Talks and Notes

Here I gather various notes and talks that might be of interest.



  • Talent Identification at the limits of Peer Review: an analysis of the EMBO Postdoctoral Fellowships Selection ProcessBernd Klaus and David del Alamo — bioRxiv preprintanalysis code and data

  • Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency — Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber — Cell Syst

  • Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts — Zelezniak A, Vowinckel J, Capuano F, Messner CB, Demichev V, Polowsky N, Mülleder M, Kamrad S, Klaus B, Keller MA, Ralser M. — Cell Syst 7(3)

  • An end to end workflow for differential gene expression using Affymetrix microarraysBernd Klaus and Stefanie Reisenauer — version 2 , 2018 — F1000Research 2018, 5:1384


  • Landscape of nuclear transport receptor cargo specificity. Mackmull MT, Klaus B, Heinze I, Chokkalingam M, Beyer A, Russell RB, Ori A, Beck M. Mol Syst Biol. 2017 Dec;13(12) 962.

  • voomDDA: discovery of diagnostic biomarkers and classification of RNA-seq data Zararsiz G, Goksuluk D, Klaus B, Korkmaz S, Eldem V, Karabulut E, Ozturk A. (2017) — PeerJ 5voomDDA webtool

  • Metabolic shifts in residual breast cancer drive tumor recurrence — