Publications by authors named "Igor Ulitsky"

73Publications

Regulation of neuronal commitment in mouse embryonic stem cells by the Reno1/Bahcc1 locus.

EMBO Rep 2020 Sep 24:e51264. Epub 2020 Sep 24.

Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.15252/embr.202051264DOI Listing
September 2020

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Authors:
Jordan A Ramilowski Chi Wai Yip Saumya Agrawal Jen-Chien Chang Yari Ciani Ivan V Kulakovskiy Mickaël Mendez Jasmine Li Ching Ooi John F Ouyang Nick Parkinson Andreas Petri Leonie Roos Jessica Severin Kayoko Yasuzawa Imad Abugessaisa Altuna Akalin Ivan V Antonov Erik Arner Alessandro Bonetti Hidemasa Bono Beatrice Borsari Frank Brombacher Christopher JF Cameron Carlo Vittorio Cannistraci Ryan Cardenas Melissa Cardon Howard Chang Josée Dostie Luca Ducoli Alexander Favorov Alexandre Fort Diego Garrido Noa Gil Juliette Gimenez Reto Guler Lusy Handoko Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Kosuke Hashimoto Norihito Hayatsu Peter Heutink Tetsuro Hirose Eddie L Imada Masayoshi Itoh Bogumil Kaczkowski Aditi Kanhere Emily Kawabata Hideya Kawaji Tsugumi Kawashima S Thomas Kelly Miki Kojima Naoto Kondo Haruhiko Koseki Tsukasa Kouno Anton Kratz Mariola Kurowska-Stolarska Andrew Tae Jun Kwon Jeffrey Leek Andreas Lennartsson Marina Lizio Fernando López-Redondo Joachim Luginbühl Shiori Maeda Vsevolod J Makeev Luigi Marchionni Yulia A Medvedeva Aki Minoda Ferenc Müller Manuel Muñoz-Aguirre Mitsuyoshi Murata Hiromi Nishiyori Kazuhiro R Nitta Shuhei Noguchi Yukihiko Noro Ramil Nurtdinov Yasushi Okazaki Valerio Orlando Denis Paquette Callum J C Parr Owen J L Rackham Patrizia Rizzu Diego Fernando Sánchez Martinez Albin Sandelin Pillay Sanjana Colin A M Semple Youtaro Shibayama Divya M Sivaraman Takahiro Suzuki Suzannah C Szumowski Michihira Tagami Martin S Taylor Chikashi Terao Malte Thodberg Supat Thongjuea Vidisha Tripathi Igor Ulitsky Roberto Verardo Ilya E Vorontsov Chinatsu Yamamoto Robert S Young J Kenneth Baillie Alistair R R Forrest Roderic Guigó Michael M Hoffman Chung Chau Hon Takeya Kasukawa Sakari Kauppinen Juha Kere Boris Lenhard Claudio Schneider Harukazu Suzuki Ken Yagi Michiel J L de Hoon Jay W Shin Piero Carninci

Genome Res 2020 07 27;30(7):1060-1072. Epub 2020 Jul 27.

RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.

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http://dx.doi.org/10.1101/gr.254219.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7397864PMC
July 2020

Gene Architecture and Sequence Composition Underpin Selective Dependency of Nuclear Export of Long RNAs on NXF1 and the TREX Complex.

Mol Cell 2020 07 5;79(2):251-267.e6. Epub 2020 Jun 5.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2020.05.013DOI Listing
July 2020

Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels.

Mol Cell 2020 05 14;78(3):434-444.e5. Epub 2020 Apr 14.

Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2020.03.022DOI Listing
May 2020

A guide to naming human non-coding RNA genes.

EMBO J 2020 03 24;39(6):e103777. Epub 2020 Feb 24.

Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.

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http://dx.doi.org/10.15252/embj.2019103777DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073466PMC
March 2020

Long Noncoding RNAs in Development and Regeneration of the Neural Lineage.

