publications

Preprints, 2020, 2019, 2018, 2017, 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007, 2006,

Preprints


In Silico Modeling of Metabolic State in Single Th17 Cells Reveals Novel Regulators of Inflammation and Autoimmunity.
A. Wagner*, C. Wang*, D. DeTomaso, J. Avila-Pacheco, S. Zaghouani, J. Fessler, E. Akama-Garren, K. Pierce, N. Ron-Harel, V. Paraskevi Douglas, M. Haigis, R.A. Sobel, C. Clish, A. Regev, V.K. Kuchroo†, N. Yosef†
bioRxiv , 2020
bioRxiv preprint
Metabolic and Epigenomic Regulation of Th17/Treg Balance by the Polyamine Pathway.
C. Wang*, A. Wagner*, J. Fessler*, J. Avila-Pacheco, J. Karminski, P. Thakore, S. Zaghouani, K. Pierce, L. Bod, A. Schnell, D. DeTomaso, N. Ron-Harel, M. Haigis, D. Puleston, E.L. Pearce, M. Soleimani, R. Sobel, C. Clish, A. Regev, N. Yosef†, V.K. Kuchroo†.
bioRxiv , 2020
bioRxiv preprint
Polyamine Metabolism Regulates the T Cell Epigenome Through Hypusination
D.J. Puleston, F. Baixauli, D.E. Sanin, M. Villa, A. Kabat, M.M. Kaminski, H. Weiss, K. Grzes, L.J. Flachsmann, C.S. Field, M. Stanckzak, L. Schimmelpfennig, F. Hassler, C. Wang, N. Yosef, V.K Kuchroo, Y. Musa, G. Mittler, J.M. Buescher, S. Balabanov, E.J. Pearce, D.R. Green, E.L. Pearce
bioRxiv , 2020
bioRxiv preprint
Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells.
A. Gayoso*, Z. Steier*, R. Lopez, J. Regier, KL. Nazor, A. Streets†, N Yosef†
bioRxiv , 2020
GitHub
bioRxiv preprint
Reproducibility code
Probabilistic Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models.
C. Xu*, R. Lopez*, E. Mehlman*, J. Regier, M.I. Jordan, N. Yosef
bioRxiv , 2020
GitHub
bioRxiv preprint
Reproducibility code
Identifying Informative Gene Modules Across Modalities of Single Cell Genomics.
D. DeTomaso and N. Yosef
bioRxiv , 2020
GitHub
bioRxiv preprint
Oleic acid Induces Tissue Resident FoxP3 Regulatory T cell Lineage Stability and Suppressive Functions.
SL. Pompura*, A. Wagner*, A. Kitz, J. LaPerche, N. Yosef†, M. Dominguez-Villar†, DA, Hafler†
bioRxiv , 2020
bioRxiv preprint
Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions.
N. Everetts*, MI .Worley*, R. Yasutomi, N. Yosef†, IK. Hariharan†
bioRxiv , 2020
bioRxiv preprint
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts.
JJ. Quinn*, MG. Jones*, RA. Okimoto, S. Nanjo, MM. Chan, N. Yosef†, TG. Bivona†, JS. Weissman†
bioRxiv ,
GitHub
bioRxiv preprint


