rinott R, Jaimovich A, Friedman N. Exploring transcription regulation through cell-to-cell variability. Proceedings of the National Academy of Sciences of the United States of America. 108: 6329-34. PMID 21444810 DOI: 10.1073/Pnas.1013148108 |
0.357 |
|
| 2011 |
Radman-Livaja M, Ruben G, Weiner A, Friedman N, Kamakaka R, Rando OJ. Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization. The Embo Journal. 30: 1012-26. PMID 21336256 DOI: 10.1038/Emboj.2011.30 |
0.364 |
|
| 2011 |
Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, ... ... Friedman N, et al. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell. 144: 296-309. PMID 21241896 DOI: 10.1016/J.Cell.2011.01.004 |
0.396 |
|
| 2011 |
Jaimovich A, Friedman N. From large-scale assays to mechanistic insights: computational analysis of interactions. Current Opinion in Biotechnology. 22: 87-93. PMID 21109421 DOI: 10.1016/J.Copbio.2010.10.017 |
0.339 |
|
| 2010 |
Friedman N, Schuldiner M. Genetics. The DNA damage road map. Science (New York, N.Y.). 330: 1327-8. PMID 21127235 DOI: 10.1126/Science.1199862 |
0.324 |
|
| 2010 |
Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biology. 11: R87. PMID 20796282 DOI: 10.1186/Gb-2010-11-8-R87 |
0.347 |
|
| 2010 |
Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nature Methods. 7: 709-15. PMID 20711195 DOI: 10.1038/Nmeth.1491 |
0.308 |
|
| 2010 |
Kim TS, Liu CL, Yassour M, Holik J, Friedman N, Buratowski S, Rando OJ. RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast. Genome Biology. 11: R75. PMID 20637075 DOI: 10.1186/Gb-2010-11-7-R75 |
0.354 |
|
| 2010 |
Jaimovich A, Rinott R, Schuldiner M, Margalit H, Friedman N. Modularity and directionality in genetic interaction maps. Bioinformatics (Oxford, England). 26: i228-36. PMID 20529911 DOI: 10.1093/Bioinformatics/Btq197 |
0.336 |
|
| 2010 |
Radman-Livaja M, Liu CL, Friedman N, Schreiber SL, Rando OJ. Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast. Plos Genetics. 6: e1000837. PMID 20140185 DOI: 10.1371/Journal.Pgen.1000837 |
0.318 |
|
| 2010 |
Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. High-resolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Research. 20: 90-100. PMID 19846608 DOI: 10.1101/Gr.098509.109 |
0.336 |
|
| 2010 |
Levin J, Adiconis X, Yassour M, Thompson D, Guttman M, Berger M, Fan L, Friedman N, Nusbaum C, Gnirke A, Regev A. Development and evaluation of RNA-seq methods Genome Biology. 11: P26. DOI: 10.1186/Gb-2010-11-S1-P26 |
0.302 |
|
| 2009 |
Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (Oxford, England). 25: i54-62. PMID 19478016 DOI: 10.1093/Bioinformatics/Btp190 |
0.301 |
|
| 2009 |
Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proceedings of the National Academy of Sciences of the United States of America. 106: 3264-9. PMID 19208812 DOI: 10.1073/Pnas.0812841106 |
0.379 |
|
| 2008 |
Capaldi AP, Kaplan T, Liu Y, Habib N, Regev A, Friedman N, O'Shea EK. Structure and function of a transcriptional network activated by the MAPK Hog1. Nature Genetics. 40: 1300-6. PMID 18931682 DOI: 10.1038/Ng.235 |
0.387 |
|
| 2008 |
Eisenberg I, Novershtern N, Itzhaki Z, Becker-Cohen M, Sadeh M, Willems PH, Friedman N, Koopman WJ, Mitrani-Rosenbaum S. Mitochondrial processes are impaired in hereditary inclusion body myopathy. Human Molecular Genetics. 17: 3663-74. PMID 18723858 DOI: 10.1093/Hmg/Ddn261 |
0.33 |
|
| 2008 |
Habib N, Kaplan T, Margalit H, Friedman N. A novel Bayesian DNA motif comparison method for clustering and retrieval. Plos Computational Biology. 4: e1000010. PMID 18463706 DOI: 10.1371/Journal.Pcbi.1000010 |
0.331 |
|
| 2008 |
Novershtern N, Itzhaki Z, Manor O, Friedman N, Kaminski N. A functional and regulatory map of asthma. American Journal of Respiratory Cell and Molecular Biology. 38: 324-36. PMID 17921359 DOI: 10.1165/Rcmb.2007-0151Oc |
0.324 |
|
| 2007 |
Wapinski I, Pfeffer A, Friedman N, Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature. 449: 54-61. PMID 17805289 DOI: 10.1038/Nature06107 |
0.367 |
|
| 2007 |
Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science (New York, N.Y.). 315: 1405-8. PMID 17347438 DOI: 10.1126/Science.1134053 |
0.304 |
|
| 2006 |
Slonim N, Friedman N, Tishby N. Multivariate information bottleneck. Neural Computation. 18: 1739-89. PMID 16771652 DOI: 10.1162/Neco.2006.18.8.1739 |
0.311 |
|
| 2006 |
Jaimovich A, Elidan G, Margalit H, Friedman N. Towards an integrated protein-protein interaction network: a relational Markov network approach. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 145-64. PMID 16597232 DOI: 10.1089/Cmb.2006.13.145 |
0.305 |
|
| 2005 |
Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, Rando OJ. Single-nucleosome mapping of histone modifications in S. cerevisiae. Plos Biology. 3: e328. PMID 16122352 DOI: 10.1371/Journal.Pbio.0030328 |