Cold Spring Harb Symp Quant Biol 2019 3;84:165-177. Epub 2020 Jan 3.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1101/sqb.2019.84.039347DOI Listing
January 2020

Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program.

Cell 2019 12;179(7):1609-1622.e16

Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signaling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Center for NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.11.010DOI Listing
December 2019

Regulation of gene expression by cis-acting long non-coding RNAs.

Nat Rev Genet 2020 02 15;21(2):102-117. Epub 2019 Nov 15.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1038/s41576-019-0184-5DOI Listing
February 2020

Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability.

Nat Commun 2019 11 8;10(1):5092. Epub 2019 Nov 8.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1038/s41467-019-13075-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6841665PMC
November 2019

Endothelial function and dysfunction in the cardiovascular system: the long non-coding road.

Cardiovasc Res 2019 Oct;115(12):1692-1704

Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, UK.

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http://dx.doi.org/10.1093/cvr/cvz154DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755355PMC
October 2019

The EXPANDER Integrated Platform for Transcriptome Analysis.

J Mol Biol 2019 06 14;431(13):2398-2406. Epub 2019 May 14.

The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2019.05.013DOI Listing
June 2019

Aging well with .

Elife 2019 03 8;8. Epub 2019 Mar 8.

Department of Biological Regulation, The Weizmann Institute of Science, Rehovot, Israel.

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https://elifesciences.org/articles/45974
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http://dx.doi.org/10.7554/eLife.45974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407920PMC
March 2019

Predictive models of subcellular localization of long RNAs.

RNA 2019 05 11;25(5):557-572. Epub 2019 Feb 11.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1261/rna.068288.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467007PMC
May 2019

Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments.

Nucleic Acids Res 2019 03;47(5):2560-2573

Non-coding RNAs and mechanisms of cytoplasmic gene regulation, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gky1270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411841PMC
March 2019

Production of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity.

Cell Syst 2018 11 14;7(5):537-547.e3. Epub 2018 Nov 14.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712183043
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http://dx.doi.org/10.1016/j.cels.2018.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542670PMC
November 2018

Regulation of Neuroregeneration by Long Noncoding RNAs.

Mol Cell 2018 11 25;72(3):553-567.e5. Epub 2018 Oct 25.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10972765183079
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http://dx.doi.org/10.1016/j.molcel.2018.09.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542662PMC
November 2018

Predicting microRNA targeting efficacy in Drosophila.

Genome Biol 2018 10 4;19(1):152. Epub 2018 Oct 4.

Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1186/s13059-018-1504-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172730PMC
October 2018

Interactions between short and long noncoding RNAs.

Authors:
Igor Ulitsky

FEBS Lett 2018 09 23;592(17):2874-2883. Epub 2018 May 23.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1002/1873-3468.13085DOI Listing
September 2018

Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells.

Nature 2018 03 24;555(7694):107-111. Epub 2018 Jan 24.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1038/nature25757DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047738PMC
March 2018

SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA.

Genes Dev 2018 01 31;32(1):70-78. Epub 2018 Jan 31.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1101/gad.309138.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828396PMC
January 2018

The human lncRNA LINC-PINT inhibits tumor cell invasion through a highly conserved sequence element.

Genome Biol 2017 10 27;18(1):202. Epub 2017 Oct 27.

Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, 31008, Spain.

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http://dx.doi.org/10.1186/s13059-017-1331-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5660458PMC
October 2017

Analysis of blood-based gene expression in idiopathic Parkinson disease.

Neurology 2017 Oct 15;89(16):1676-1683. Epub 2017 Sep 15.