2020


Decision-Making with Auto-Encoding Variational Bayes.
R. Lopez, P. Boyeau, N. Yosef, M. Jordan & J. Regier.
Advances in Neural Information Processing Systems , 2020
GitHub
arXiv preprint
Enhancing Scientific Discoveries in Molecular Biology with Deep Generative Models.
R. Lopez, A. Gayoso & N. Yosef.
Molecular Systems Biology , 2020
10.15252/msb.20199198
Integrated single cell analysis of blood and cerebrospinal fluid leukocytes in multiple sclerosis.
D. Schafflick*, C. Xu*, M. Hartlehnert*, M. Cole*, T. Lautwein, K. Buscher, J.Wolbert, SG. Meuth, T. Kuhlmann, C. Gross, H. Wiendl, N. Yosef† , G.M zu Horste†
Nature Communications , 2020
10.1038/s41467-019-14118-w
Inference of Single-Cell Phylogenies from Lineage Tracing Data.
MG. Jones*, A. Khodaverdian*, JJ. Quinn*, MM. Chan, JA. Hussmann, R. Wang, C. Xu, JS. Weissman†, N. Yosef†
Genome Biology , 2020
10.1186/s13059-020-02000-8
GitHub
Interpretable factor models of single-cell RNA-seq via variational autoencoders.
V. Svensson, A. Gayoso, N. Yosef, L. Pachter.
Bioinformatics , 2020
10.1093/bioinformatics/btaa169
Coverage-dependent bias creates the appearance of binary splicing in single cells.
CF. Buen Abad Najar, N. Yosef†, LF. Lareau†.
eLife , 2020
10.7554/eLife.54603
LentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
Gordon, M. G., Inoue, F., Martin, B., Schubach, M., Agarwal, V., Whalen, S., Feng, S., Zhao, J., Ashuach, T., Ziffra, R., Kreimer, A., Georgakopoulous-Soares, I., Yosef, N., Ye, C. J., Pollard, K. S., Shendure, J., Kircher, M., & Ahituv, N.
Nature Protocols , 2020
10.1038/s41596-020-0333-5


2019


Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.
F. Inoue*, A. Kreimer*, T. Ashuach, N. Ahituv†, N. Yosef†
Cell Stem Cell , 2019
10.1016/j.stem.2019.09.010
MPRAnalyze—A statistical framework for Massively Parallel Reporter Assays.
T. Ashuach*, DS Fischer*, FJ Theis, N. Yosef.
Genome Biology , 2019
10.1186/s13059-019-1787-z
Functional Interpretation of Single-Cell Similarity Maps.
D. Detomaso*, M. Jones*, M. Subramanian, J. Ye, N. Yosef.
Nature Communications , 2019
10.1038/s41467-019-12235-0
GitHub
Simulating multi-faceted variability in single cell RNA sequencing.
X. Zhang*, C. Xu*, N. Yosef.
Nature Communications , 2019
10.1038/s41467-019-10500-w
GitHub
Reconstructing B cell receptor sequences from short-read single cell RNA-sequencing with BRAPeS.
S. Afik*, G. Raulet* and N. Yosef.
Life Science Alliance , 2019
10.26508/lsa.201900371
Meta-analysis of massively parallel reporter assays enables the prediction of regulatory elements.
A. Kreimer*, Z. Yan*, N. Ahituv, N. Yosef
Human Mutation , 2019
10.1002/humu.23820
Connectivity Problems on Heterogeneous Graphs
J. Wu, A. Khodaverdian, B.Weitz, N. Yosef
Algorithms for Molecular Biology , 2019
10.1186/s13015-019-0141-z
Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.
MB. Cole, D. Risso, A. Wagner, D. DeTomaso, J. Ngai, E. Purdom, S. Dudoit†, N. Yosef†
Cell Systems , 2019
10.1016/j.cels.2019.03.010
GitHub
Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets.
AK Morrow, GZ He, FA Nothaft, ET Tu, J Paschall, N Yosef, AD. Joseph
Cell Systems , 2019
10.1016/j.cels.2019.11.002
Molecular recording of mammalian embryogenesis.
MM. Chan, ZD. Smith, S. Grosswendt, H. Kretzmer, TM. Norman, B. Adamson, M. Jost, JJ. Quinn, D. Yang, MG. Jones, A. Khodaverdian, N. Yosef, A. Meissner, JS. Weissman
Nature , 2019
10.1038/s41586-019-1184-5
A joint model of unpaired data from scRNA-seq and spatial transcriptomics for imputing missing gene expression measurements.
R. Lopez*, A. Nazaret*, M. Langevin*, J. Samaran, J. Regier, M.I. Jordan, N. Yosef
ICML 2019 Workshop on Computational Biology (spotlight presentation; best student’s poster) , 2019
arXiv preprint
Reproducibility code
Deep Generative Models for Detecting Differential Expression in Single Cells.
P. Boyeau, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N. Yosef
Machine Learning in Computational Biology meeting , 2019
bioRxiv preprint
Detecting Zero-Inflated Genes in Single-Cell Transcriptomics Data.
O. Clivio, R. Lopez, J. Regier, A. Gayoso, MI. Jordan, N Yosef
Machine Learning in Computational Biology meeting (spotlight presentation) , 2019
bioRxiv preprint
Reproducibility code
A Joint Model of RNA Expression and Surface Protein Abundance in Single Cells
A. Gayoso, R. Lopez, ZR. Steier, J. Regier, AM Streets, N. Yosef
Machine Learning in Computational Biology meeting , 2019
bioRxiv preprint


