Program

Subject

Journal

2008-10-06 - Sebastien Li-Thiao-Te.

One-factor-at-a-time versus Designed experiments

2008-10-13 - Pascal Bochet.

Proteome wide modulation of protein expression by microRNA

(two recent papers in Nature)

2008-10-27 & 2008-10-30 - Mathias Vandenbogaert.

Modeling the electron transport chain of purple non-sulfur bacteria
Steffen Klamt, Hartmut Grammel, Ronny Straube, Robin Ghosh and Ernst Dieter Gilles

Molecular Systems Biology, 4:156, Jan 2008

2008-11-04 - Aurelien Mazurie

Functional Modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage.
Sameith K, Antczak P, Marston E, Turan N, Maier D, Stankovic T,Falciani F.

Bioinformatics. 2008 Sep 17.

2008-11-12 - Benno

Finding multiple target optimal intervention in disease-related molecular network
Kun Yang, Hongjun Bai, Qi Ouyang, Luhua Lai and Chao Tang

Molecular Systems Biology 4:228, 2008

2008-11-17 - Frank Rügheimer

Computational expansion of genetic networks
Amos Tanay and Ron Shamir

Bioinformatics. 2001;17

2008-11-28 - Sebastien Li-Thiao-Te

Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome
Matthias Mann, Shao-En Ong, Mads Gronborg, Hanno Steen, Ole N. Jensen, Akhilesh Pandey

Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements
Steen Hanno; Jebanathirajah Judith A; Rush John; Morrice Nicolas; Kirschner Marc W

Trends in Biotechnology, 20, 6, June 02, pp 261-268

Molecular & cellular proteomics : MCP 2006;5(1):172-81

2008-12-01 - Aurelien Mazurie

Inferring pathway activity toward precise disease classification
Lee E, Chuang HY, Kim JW, Ideker T, Lee D.

PLoS Comput Biol. 2008 Nov;4(11)

2008-12-15 - Pascal Bochet

2009-01-23 - Sebastien Li-Thiao-Te

2009-02-02 - Thomas Rolland

Large-scale assignment of orthology: back to phylogenetics?
Toni Gabaldón

Genome Biology 2008, 9:235

2009-02-16 - Frank Rügheimer

2009-02-26 - Mathieu Michaud

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks
Jun Zhu, Bin Zhang, Erin N Smith, Becky Drees, Rachel B Brem, Leonid Kruglyak, Roger E Bumgarner and Eric E Schadt

Nature Genetics 40, 854 - 861 (2008)

2009-03-02 - Pascal Bochet

A protocol for unraveling gene regulatory networks
Stefan C Materna & Paola Oliveri

Nature Protocols Vol.3 No.12 2008

2009-03-04 - Aurelien Mazurie

Metabolic systems cost-benefit analysis for interpreting network structure and regulation
Ross P. Carlson

Bioinformatics. 2007 May 15;23(10):1258-64

2009-04-01 - Sebastien Li-Thiao-Te

2009-04-06 - Mathias Vandenbogaert

Retention time alignment algorithms for LC/MS data must consider non-linear shifts.
Katharina Podwojski, Arno Fritsch, Daniel C. Chamrad, Wolfgang Paul, Barbara Sitek, Kai Stühler, Petra Mutzel, Christian Stephan, Helmut E. Meyer, Wolfgang Urfer, Katja Ickstadt and Jörg Rahnenführer

Bioinformatics Vol. 25 no. 6 2009, pages 758–764

2009-04-17 - Maxime Venin & Frank Ruegheimer

Frequent Item Sets (Part I)

N/A

2009-05-04 - Benno

Models from experiments: combinatorial drug perturbations of cancer cells
Sven Nelander, Weiqing Wang, Bjorn Nilsson, Qing-Bai She, Christine Pratilas, Neal Rosen, Peter Gennemark and Chris Sander

Molecular Systems Biology 4:216

2009-05-18 - Aurelien

N/A

N/A

2009-05-25 - Frank & Maxime

Frequent Item Sets (Part II)

N/A

2009-06-04 - Mathieu

Dynamic modularity in protein interaction networks predicts breast cancer outcome
Taylor I, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana J

Nature Biotechnology 27, 199-204 (2009 February)

2009-06-08 - Thomas

Population genomics of domestic and wild yeasts.
Liti G. et al.

