Molecular Systems Biology

Bioinformatics

2009

Predicting and controlling the reactivity of immune cell populations against cancer

Kfir Oved, Eran Eden, Martin Akerman, Roy Noy, Ron Wolchinsky, Orit Izhaki, Ester Schallmach, Adva Kubi, Naama Zabari, Jacob Schachter, Uri Alon, Yael Mandel-Gutfreund, Michal J Besser & Yoram Reiter

doi:10.1038/msb.2009.15
Published online: 28 April 2009

Synopsis | Full Text | PDF (3,394K) | Supplementary information

The impact of cellular networks on disease comorbidity

Juyong Park, Deok-Sun Lee, Nicholas A Christakis & Albert-László Barabási

doi:10.1038/msb.2009.16
Published online: 07 April 2009

Full Text | PDF (587K) | Supplementary information

Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Thanasis Margaritis, Philip Lijnzaad, Dik van Leenen, Diane Bouwmeester, Patrick Kemmeren, Sander R van Hooff & Frank CP Holstege

doi:10.1038/msb.2009.21
Published online: 28 April 2009

Full Text | PDF (2,109K) | Supplementary information

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

Barrett C Foat & Gary D Stormo

doi:10.1038/msb.2009.24
Published online: 28 April 2009

Synopsis | Full Text | PDF (654K) | Supplementary information

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

Anna Bauer-Mehren, Laura I Furlong & Ferran Sanz

doi:10.1038/msb.2009.47
Published online: 28 July 2009

Full Text | PDF (2,047K) | Supplementary information

A simple and efficient algorithm for genome-wide homozygosity analysis in disease

Wei Liu, Jinhui Ding, Jesse Raphael Gibbs, Sue Jane Wang, John Hardy & Andrew Singleton

doi:10.1038/msb.2009.53
Published online: 15 September 2009

Full Text | PDF (1,823K) | Supplementary information

Disease signatures are robust across tissues and experiments

Joel T Dudley, Robert Tibshirani, Tarangini Deshpande & Atul J Butte

doi:10.1038/msb.2009.66
Published online: 15 September 2009

Full Text | PDF (1,317K) | Supplementary information

Complex topology rather than complex membership is a determinant of protein dosage sensitivity

Richard Oberdorf & Tanja Kortemme

doi:10.1038/msb.2009.9
Published online: 17 March 2009

Synopsis | Full Text | PDF (1,241K) | Supplementary information

2008

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

Arun K Ramani, Zhihua Li, G Traver Hart, Mark W Carlson, Daniel R Boutz & Edward M Marcotte

doi:10.1038/msb.2008.19
Published online: 15 April 2008

Synopsis | Full Text | PDF (4,872K) | Supplementary information

Life Sciences and the web: a new era for collaboration

Jonathan A Sagotsky, Le Zhang, Zhihui Wang, Sean Martin & Thomas S Deisboeck

doi:10.1038/msb.2008.39
Published online: 01 July 2008

Full Text | PDF (348K)

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

Igor Ulitsky, Tomer Shlomi, Martin Kupiec & Ron Shamir

doi:10.1038/msb.2008.42
Published online: 15 July 2008

Synopsis | Full Text | PDF (7,159K) | Supplementary information

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

David J Lynn, Geoffrey L Winsor, Calvin Chan, Nicolas Richard, Matthew R Laird, Aaron Barsky, Jennifer L Gardy, Fiona M Roche, Timothy H W Chan, Naisha Shah, Raymond Lo, Misbah Naseer, Jaimmie Que, Melissa Yau, Michael Acab, Dan Tulpan, Matthew D Whiteside, Avinash Chikatamarla, Bernadette Mah, Tamara Munzner, Karsten Hokamp, Robert E W Hancock & Fiona S L Brinkman

doi:10.1038/msb.2008.55
Published online: 02 September 2008

Synopsis | Full Text | PDF (3,173K) | Supplementary information

p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation

Ran Brosh, Reut Shalgi, Atar Liran, Gilad Landan, Katya Korotayev, Giang Huong Nguyen, Espen Enerly, Hilde Johnsen, Yosef Buganim, Hilla Solomon, Ido Goldstein, Shalom Madar, Naomi Goldfinger, Anne-Lise Børresen-Dale, Doron Ginsberg, Curtis C Harris, Yitzhak Pilpel, Moshe Oren & Varda Rotter

doi:10.1038/msb.2008.65
Published online: 25 November 2008

Synopsis | Full Text | PDF (6,255K) | Supplementary information

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

Lukas Burger & Erik van Nimwegen

doi:10.1038/msb4100203
Published online: 12 February 2008

Synopsis | Full Text | PDF (409K) | Supplementary information

¹H NMR metabonomics approach to the disease continuum of diabetic complications and premature death