0.316 |
|
| 2005 |
Kaplan T, Friedman N, Margalit H. Ab initio prediction of transcription factor targets using structural knowledge. Plos Computational Biology. 1: e1. PMID 16103898 DOI: 10.1371/Journal.Pcbi.0010001 |
0.357 |
|
| 2005 |
Segal E, Friedman N, Kaminski N, Regev A, Koller D. From signatures to models: understanding cancer using microarrays. Nature Genetics. 37: S38-45. PMID 15920529 DOI: 10.1038/Ng1561 |
0.541 |
|
| 2005 |
Segman RH, Shefi N, Goltser-Dubner T, Friedman N, Kaminski N, Shalev AY. Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors. Molecular Psychiatry. 10: 500-513. PMID 15685253 DOI: 10.1038/Sj.Mp.4001636 |
0.315 |
|
| 2005 |
Barash Y, Elidan G, Kaplan T, Friedman N. CIS: compound importance sampling method for protein--DNA binding site p-value estimation Bioinformatics. 21: 596-600. PMID 15454407 DOI: 10.1093/Bioinformatics/Bti041 |
0.301 |
|
| 2004 |
Segal E, Friedman N, Koller D, Regev A. A module map showing conditional activity of expression modules in cancer. Nature Genetics. 36: 1090-8. PMID 15448693 DOI: 10.1038/Ng1434 |
0.531 |
|
| 2004 |
Marion RM, Regev A, Segal E, Barash Y, Koller D, Friedman N, O'Shea EK. Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proceedings of the National Academy of Sciences of the United States of America. 101: 14315-22. PMID 15353587 DOI: 10.1073/Pnas.0405353101 |
0.583 |
|
| 2004 |
Achiron A, Gurevich M, Friedman N, Kaminski N, Mandel M. Blood transcriptional signatures of multiple sclerosis: unique gene expression of disease activity. Annals of Neurology. 55: 410-7. PMID 14991819 DOI: 10.1002/Ana.20008 |
0.318 |
|
| 2004 |
Friedman N. Inferring cellular networks using probabilistic graphical models. Science (New York, N.Y.). 303: 799-805. PMID 14764868 DOI: 10.1126/Science.1094068 |
0.359 |
|
| 2004 |
Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, Kaminski N. Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics (Oxford, England). 20: 839-46. PMID 14751998 DOI: 10.1093/Bioinformatics/Btg487 |
0.307 |
|
| 2003 |
Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nature Genetics. 34: 166-76. PMID 12740579 DOI: 10.1038/Ng1165 |
0.69 |
|
| 2003 |
Friedman N, Koller D. Being Bayesian about network structure. A Bayesian approach to structure discovery in Bayesian networks Machine Learning. 50: 95-125. DOI: 10.1023/A:1020249912095 |
0.53 |
|
| 2002 |
Kaminski N, Friedman N. Practical approaches to analyzing results of microarray experiments. American Journal of Respiratory Cell and Molecular Biology. 27: 125-32. PMID 12151303 DOI: 10.1165/Ajrcmb.27.2.F247 |
0.333 |
|
| 2002 |
Barash Y, Friedman N. Context-specific Bayesian clustering for gene expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 169-91. PMID 12015876 DOI: 10.1089/10665270252935403 |
0.402 |
|
| 2001 |
Segal E, Taskar B, Gasch A, Friedman N, Koller D. Rich probabilistic models for gene expression. Bioinformatics (Oxford, England). 17: S243-52. PMID 11473015 DOI: 10.1093/Bioinformatics/17.Suppl_1.S243 |
0.581 |
|
| 2001 |
Pe'er D, Regev A, Elidan G, Friedman N. Inferring subnetworks from perturbed expression profiles Bioinformatics. 17: S215-S224. PMID 11473012 DOI: 10.1093/Bioinformatics/17.Suppl_1.S215 |
0.626 |
|
| 2001 |
Ben-Dor A, Friedman N, Yakhini Z. Statistical benchmarking and class discovery in gene expression data Nature Genetics. 27: 96-96. DOI: 10.1038/87368 |
0.348 |
|
| 2000 |
Friedman N, Linial M, Nachman I, Pe'er D. Using Bayesian networks to analyze expression data Journal of Computational Biology. 7: 601-620. PMID 11108481 DOI: 10.1089/106652700750050961 |
0.617 |
|
| 2000 |
Ben-Dor A, Bruhn L, Friedman N, Nachman I, Schummer M, Yakhini Z. Tissue classification with gene expression profiles. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 559-83. PMID 11108479 DOI: 10.1089/106652700750050943 |
0.353 |
|
| 2000 |
Friedman N, Halpern JY, Koller D. First-order conditional logic for default reasoning revisited Acm Transactions On Computational Logic. 1: 175-207. DOI: 10.1145/359496.359500 |
0.594 |
|
| 1999 |
Friedman N, Halpern JY. Modeling belief in dynamic systems part II: revision and update Journal of Artificial Intelligence Research. 10: 117-167. DOI: 10.1613/Jair.506 |
0.477 |
|
| 1999 |
Friedman N, Halpern JY. Belief Revision: A Critique Journal of Logic, Language and Information. 8: 401-420. DOI: 10.1023/A:1008314832430 |
0.478 |
|
| 1997 |
Friedman N, Halpern JY. Modeling belief in dynamic systems, part I: foundations Artificial Intelligence. 95: 257-316. DOI: 10.1016/S0004-3702(97)00040-4 |
0.471 |
|
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