From the School of Computer Science (R.S., D.A., H.S.), Tel Aviv University, Israel; Institute of Neurogenetics (C.K., E.-J.V., H.P., M.K.), University of Lübeck, Germany; Department of Psychiatry and Psychotherapy (E.-J.V., M.K.), University of Lübeck, Germany; Institute of Medical Genetics and Applied Genomics (M.B., S.P., O.R.), University of Tübingen, Germany; IMGM Laboratories GmbH (M.B.), Martinsried, Germany; Mediterranean Institute for Life Sciences (M.U.), Split, Croatia; Department of Neurology (Y.C.W., D.K.), Northwestern University Feinberg School of Medicine, Chicago, IL; Clinical Institute of Medical Genetics (A.M., B.P.), University Medical Center Ljubljana, Slovenia; Sorbonne Universités (J.C.-C., S.L., A.B.), UPMC Université Paris 6 UMR S 1127, Inserm U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Centre d'Investigation Clinique Pitié Neurosciences CIC-1422 (J.C.-C.), Paris, France; Machine Learning Technologies Group (O.L.), IBM Research-Haifa, Mount Carmel, Israel; Department of Neurology (G.D., G.K.), Kiel University, Germany; and Department of Biological Regulation (I.U.), Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1212/WNL.0000000000004516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644465PMC
October 2017

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.

Genome Biol 2017 08 30;18(1):162. Epub 2017 Aug 30.

Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St., Rehovot, 76100, Israel.

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http://dx.doi.org/10.1186/s13059-017-1293-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577775PMC
August 2017

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems.

Sci Rep 2017 08 17;7(1):8637. Epub 2017 Aug 17.

Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.

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http://dx.doi.org/10.1038/s41598-017-08320-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5561060PMC
August 2017

The functions of long noncoding RNAs in development and stem cells.

Development 2016 11;143(21):3882-3894

Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl St, Rehovot 76100, Israel

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http://dev.biologists.org/lookup/doi/10.1242/dev.140962
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http://dx.doi.org/10.1242/dev.140962DOI Listing
November 2016

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.

Authors:
Igor Ulitsky

Nat Rev Genet 2016 10 30;17(10):601-14. Epub 2016 Aug 30.

Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, Rehovot 76100, Israel.

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http://dx.doi.org/10.1038/nrg.2016.85DOI Listing
October 2016

A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells.

Nat Commun 2016 07 13;7:12209. Epub 2016 Jul 13.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1038/ncomms12209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947167PMC
July 2016

Nuclear Retention of mRNA in Mammalian Tissues.

Cell Rep 2015 Dec 17;13(12):2653-62. Epub 2015 Dec 17.

Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.11.036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4700052PMC
December 2015

Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor.

Nucleic Acids Res 2016 Feb 10;44(3):1370-83. Epub 2015 Dec 10.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel

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http://dx.doi.org/10.1093/nar/gkv1367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756822PMC
February 2016

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs.

Biochim Biophys Acta 2016 Jan 8;1859(1):31-40. Epub 2015 Aug 8.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.bbagrm.2015.07.017DOI Listing
January 2016

Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

Cell Rep 2015 May 7;11(7):1110-22. Epub 2015 May 7.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247150041
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http://dx.doi.org/10.1016/j.celrep.2015.04.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576741PMC
May 2015

lincRNAs: genomics, evolution, and mechanisms.

Cell 2013 Jul;154(1):26-46

Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.

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http://dx.doi.org/10.1016/j.cell.2013.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3924787PMC
July 2013

Extensive alternative polyadenylation during zebrafish development.

Genome Res 2012 Oct 21;22(10):2054-66. Epub 2012 Jun 21.

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/gr.139733.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460199PMC
October 2012

A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression.

PLoS One 2011 31;6(10):e26992. Epub 2011 Oct 31.

Department of Cell Research and Immunology, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026992PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205039PMC
March 2012

SPIKE: a database of highly curated human signaling pathways.

Nucleic Acids Res 2011 Jan 19;39(Database issue):D793-9. Epub 2010 Nov 19.

Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1093/nar/gkq1167DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014840PMC
January 2011

DEGAS: de novo discovery of dysregulated pathways in human diseases.

PLoS One 2010 Oct 19;5(10):e13367. Epub 2010 Oct 19.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0013367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2957424PMC
October 2010

Towards computational prediction of microRNA function and activity.

Nucleic Acids Res 2010 Aug 24;38(15):e160. Epub 2010 Jun 24.

Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 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/gkq570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926627PMC
August 2010

Different sets of QTLs influence fitness variation in yeast.

Mol Syst Biol 2010 16;6:346. Epub 2010 Feb 16.

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

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http://dx.doi.org/10.1038/msb.2010.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835564PMC
May 2010

Expander: from expression microarrays to networks and functions.

Nat Protoc 2010 Feb 28;5(2):303-22. Epub 2010 Jan 28.

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

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http://dx.doi.org/10.1038/nprot.2009.230DOI Listing
February 2010

Towards accurate imputation of quantitative genetic interactions.

Genome Biol 2009 10;10(12):R140. Epub 2009 Dec 10.

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

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http://dx.doi.org/10.1186/gb-2009-10-12-r140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812947PMC
May 2010

Identifying functional modules using expression profiles and confidence-scored protein interactions.

Bioinformatics 2009 May 17;25(9):1158-64. Epub 2009 Mar 17.

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

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http://dx.doi.org/10.1093/bioinformatics/btp118DOI Listing
May 2009

Allegro: analyzing expression and sequence in concert to discover regulatory programs.

Nucleic Acids Res 2009 Apr 16;37(5):1566-79. Epub 2009 Jan 16.

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

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http://dx.doi.org/10.1093/nar/gkn1064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655690PMC
April 2009

Regulatory networks define phenotypic classes of human stem cell lines.

Nature 2008 Sep 24;455(7211):401-5. Epub 2008 Aug 24.

Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature07213DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637443PMC
September 2008

From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions.

Mol Syst Biol 2008 15;4:209. Epub 2008 Jul 15.

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

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http://msb.embopress.org/cgi/doi/10.1038/msb.2008.42
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http://dx.doi.org/10.1038/msb.2008.42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2516364PMC
December 2008

Comprehensive microRNA profiling reveals a unique human embryonic stem cell signature dominated by a single seed sequence.

Stem Cells 2008 Jun 10;26(6):1506-16. Epub 2008 Apr 10.

The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1634/stemcells.2007-1081DOI Listing
June 2008

SPIKE--a database, visualization and analysis tool of cellular signaling pathways.

BMC Bioinformatics 2008 Feb 20;9:110. Epub 2008 Feb 20.

The David and Inez Myers Laboratory for Genetic Research, Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.

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http://dx.doi.org/10.1186/1471-2105-9-110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2263022PMC
February 2008

MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data.

Genome Biol 2008 Jan 2;9(1):R1. Epub 2008 Jan 2.

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

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http://dx.doi.org/10.1186/gb-2008-9-1-r1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395235PMC
January 2008

Detecting pathways transcriptionally correlated with clinical parameters.

Comput Syst Bioinformatics Conf 2008 ;7:249-58

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

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August 2009

Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks.

Mol Syst Biol 2007 17;3:104. Epub 2007 Apr 17.

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

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http://dx.doi.org/10.1038/msb4100144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1865586PMC
May 2007

Identification of functional modules using network topology and high-throughput data.

BMC Syst Biol 2007 Jan 26;1. Epub 2007 Jan 26.

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

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http://dx.doi.org/10.1186/1752-0509-1-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839897PMC
January 2007

Network-based prediction of protein function.

Mol Syst Biol 2007 13;3:88. Epub 2007 Mar 13.

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

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http://dx.doi.org/10.1038/msb4100129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847944PMC
May 2007

The average common substring approach to phylogenomic reconstruction.

J Comput Biol 2006 Mar;13(2):336-50

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

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http://dx.doi.org/10.1089/cmb.2006.13.336DOI Listing
March 2006