Ville-Petteri Mäkinen, Pasi Soininen, Carol Forsblom, Maija Parkkonen, Petri Ingman, Kimmo Kaski, Per-Henrik Groop & Mika Ala-Korpela for the FinnDiane Study Group

doi:10.1038/msb4100205
Published online: 12 February 2008

Synopsis | Full Text | PDF (1,017K) | Supplementary information

2007

Large-scale mapping of human protein–protein interactions by mass spectrometry

Rob M Ewing, Peter Chu, Fred Elisma, Hongyan Li, Paul Taylor, Shane Climie, Linda McBroom-Cerajewski, Mark D Robinson, Liam O'Connor, Michael Li, Rod Taylor, Moyez Dharsee, Yuen Ho, Adrian Heilbut, Lynda Moore, Shudong Zhang, Olga Ornatsky, Yury V Bukhman, Martin Ethier, Yinglun Sheng, Julian Vasilescu, Mohamed Abu-Farha, Jean-Philippe Lambert, Henry S Duewel, Ian I Stewart, Bonnie Kuehl, Kelly Hogue, Karen Colwill, Katharine Gladwish, Brenda Muskat, Robert Kinach, Sally-Lin Adams, Michael F Moran, Gregg B Morin, Thodoros Topaloglou & Daniel Figeys

doi:10.1038/msb4100134
Published online: 13 March 2007

Synopsis | Full Text | PDF (440K) | Supplementary information

2006

Integration of metabolome data with metabolic networks reveals reporter reactions

Tunahan Çakir, Kiran Raosaheb Patil, Zeynep Ilsen Önsan, Kutlu Özergin Ülgen, Betül Kirdar & Jens Nielsen

doi:10.1038/msb4100085
Published online: 03 October 2006

Synopsis | Full Text | PDF (297K) | Supplementary information

Depicting combinatorial complexity with the molecular interaction map notation

Kurt W Kohn, Mirit I Aladjem, Sohyoung Kim, John N Weinstein & Yves Pommier

doi:10.1038/msb4100088
Published online: 03 October 2006

Full Text | PDF (353K) | Supplementary information

Principles of microRNA regulation of a human cellular signaling network

Qinghua Cui, Zhenbao Yu, Enrico O Purisima & Edwin Wang

doi:10.1038/msb4100089
Published online: 12 September 2006

Full Text | PDF (208K) | Supplementary information

2005

A global view of pleiotropy and phenotypically derived gene function in yeast

Aimée Marie Dudley, Daniel Maarten Janse, Amos Tanay, Ron Shamir & George McDonald Church

doi:10.1038/msb4100004
Published online: 29 March 2005

Synopsis | Full Text | PDF (412K) | Supplementary information

Expression dynamics of a cellular metabolic network

Peter Kharchenko, George M Church & Dennis Vitkup

doi:10.1038/msb4100023
Published online: 02 August 2005

Full Text | PDF (128K)

The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation

Yuval Tabach, Michael Milyavsky, Igor Shats, Ran Brosh, Or Zuk, Assif Yitzhaky, Roberto Mantovani, Eytan Domany, Varda Rotter & Yitzhak Pilpel

doi:10.1038/msb4100030
Published online: 18 October 2005

Synopsis | Full Text | PDF (383K) | Supplementary information

Gene function prediction from congruent synthetic lethal interactions in yeast

Ping Ye, Brian D Peyser, Xuewen Pan, Jef D Boeke, Forrest A Spencer & Joel S Bader

doi:10.1038/msb4100034
Published online: 22 November 2005

Synopsis | Full Text | PDF (257K) | Supplementary information

Subject archive

Bioinformatics

2009

Predicting and controlling the reactivity of immune cell populations against cancer

The impact of cellular networks on disease comorbidity

Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

A simple and efficient algorithm for genome-wide homozygosity analysis in disease

Disease signatures are robust across tissues and experiments

Complex topology rather than complex membership is a determinant of protein dosage sensitivity

2008

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

Life Sciences and the web: a new era for collaboration

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

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

¹H NMR metabonomics approach to the disease continuum of diabetic complications and premature death

2007

Large-scale mapping of human protein–protein interactions by mass spectrometry

2006

Integration of metabolome data with metabolic networks reveals reporter reactions

Depicting combinatorial complexity with the molecular interaction map notation

Principles of microRNA regulation of a human cellular signaling network

2005

A global view of pleiotropy and phenotypically derived gene function in yeast

Expression dynamics of a cellular metabolic network

The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation

Gene function prediction from congruent synthetic lethal interactions in yeast

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Subject archive

Bioinformatics

2009

Predicting and controlling the reactivity of immune cell populations against cancer

The impact of cellular networks on disease comorbidity

Adaptable gene-specific dye bias correction for two-channel DNA microarrays

Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

A simple and efficient algorithm for genome-wide homozygosity analysis in disease

Disease signatures are robust across tissues and experiments

Complex topology rather than complex membership is a determinant of protein dosage sensitivity

2008

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

Life Sciences and the web: a new era for collaboration

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

InnateDB: facilitating systems-level analyses of the mammalian innate immune response

p53-repressed miRNAs are involved with E2F in a feed-forward loop promoting proliferation

Accurate prediction of protein–protein interactions from sequence alignments using a Bayesian method

1H NMR metabonomics approach to the disease continuum of diabetic complications and premature death

2007

Large-scale mapping of human protein–protein interactions by mass spectrometry

2006

Integration of metabolome data with metabolic networks reveals reporter reactions

Depicting combinatorial complexity with the molecular interaction map notation

Principles of microRNA regulation of a human cellular signaling network

2005

A global view of pleiotropy and phenotypically derived gene function in yeast

Expression dynamics of a cellular metabolic network

The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation

Gene function prediction from congruent synthetic lethal interactions in yeast

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by Subject Area

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¹H NMR metabonomics approach to the disease continuum of diabetic complications and premature death