Publications by authors named "Nir Yosef"

90Publications

Evaluation of Davis et al.: Exploring Sequence of Determinants of Transcriptional Regulation-The Case of c-AMP Response Element.

Cell Syst 2020 Jul 22;11(1):2-4. Epub 2020 Jul 22.

Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2020.07.001DOI Listing
July 2020

Coverage-dependent bias creates the appearance of binary splicing in single cells.

Elife 2020 Jun 29;9. Epub 2020 Jun 29.

Center for Computational Biology, University of California, Berkeley, Berkeley, United States.

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http://dx.doi.org/10.7554/eLife.54603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7498265PMC
June 2020

The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.

J Biol Chem 2020 Aug 9;295(33):11435-11454. Epub 2020 Jun 9.

Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel

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http://dx.doi.org/10.1074/jbc.RA120.013426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7450105PMC
August 2020

Implications of the Upper Bound on h→μ^{+}μ^{-} on the Baryon Asymmetry of the Universe.

Phys Rev Lett 2020 May;124(18):181801

Department of Particle Physics and Astrophysics, Weizmann Institute of Science, Rehovot 7610001, Israel.

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http://dx.doi.org/10.1103/PhysRevLett.124.181801DOI Listing
May 2020

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

Genome Biol 2020 04 14;21(1):92. Epub 2020 Apr 14.

Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1186/s13059-020-02000-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155257PMC
April 2020

Interpretable factor models of single-cell RNA-seq via variational autoencoders.

Bioinformatics 2020 Jun;36(11):3418-3421

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267837PMC
June 2020

Mango: Exploratory Data Analysis for Large-Scale Sequencing Datasets.

Cell Syst 2019 12 4;9(6):609-613.e3. Epub 2019 Dec 4.

Electrical Engineering and Computer Science Department, University of California Berkeley, 465 Soda Hall, Berkeley, CA 94720-1776, USA; Center for Computational Biology, University of California Berkeley, 108 Stanley Hall, Berkeley, CA 94720-3220, USA; Unite Genomics, Inc., 1301 Marina Village Pkwy, Suite 320, Alameda, CA 94501, USA.

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http://dx.doi.org/10.1016/j.cels.2019.11.002DOI Listing
December 2019

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.

Cell Stem Cell 2019 Nov 17;25(5):713-727.e10. Epub 2019 Oct 17.

Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850896PMC
November 2019

Functional interpretation of single cell similarity maps.

Nat Commun 2019 09 26;10(1):4376. Epub 2019 Sep 26.

Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41467-019-12235-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763499PMC
September 2019

MPRAnalyze: statistical framework for massively parallel reporter assays.

Genome Biol 2019 09 2;20(1):183. Epub 2019 Sep 2.

Department of Electrical Engineering and Computer Sciences, University of California Berkeley, Berkeley, California, USA.

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http://dx.doi.org/10.1186/s13059-019-1787-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717970PMC
September 2019

Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS.

Life Sci Alliance 2019 08 26;2(4). Epub 2019 Aug 26.

Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA

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http://dx.doi.org/10.26508/lsa.201900371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6709718PMC
August 2019

Simulating multiple faceted variability in single cell RNA sequencing.

Nat Commun 2019 06 13;10(1):2611. Epub 2019 Jun 13.

Department of Electrical Engineering and Computer Sciences, Center for Computational Biology, UC Berkeley, Berkeley, CA, 94720, USA.

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http://dx.doi.org/10.1038/s41467-019-10500-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6565723PMC
June 2019

Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.

Hum Mutat 2019 09 18;40(9):1299-1313. Epub 2019 Jun 18.

Department of Electrical Engineering and Computer Sciences, Center for Computational Biology, University of California, Berkeley, California.

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https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23820
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http://dx.doi.org/10.1002/humu.23820DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771677PMC
September 2019

Molecular recording of mammalian embryogenesis.

Nature 2019 06 13;570(7759):77-82. Epub 2019 May 13.

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1184-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229772PMC
June 2019

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq.

Cell Syst 2019 04;8(4):315-328.e8

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712193008
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http://dx.doi.org/10.1016/j.cels.2019.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544759PMC
April 2019

Connectivity problems on heterogeneous graphs.

Algorithms Mol Biol 2019 8;14. Epub 2019 Mar 8.

2Department of Electrical Engineering and Computer Science, UC Berkeley, Berkeley, CA USA.

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http://dx.doi.org/10.1186/s13015-019-0141-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408827PMC
March 2019

Deep generative modeling for single-cell transcriptomics.

Nat Methods 2018 12 30;15(12):1053-1058. Epub 2018 Nov 30.

Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41592-018-0229-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6289068PMC
December 2018

Impulse model-based differential expression analysis of time course sequencing data.

Nucleic Acids Res 2018 11;46(20):e119

Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/nar/gky675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237758PMC
November 2018

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.

BMC Genomics 2018 Jun 19;19(1):477. Epub 2018 Jun 19.

Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.

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http://dx.doi.org/10.1186/s12864-018-4772-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6007078PMC
June 2018

Computation Resources for Molecular Biology: Special Issue 2018.

J Mol Biol 2018 07 31;430(15):2181-2183. Epub 2018 May 31.

Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub Investigator. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.05.041DOI Listing
July 2018

Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon.

Cell Syst 2018 Mar 14;6(3):381-394.e7. Epub 2018 Feb 14.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA; Bioinformatics Core, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5876141PMC
March 2018

Injury Activates Transient Olfactory Stem Cell States with Diverse Lineage Capacities.

Cell Stem Cell 2017 Dec 22;21(6):775-790.e9. Epub 2017 Nov 22.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.stem.2017.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5728414PMC
December 2017

Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state.

Nucleic Acids Res 2017 Sep;45(16):e148

Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.

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http://dx.doi.org/10.1093/nar/gkx615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766189PMC
September 2017

Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation.

Sci Rep 2017 08 8;7(1):7533. Epub 2017 Aug 8.

Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.

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http://dx.doi.org/10.1038/s41598-017-07757-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5548911PMC
August 2017

Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution.

Cell Stem Cell 2017 06 11;20(6):817-830.e8. Epub 2017 May 11.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720, USA; QB3 Functional Genomics Laboratory, University of California, Berkeley, CA 94720, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.04.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484588PMC
June 2017

A new way to build cell lineages.

Elife 2017 03 23;6. Epub 2017 Mar 23.

Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, United States.

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http://dx.doi.org/10.7554/eLife.25654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364025PMC
March 2017

Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation.

Nat Immunol 2017 04 6;18(4):412-421. Epub 2017 Feb 6.

Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ni.3683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5901650PMC
April 2017

Writ large: Genomic dissection of the effect of cellular environment on immune response.

Science 2016 10;354(6308):64-68

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/science.aaf5453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111631PMC
October 2016

Revealing the vectors of cellular identity with single-cell genomics.

Nat Biotechnol 2016 Nov;34(11):1145-1160

Department of Electrical Engineering and Computer Science and the Center for Computational Biology, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nbt.3711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465644PMC
November 2016

Protein C receptor (PROCR) is a negative regulator of Th17 pathogenicity.

J Exp Med 2016 10 26;213(11):2489-2501. Epub 2016 Sep 26.

Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115

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http://dx.doi.org/10.1084/jem.20151118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068226PMC
October 2016

ImpulseDE: detection of differentially expressed genes in time series data using impulse models.

Bioinformatics 2017 03;33(5):757-759

Electrical Engineering and Computer Science, Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720-1776, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859984PMC
March 2017

Antiviral CD8 T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion.

Immunity 2016 10;45(4):917-930

Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 01239, USA; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 01239, USA; Broad Institute, Cambridge, MA 01239, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2016.09.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5077698PMC
October 2016

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data.

BMC Bioinformatics 2016 Aug 23;17(1):315. Epub 2016 Aug 23.

Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California, Berkeley, 97420, CA, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/s12859-016-1176-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995760PMC
August 2016

Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity.

ACS Chem Biol 2016 08 22;11(8):2131-9. Epub 2016 Jul 22.

Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley , Berkeley, California 94720, United States.

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http://dx.doi.org/10.1021/acschembio.6b00433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4994060PMC
August 2016

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

Cell 2015 Dec 19;163(6):1400-12. Epub 2015 Nov 19.

Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and David H. Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671824PMC
December 2015

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity.

Cell 2015 Dec 19;163(6):1413-27. Epub 2015 Nov 19.

Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.10.068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671820PMC
December 2015

Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor.

Proc Natl Acad Sci U S A 2015 Mar 17;112(13):E1594-603. Epub 2015 Mar 17.

Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8.

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http://dx.doi.org/10.1073/pnas.1503286112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386406PMC
March 2015

Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion.

Mol Cell Biol 2015 Mar 12;35(6):1014-25. Epub 2015 Jan 12.

Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA

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http://dx.doi.org/10.1128/MCB.01105-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333097PMC
March 2015

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Nature 2014 Jun 11;510(7505):363-9. Epub 2014 Jun 11.

1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA.

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http://dx.doi.org/10.1038/nature13437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193940PMC
June 2014

Understanding Th17 cells through systematic genomic analyses.

Curr Opin Immunol 2014 Jun 6;28:42-8. Epub 2014 Mar 6.

Center for Neurologic Diseases, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, United States; Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, United States. Electronic address:

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http://dx.doi.org/10.1016/j.coi.2014.01.017DOI Listing
June 2014

The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells.

Nat Immunol 2014 Apr 2;15(4):373-83. Epub 2014 Mar 2.

1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Division of Hematology/Oncology, Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA. [4].

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http://dx.doi.org/10.1038/ni.2834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000237PMC
April 2014

Particle physics: let it B.

Authors:
Yosef Nir

Nature 2013 Jul;499(7458):290-1

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http://dx.doi.org/10.1038/499290aDOI Listing
July 2013

Metallothioneins negatively regulate IL-27-induced type 1 regulatory T-cell differentiation.

Proc Natl Acad Sci U S A 2013 May 29;110(19):7802-7. Epub 2013 Apr 29.

Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1073/pnas.1211776110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651423PMC
May 2013

Implications of Higgs searches on the four-generation standard model.

Phys Rev Lett 2013 Mar 25;110(9):091801. Epub 2013 Feb 25.

Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel.

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http://dx.doi.org/10.1103/PhysRevLett.110.091801DOI Listing
March 2013

Sodium chloride drives autoimmune disease by the induction of pathogenic TH17 cells.

Nature 2013 Apr 6;496(7446):518-22. Epub 2013 Mar 6.

Departments of Neurology and Immunobiology, Yale School of Medicine, 15 York Street, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/nature11868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3746493PMC
April 2013

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1.

Nature 2013 Apr 6;496(7446):513-7. Epub 2013 Mar 6.

Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://www.nature.com/doifinder/10.1038/nature11984
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http://dx.doi.org/10.1038/nature11984DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637879PMC
April 2013

Asymmetric Higgsino dark matter.

Phys Rev Lett 2012 Aug 31;109(5):051302. Epub 2012 Jul 31.

Institute for Advanced Study, Princeton, New Jersey 08540, USA.

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http://dx.doi.org/10.1103/PhysRevLett.109.051302DOI Listing
August 2012

Relating direct CP violation in D decays and the forward-backward asymmetry in tt[over ¯] production.

Phys Rev Lett 2012 Jun 26;108(26):261601. Epub 2012 Jun 26.

Department of Particle Physics and Astrophysics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1103/PhysRevLett.108.261601DOI Listing
June 2012

Induction and molecular signature of pathogenic TH17 cells.

Nat Immunol 2012 Oct 9;13(10):991-9. Epub 2012 Sep 9.

Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/ni.2416DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3459594PMC
October 2012

Systematic identification of gene annotation errors in the widely used yeast mutation collections.