2018


Deep Generative Modeling for Single-cell Transcriptomics.
R. Lopez, J. Regier, MB. Cole, M. Jordan, N. Yosef.
Nature Methods , 2018
10.1038/s41592-018-0229-2
GitHub
News and Views
A Reproducibility-Based Computational Framework Identifies An Inducible Enhanced Antiviral Dendritic Cell State In HIV-1 Elite Controllers.
EM Gayo, MB. Cole, KE Kolb*, Z. Ouyang, J. Cronin, SW. Kazer, J. Ordovas-Montanes, M. Lichterfeld, BD. Walker, N Yosef†, AK. Shalek†, XG. Yu†
Genome Biology , 2018
10.1186/s13059-017-1385-x
GitHub
Impulse model-based differential expression analysis of time course sequencing data.
DS Fischer, FJ Theis, N. Yosef.
Nucleic Acids Research , 2018
10.1093/nar/gky675
GitHub
Information Constraints on Auto-Encoding Variational Bayes.
R. Lopez, J. Regier, M. Jordan, N. Yosef.
Advanced in Neural Information Processing Systems , 2018
arXiv preprint
A Deep Generative Model for Semi-Supervised Classification with Noisy Labels.
M. Langevin, E. Mehlman, J. Regier, R. Lopez, M. Jordan, N. Yosef.
Bay Area Machine Learning Symposium (oral presentation) , 2018
arXiv preprint


2017


A deep generative model for gene expression profiles from single-cell RNA sequencing.
R. Lopez, J. Regier, M. Jordan, N. Yosef.
BayLearn Symposium (oral presentation) and NIPS Workshop on Machine Learning in Computational Biology (spotlight talk) , 2017
arXiv preprint
A new way to build cell lineages.
X. Zhang and N. Yosef.
eLife , 2017
10.7554/eLife.25654
Predicting gene expression in massively parallel reporter assays: a comparative study.
A. Kreimer, H. Zeng, MD. Edwards, Y. Guo, K. Tian, S. Shin, R. Welch, M. Wainberg, R. Mohan, NA. Sinnott-Armstrong, Y. Li, G. Eraslan, T.l Bin AMIN, J. Goke, NS. Mueller, M. Kellis, A. Kundaje, MA Beer, S. Keles, DK. Gifford and N. Yosef†.
Human Mutation , 2017
10.1002/humu.23197
An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.
P. Mertins, D. Przybylski, N. Yosef, J. Qiao, K. Clauser, R. Raychowdhury, TM. Eisenhaure, T. Maritzen, V. Haucke, T. Satoh, S. Akira, SA. Carr, A. Regev, N. Hacohen, N. Chevrier.
Cell Reports , 2017
10.1016/j.celrep.2017.06.016
Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.
RB. Fletcher, D. Das, L. Gadye, KN. Street, A. Baudhuin, A. Wagner, MB. Cole, Q. Flores, YG. Choi, N. Yosef, E. Purdom, S. Dudoit, D. Risso, J. Ngai.
Cell Stem Cell , 2017
10.1016/j.stem.2017.04.003
Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.
L. Gadye, D. Das, MA. Sanchez, K. Street, A. Bauduin, A. Wagner, MB. Cole, YG Choi, N. Yosef ,E. Purdom, S. Dudoit, D. Risso, J. Ngai, RB. Fletcher.
Cell Stem Cell , 2017
10.1016/j.stem.2017.10.014
Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.
AH. Ryu, WL. Eckalbar, A. Kreimer, N. Yosef, Nadav Ahituv.
Scientific Reports , 2017
10.1038/s41598-017-07757-w
Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.
K. Karwacz, ER. Miraldi, M. Pokrovskii, A. Madi, N. Yosef, I. Wortman, X. Chen, A. Watters, N. Carriero, A. Awasthi, A. Regev, R. Bonneau, D. Littman, VK. Kuchroo.
Nature Immunology , 2017
10.1038/ni.3683


2016


The Epigenetic Landscape of T Cell Exhaustion
D.R. Sen*, J. Kaminski*, R.A Barnitz, M. Kurachi, U. Gerdemann, K.B. Yates, H Tsao, J. Godec, M.W. LaFleur, F.D. Brown, P. Tonnerre, R.T. Chung, D.C. Tully, T.M. Allen, N. Frahm, G.M. Lauer, E. J. Wherry, N. Yosef†, and W.N. Haining†.
Science , 2016
10.1126/science.aae0491
Featured on journal’s cover, Perspectives: [Science], [Nature]
Writ large: Genomic Dissection of the Effect of Cellular Environment on Immune Response.
N. Yosef† and A. Regev†
Science , 2016
10.1126/science.aaf5453
Revealing the vectors of cellular identity with single cell genomics
A. Wagner, A. Regev*, N. Yosef*
Nature Biotechnology , 2016
10.1038/nbt.3711
FastProject: A Tool for Low-Dimensional Analysis of Single-Cell RNA-Seq Data
D. DeTomaso, N. Yosef.
BMC Bioinformatics , 2016
10.1186/s12859-016-1176-5
GitHub
ImpulseDE: detection of differentially expressed genes in time series data using impulse models/
J. Sander, J. Schultze, N. Yosef.
Bioinformatics , 2016
GitHub
Available on Bioconductor
Convolutional Kitchen Sinks for Transcription Factor Binding Site Prediction
A. Morrow*, V. Shankar*, A. Joseph, B. Recht, and N. Yosef.
NeurIps Workshop on Machine Learning in Computational Biology , 2016
Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity
Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK
ACS Chem Biol , 2016


2015


Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
JT. Gaublomme*, N. Yosef*, Y. Lee, RS. Gertner, LV. Yang, PP. Pandolfi, T. Mak, R. Satija, AK. Shalek, VK. Kuchroo, A. Regev, H. Park.
Cell , 2015
10.1016/j.cell.2015.11.009
News and Views
Featured on journal’s cover
CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity
C. Wang, N. Yosef, JT. Gaublomme, C. Wu, Y. Lee, CB. Clish, J. Kaminski, S. Xiao, G. Meyer Zu Horste, M. Pawlak, Y. Kishi, N. Joller, K. Karwacz, C. Zhu, M. Ordovas-Montanes, A. Madi, I. Wortman, T. Miyazaki, RA. Sobel, H. Park, A. Regev, VK. Kuchroo.
Cell , 2015
10.1016/j.cell.2015.10.068
Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor
R. Tian, H. Wang, GD. Gish, E. Petsalaki, A. Pasculescu, Y. Shi, M. Mollenauer, RD. Bagshaw, N. Yosef, T. Hunter, AC. Gingras, A. Weiss, and T. Pawson.
PNAS , 2015
10.1073/pnas.1503286112-2
Oct1 and OCA-B are selectively required for CD4 memory T cell function
Shakya A, Goren A, Shalek A, German CN, Snook J, Kuchroo VK, Yosef N, Chan RC, Regev A, Williams MA, Tantin D.
J Exp Med. , 2015
10.1084/jem.20150363
Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion
A. Shakya, C. Callister C, A. Goren, N. Yosef, N. Garg, V. Khoddami V, D. Nix, A. Regev, D. Tantin D.
Molecular and cellular biology , 2015
MicroRNA-21 promotes Th17 differentiation and mediates experimental autoimmune encephalomyelitis
G. Murugaiyan G, AP. da Cunha, AK. Ajay, N. Joller, LP. Garo, S. Kumaradevan, N. Yosef, VS Vaidya, HL. Weiner.
The Journal of clinical investigation , 2015