Nature 2009

2009-06-15 - Aurelien

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
Thomas R, Gohlke J, Stopper G, Parham F, Portier C.

Genome Biology 2009, 10:R44

2009-06-26 - Pascal

Development and assessment of scoring functions for protein identification using PMF data
Zhao Song,Luonan Chen,Ashwin Ganapathy,Xiu-Feng Wan,Laurent Brechenmacher,Nengbing Tao,David Emerich,Gary Stacey,Dong Xu

Electrophoresis 2007, 28, 864–870

2009-07-08 - Samad

Network component analysis: Reconstruction of regulatory signals in biological systems
James C. Liao, Riccardo Boscolo, Young-Lyeol Yang, Linh My Tran, Chiara Sabatti, and Vwani P. Roychowdhury

NAS December 23, 2003 vol. 100 no. 26

2009-09-09 - Mathias

PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling
Ari Frank and Pavel Pevzner

Anal. Chem. 2005, 77, 964-973

2009-09-14 - Frank

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments
Ewa Szczurek, Irit Gat-Viks, Jerzy Tiuryn and Martin Vingron

Mol. Systems Biology 5:287, July 2009

2009-10-05 - Pascal

Backup in gene regulatory networks explains differences between binding and knockout results
Anthony Gitter, Zehava Siegfried, Michael Klutstein, Oriol Fornes, Baldo Oliva, Itamar Simon and Ziv Bar-Joseph

Molecular Systems Biology 5:276

2009-10-23 - Samad

Assessing the limits of genomic data integration for predicting protein networks
Long J. Lu, Yu Xia, Alberto Paccanaro, Haiyuan Yu, and Mark Gerstein

Genome Res. 2005 15: 945-953

2009-10-30 - Thomas

A yeast hybrid provides insight into the evolution of gene expression regulation.
Tirosh I, Reikhav S, Levy AA, Barkai N.

Science. 2009 May 1;324(5927):659-62.

2009-11-09 - Ashish

N/A

N/A

2009-11-16 - Olivia

ASMS Fall Workshop in Baltimore : Bioinformatics for Protein Identification

N/A

2009-11-23 - Frank

Learning a prior on regulatory potential from eQTL data.
Lee et al.

PLoS Genet. 2009 Jan;5(1)

2009-11-30 - Samuel

A comprehensive library of fluorescent transcriptional reporters for Esherichia coli.
Zaslaver et al.

Nature methods (2006) vol. 3 (8) pp. 623

2009-12-07 - Benno

N/A

N/A

2009-12-14 - Pascal

N/A

N/A

2009-12-21 - N/A

N/A

N/A

2010-01-12 - Pascal

N/A

N/A

2010-01-18 - Thomas

N/A

N/A

2010-01-25 - Ashish

Predicting functionality of protein–DNA interactions by integrating diverse evidence
Duygu Ucar, Andreas Beyer, Srinivasan Parthasarathy and Christopher T. Workman

Bioinformatics, Vol. 25, 2009, pages i137–i144

2010-02-03 - Frank

Metrics for GO based protein semantic similarity: a systematic evaluation.
Pesquita et al.

BMC Bioinformatics. 2008; 9(Suppl 5): S4

2010-02-15 - Olivia

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.
Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M.

Cell. 2006 Nov 3;127(3):635-48.

2010-02-22 - Mathias

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies
Brian C. Searle, Mark Turner, and Alexey I. Nesvizhskii

J Proteome Res. 2008 Jan;7(1):245-53.