Nat Methods 2012 Feb 5;9(4):373-8. Epub 2012 Feb 5.

Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel.

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http://dx.doi.org/10.1038/nmeth.1890DOI Listing
February 2012

ANAT: a tool for constructing and analyzing functional protein networks.

Sci Signal 2011 Oct 25;4(196):pl1. Epub 2011 Oct 25.

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1126/scisignal.2001935DOI Listing
October 2011

Impulse control: temporal dynamics in gene transcription.

Cell 2011 Mar;144(6):886-96

Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.cell.2011.02.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148525PMC
March 2011

Network-free inference of knockout effects in yeast.

PLoS Comput Biol 2010 Jan 8;6(1):e1000635. Epub 2010 Jan 8.

Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1371/journal.pcbi.1000635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795781PMC
January 2010

Testing new indirect CP violation.

Phys Rev Lett 2009 Aug 14;103(7):071602. Epub 2009 Aug 14.

Institute for High Energy Phenomenology, Newman Laboratory of Elementary Particle Physics, Cornell University, Ithaca, New York 14853, USA.

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http://dx.doi.org/10.1103/PhysRevLett.103.071602DOI Listing
August 2009

Combining K0-K0 mixing and D0-D0 mixing to constrain the flavor structure of new physics.

Phys Rev Lett 2009 May 28;102(21):211802. Epub 2009 May 28.

Department of Particle Physics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1103/PhysRevLett.102.211802DOI Listing
May 2009

Metabolic-network-driven analysis of bacterial ecological strategies.

Genome Biol 2009 5;10(6):R61. Epub 2009 Jun 5.

The Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/gb-2009-10-6-r61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718495PMC
September 2009

A complex-centric view of protein network evolution.

Nucleic Acids Res 2009 Jul 22;37(12):e88. Epub 2009 May 22.

The Blavatnik School of Computer Science, Department of Molecular Microbiology and Biotechnology and School of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkp414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709590PMC
July 2009

A genome-wide screen for essential yeast genes that affect telomere length maintenance.

Nucleic Acids Res 2009 Jul 22;37(12):3840-9. Epub 2009 Apr 22.

Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkp259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709559PMC
July 2009

Toward accurate reconstruction of functional protein networks.

Mol Syst Biol 2009 17;5:248. Epub 2009 Mar 17.

The Blavatnik School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1038/msb.2009.3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671920PMC
July 2009

From sequence to structure to networks.

Genome Biol 2008 4;9(11):326. Epub 2008 Nov 4.

School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/gb-2008-9-11-326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614487PMC
February 2009

Improved network-based identification of protein orthologs.

Bioinformatics 2008 Aug;24(16):i200-6

School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btn277DOI Listing
August 2008

Importance of the heavier singlet neutrinos in leptogenesis.

Phys Rev Lett 2007 Aug 24;99(8):081802. Epub 2007 Aug 24.

Department of Particle Physics, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1103/PhysRevLett.99.081802DOI Listing
August 2007

Constraining the phase of Bs-Bs mixing.

Phys Rev Lett 2006 Oct 10;97(15):151801. Epub 2006 Oct 10.

Department of Physics, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel.

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October 2006

Inferring functional pathways from multi-perturbation data.

Bioinformatics 2006 Jul;22(14):e539-46

School of Computer Science, Tel-Aviv University, Tel-Aviv, Israel.

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http://dx.doi.org/10.1093/bioinformatics/btl204DOI Listing
July 2006

Baryogenesis from the Kobayashi-Maskawa phase.

Phys Rev Lett 2004 Jul 27;93(5):051301. Epub 2004 Jul 27.

Department of Particle Physics, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1103/PhysRevLett.93.051301DOI Listing
July 2004

Leptogenesis from supersymmetry breaking.

Phys Rev Lett 2003 Dec 16;91(25):251801. Epub 2003 Dec 16.

Department of Physics, Technion-Israel Institute of Technology, Technion City, 32000 Haifa, Israel.

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December 2003