2014


Small-Molecule RORγt Antagonists Inhibit T Helper 17 Cell Transcriptional Network by Divergent Mechanisms
S. Xiao*, N. Yosef*, J. Yang, Y. Wang, L. Zhou, C. Zhu, E Baloglu, D. Schmidt, R. Ramesh, M. Lobera, M.S. Sundrud, P. Tsai, Z. Xiang, J. Wang, Y. Xu, X. Lin, K. Kretschmer, P.B. Rahl, R.A. Young, Z. Zhong, D.A. Hafler, A. Regev, S. Ghosh, A. Marson, V.K. Kuchroo.
Immunity , 2014
10.1016/j.immuni.2014.04.004
Understanding Th17 cells through systematic genomic analyses
A. Peters, N. Yosef
Current Opinion in Immunology , 2014
10.1016/j.coi.2014.01.017
The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells
M. Kurachi, R.A. Barnitz, N. Yosef, P.M. Odorizzi, M.A. Dilorio, M.E. Lemieux, K. Yates, J. Godec, M.G. Klatt, A. Regev, E.J Wherry, W.N. Haining
Nature Immunology , 2014
10.1038/ni.2834
Single cell RNA Seq reveals dynamic paracrine control of cellular variation
A. Shalek, R. Satija, J. Shuga, J. Trombetta, D. Gennert, D. Lu, P. Chen, R. Gertner, J. Gaublomme, N. Yosef, S. Schwartz, B. Fowler, S. Weaver, J. Wang, X. Wang, R. Ding, R. Raychowdhury, N. Friedman, N. Hacohen, H. Park, A. May, A. Regev.
Nature , 2014
10.1038/nature13437


2013


Dynamic regulatory network controlling TH17 cell differentiation
N. Yosef*, A.K. Shalek*, J. Gaublomme*, Y. Lee, A. Awasthi, H. Jin, C. Wu, K. Karwacz, S. Xiao, M. Jorgolli, D. Gennert, R. Satija, A. Shakya, D.Y. Lu, J.J. Trombetta, M. Pillai, P.J. Ratcliffe, M.L. Coleman, M. Bix, D. Tantin, H. Park, V.K Kuchroo, A. Regev.
Nature , 2013
10.1038/nature11981
Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1
C. Wu*, N.Yosef*, T. Thalhamer*, C. Zhu, S. Xiao, Y. Kishi, A. Regev, V.K. Kuchroo.
Nature , 2013
10.1038/nature11984
Sodium Chloride Drives Autoimmune Disease by the Induction of Pathogenic Th17 Cells
M. Kleinewietfeld, A. Manzel, J. Titze, H. Kvakan, N. Yosef, R.A. Linker, D.N. Muller, D.A. Hafler.
Nature , 2013
10.1038/nature11868
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
AK. Shalek, R. Satija, X. Adiconis, RS. Gertner, JT. Gaublomme, R. Raychowdhury, S. Schwartz, N. Yosef, C. Malboeuf, D. Lu, JT. Trombetta, D. Gennert, A. Gnirke, A. Goren, N. Hacohen, JZ. Levin, H. Park, Aviv Regev.
Nature , 2013
10.1038/nature1217
Metallothioneins negatively regulate IL-27-induced type 1 regulatory T-cell differentiation
C. Wu, C. Pot, L. Apetoh, T. Thalhamer, B. Zhu, G. Murugaiyan, S. Xiao, Y. Lee, M. Rangachari, N. Yosef, VK. Kuchroo.
Proc Natl Acad Sci USA , 2013
10.1073/pnas.1211776110


2012


A high throughput in vivo protein-DNA mapping approach reveals principles of dynamic gene regulation in mammals
M. Garber*, N. Yosef*, A. Goren, R. Raychowdhury, A. Thielke, M. Guttman, J. Robinson, B. Minie, N. Chevrier, Z. Itzhaki, A. Weiner, D. Friedrich, J. Meldrim, O. Ram, C. Chang, A. Gnirke, S. Fisher, N. Friedman, B. Wong, B. Bernstein, C. Nusbaum, N. Hacohen, A. Regev, I. Amit.
Molecular Cell , 2012
0.1016/j.molcel.2012.07.030
Systematic identification of gene annotation errors in the widely used yeast mutation collections
T. Ben-Shitrit*, N. Yosef*, K. Shemesh, R. Sharan, E. Ruppin and M. Kupiec
Nature Methods , 2012
10.1038/nmeth.1890
Induction and molecular signature of pathogenic TH17 cells
Y. Lee, A. Awasthi, N. Yosef, F.J. Quintana, S. Xiao, S. Kunder, R.A. Sobel, A. Regev, V.K. Kuchroo.
Nature Immunology , 2012
10.1038/ni.2416
Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
A.K. Shalek, J. Gaublomme, L. Wang, N. Yosef, N. Chevrier, M.S. Andersen, J.T. Robinson, N. Pochet, D. Neuberg, R.S. Gertner, I. Amit, J.R. Brown, N. Hacohen, A. Regev, C.V. Wu, H. Park.
Nano Letters , 2012
10.1021/nl3042917
Met kinetic signature derived from the response to HGF/SF in a cellular model predicts breast cancer patient survival
G.Y. Stein, N. Yosef, H. Reichman, J. Horev, A. Laser-Azogui, A. Berens, J. Resau, E. Ruppin, R. Sharan and I. Tsarfaty.
PLoS One , 2012
10.1371/journal.pone.0045969


2011


Impulse control: Temporal dynamics in gene transcription
N. Yosef, A. Regev.
Cell , 2011
Included in Cell’s top reviews for 2011. Featured on journal’s cover.
ANAT – A Software Tool for Reconstructing and Analyzing Functional Networks of Proteins
N. Yosef, E. Zalckvar, N. Atias, AD. Rubinstein, M. Homilius, L. Vardi, H. Zur, A. Kimchi, E. Ruppin, and R. Sharan.
Science Signaling , 2011
Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
N.Novershtern, A. Subramanian, L. Lawton, RH. Mak, W. Haining, ME. McConkey, N. Habib, N. Yosef, CY. Chang, T. Shay, GM. Frampton, ACB. Drake, I. Leskov, B. Nilsson, F. Preffer, D. Dombkowski, JW. Evans, T. Liefeld, JS. Smutko, J. Chen, N. Friedman, R. Young, T. Golub, A. Regev, BL. Ebert.
Cell , 2011
Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
O. Ram, A. Goren, I. Amit, N. Shoresh, N. Yosef, J. Ernst, M. Kellis, M. Gymrek, R. Issner, M. Coyne, T. Durham, X. Zhang, J. Donaghey, CB. Epstein, A. Regev, and BE. Bernstein.
Cell , 2011
Systematic Discovery of Signaling Components Identifies New Branches in Viral-Sensing Pathways
N. Chevrier P. Mertins, MN Artyomov, AK Shalek, M Iannacone, MF Ciaccio, I Gat-Viks, E Tonti, MM DeGrace, KR Clauser, M Garber, TM Eisenhaure, N Yosef, JT Robinson, A Sutton, MS Andersen, DE Root U von Andrian, RB Jones, H Park, SA Carr, A Regev, I Amit, N Hacohen.
Cell , 2011


2010


Network-free inference of knockout effects in yeast
T. Peleg, N. Yosef, E. Ruppin, and R. Sharan.
PLoS Computational Biology , 2010
Prediction of Phenotype Information from Genotype Data
N.Yosef, J. Gramm, Q. Wang, W.S. Noble, R. Karp, and R. Sharan.
Communications in Information and Systems , 2010
A Systems Level Strategy for Analyzing the Cell Death Network: implications in exploring the apoptosis/ autophagy connection
E. Zalckvar, N. Yosef, S. Reef, R. Sharan, E. Ruppin, and A. Kimchi.
Cell Death and Differentiation , 2010
10.1038/cdd.2010.7
Transcription Regulation by CHIP/LDB Complexes
R. Bronstein, L. Levkovitz, N. Yosef, E. Ruppin, R. Sharan, He. Westphal, B. Oliver, D. Segal.
PLoS Genetics , 2010
A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology
L. Levkovitz, N. Yosef, MC. Gershengorn, E. Ruppin, R. Sharan and Y. Oron.
PLoS ONE , 2010


2009


Toward Accurate Reconstruction of Functional Protein Networks
N.Yosef*, L. ungar*, E. Zalckvar, A.Kimchi, M.Kupeic, E. Ruppin and R. Sharan.
Molecular Systems Biology , 2009
A Complex-Centric View of Protein Network Evolution
N.Yosef, M.Kupeic, E. Ruppin and R. Sharan.
Nucleic Acids Research , 2009
10.1093/nar/gkp414
A genome-wide screen for essential yeast genes that affect telomere length maintenance
L. Ungar*, N.Yosef*, Y. Sela, R. Sharan, E. Ruppin, M. Kupiec.
Nucleic Acids Research , 2009
10.1093/nar/gkp259
Metabolic environmental modeling predicts ecological strategies for bacterial growth
S. Freilich, A. Kreimer, E. Borenstein, N.Yosef, R. Sharan, U. Gophna, E. Ruppin.
Genome Biology , 2009
10.1186/gb-2009-10-6-r61


2008


Cross-species Analysis of Protein-protein Interaction Networks
N.Yosef, E. Ruppin and R. Sharan.
In Protein-protein interactions and networks: identification analysis and prediction, Panchenko& Przytycka (ed) pp 163-186. Springer , 2008
Improved Network-based Identification of Protein Orthologs
N.Yosef, R. Sharan and W. S. Noble.
Bioinformatics 24 (ECCB 2008) , 2008
From sequence to structure to networks
N. Yosef, L. Käll.
Genome Biology , 2008


2007


A Supervised Approach for Identifying Discriminating Genotype Patterns and its Application to Breast Cancer Data
N.Yosef, Z.Yakhini, A.Tsalenko, E.Ruppin and R.Sharan
Bioinformatics 23 (ECCB 2006) , 2007
Medical sequencing at the extremes of human body mass
N. Ahituv, N. Kavaslar, W. Schackwitz, A. Ustaszewska, J. Martin, S. Hébert, H. Doelle, B. Ersoy, G. Kryukov, S. Schmidt, N. Yosef, E. Ruppin, R. Sharan, C. Vaisse, S. Sunyaev, R. Dent, J. Cohen, R. McPherson, and L.A. Pennacchio.
American Journal of Human Genetics , 2007


2006


Inferring Functional Pathways from Multi-Perturbation Data
N. Yosef, A. Kaufman and E. Ruppin
Bioinformatics (ISMB 2006) , 2006