2010-03-01 - Samuel

Improving the performance of dictionary-based approaches in protein name recognition.
Tsuruoka et Tsujii.

J Biomed Inform (2004) vol. 37 (6) pp. 461-70

2010-03-03 - Benno

Population context determines cell-to-cell variability in endocytosis and virus infection
Berend Snijder, Raphael Sacher, Pauli Rämö, Eva-Maria Damm, Prisca Liberali & Lucas Pelkmans

Nature 461, 520-523(24 September 2009)

2010-03-21 - Frederik

Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
Eran Segal, Michael Shapira, Aviv Regev, Dana Pe’er, David Botstein, Daphne Koller & Nir Friedman

NATURE GENETICS VOLUME 34 NUMBER 2 JUNE 2003

2010-04-08 - Ashish

Probit Regression: Particular Case of Generalized Linear Model
N/A

N/A

2010-04-12 - Frank

Gaussian Graphical Models / Covariance Selection
Søren Højsgaard and Steffen Lauritzen / Arthur Dempster

J. R. Statist. Soc B (2008) 70, pp 1005--1027 / Biometrics 28, 157-175, 1972

2010-04-17 - Mathias V.

Accurate and Sensitive Peptide Identification with Mascot Percolator
Markus Brosch, Lu Yu, Tim Hubbard, and Jyoti Choudhary

Journal of Proteome Research 8 3176-3181 (2009)

2010-04-19 - Pascal

N/A
N/A

N/A

2010-05-03 - Benno

N/A
N/A

N/A

2010-05-10 - Thomas

N/A
N/A

N/A

2010-05-17 - Olivia

N/A
N/A

N/A

2010-05-26 - Frederik

Inferring cluster-based networks from differently stimulated multiple time-course gene expression data
Yuichi Shiraishi, Shuhei Kimura and Mariko Okada

Bioinformatics 2010 26(8):1073-1081

2010-05-31 - Benno

N/A
N/A

N/A

2010-06-11 - Ashish

N/A
N/A

N/A

2010-06-14 - Pascal

N/A
N/A

N/A

2010-06-21 - Olivia

N/A
N/A

N/A

2010-06-28 - Mathias

PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data
Brian E. Ruttenberg, Trairak Pisitkun, Mark A. Knepper, and Jason D. Hoffert

Journal of Proteome Research, Jul;7(7):3054-3059 (2008)

2010-07-12 - Benno

N/A
N/A

N/A

2010-07-26 - Samuel

N/A
N/A

N/A

2010-09-24 - Frederik

Network Legos: Building Blocks of Cellular Wiring Diagrams
T. M. Murali and C. G. Rivera

Journal of Computational Biology 2008, Vol 15,Num 7,Pp 829-844

2010-09-24 - Frank

Nonparametric identification of regulatory interactions from spatial and temporal gene expression data
Anil Aswani, Soile Keränen, James Brown, Charless Fowlkes, David Knowles, Mark Biggin, Peter Bickel, Claire Tomlin

BMC Bioinformatics 2010, 11:413

2010-11-04 - Mathias

Feasibility of Large-Scale Phosphoproteomics with Higher Energy Collisional Dissociation Fragmentation
Nagarjuna Nagaraj, Rochelle C. J. D’Souza, Juergen Cox, Jesper V. Olsen, and Matthias Mann

J Proteome Res. 2010 Oct 26. [Epub ahead of print]

2011-01-28 - Frank

Towards Evidence-Based Medical Statistics 1: The P Value Fallacy
Steven N. Goodman

Ann Intern Med. 1999; 130:995-1004.

2011-05-24 - Mathias

More than 100,000 Detectable Peptide Species Elute in Single Shotgun Proteomics Runs but the Majority is Inaccessible to Data-Dependent LC-MS/MS
Annette Michalski, Juergen Cox, and Matthias Mann

J. Proteome Res. 2011, 10, 1785–1793