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|| '''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 [[BR]]''Annette Michalski, Juergen Cox, and Matthias Mann''|| J. Proteome Res. 2011, 10, 1785–1793||

Journal Club

Every Monday, the lab is having a Journal Club held in the conference room at 11:30am. Please join! The list of the [:Journal Club Suggested Topics:suggested topics] is also available.

The Journal club takes place on Monday every week, start at 11:30am and last about an hour. The suggestions are:

  • have the talk first, then the questions/discussions. It will help keeping the JC within an hour, and focus the discussion by letting people think about their questions. In case we have more questions than can be managed before the end of the hour, we can continue the discussions over lunch.
  • good article sources:
  • ideally, having a last slide with answers to the question 'What did it bring to this research field?' and 'Why did you think it was interesting?' (plus, maybe, 'Why have you been disappointed by this paper?') would provide a nice take-home message




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 BR 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.BRSameith 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 BR 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 BRAmos Tanay and Ron Shamir

Bioinformatics. 2001;17

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

Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteomeBRMatthias Mann, Shao-En Ong, Mads Gronborg, Hanno Steen, Ole N. Jensen, Akhilesh PandeyBRBRPhosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurementsBRSteen Hanno; Jebanathirajah Judith A; Rush John; Morrice Nicolas; Kirschner Marc W

Trends in Biotechnology, 20, 6, June 02, pp 261-268BRBRMolecular & cellular proteomics : MCP 2006;5(1):172-81

2008-12-01 - Aurelien Mazurie

Inferring pathway activity toward precise disease classificationBRLee 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?BRToni 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 BR 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 BRStefan 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 regulationBRRoss 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.BR 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)


2009-05-04 - Benno

Models from experiments: combinatorial drug perturbations of cancer cellsBRSven 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



2009-05-25 - Frank & Maxime

Frequent Item Sets (Part II)


2009-06-04 - Mathieu

Dynamic modularity in protein interaction networks predicts breast cancer outcomeBRTaylor 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.BRLiti G. et al.

Nature 2009

2009-06-15 - Aurelien

Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structureBRThomas 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 dataBRZhao 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 systemsBRJames 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 ModelingBR 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 experimentsBREwa 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 resultsBRAnthony 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 BRLong 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.BRTirosh I, Reikhav S, Levy AA, Barkai N.

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

2009-11-09 - Ashish



2009-11-16 - Olivia

ASMS Fall Workshop in Baltimore : Bioinformatics for Protein Identification


2009-11-23 - Frank

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

PLoS Genet. 2009 Jan;5(1)

2009-11-30 - Samuel

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

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

2009-12-07 - Benno



2009-12-14 - Pascal



2009-12-21 - N/A



2010-01-12 - Pascal



2010-01-18 - Thomas



2010-01-25 - Ashish

Predicting functionality of protein–DNA interactions by integrating diverse evidenceBRDuygu 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.BRPesquita et al.

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

2010-02-15 - Olivia

Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.BROlsen 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 MethodologiesBRBrian 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.BRTsuruoka 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 infectionBRBerend 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 dataBREran Segal, Michael Shapira, Aviv Regev, Dana Pe’er, David Botstein, Daphne Koller & Nir Friedman


2010-04-08 - Ashish

Probit Regression: Particular Case of Generalized Linear ModelBRN/A


2010-04-12 - Frank

Gaussian Graphical Models / Covariance SelectionBR 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 PercolatorBRMarkus Brosch, Lu Yu, Tim Hubbard, and Jyoti Choudhary

Journal of Proteome Research 8 3176-3181 (2009)

2010-04-19 - Pascal



2010-05-03 - Benno



2010-05-10 - Thomas



2010-05-17 - Olivia



2010-05-26 - Frederik

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

Bioinformatics 2010 26(8):1073-1081

2010-05-31 - Benno



2010-06-11 - Ashish



2010-06-14 - Pascal



2010-06-21 - Olivia



2010-06-28 - Mathias

PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn DataBRBrian 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



2010-07-26 - Samuel



2010-09-24 - Frederik

Network Legos: Building Blocks of Cellular Wiring DiagramsBRT. 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 dataBRAnil 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 FragmentationBRNagarjuna 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 BRSteven 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 BRAnnette Michalski, Juergen Cox, and Matthias Mann

J. Proteome Res. 2011, 10, 1785–1793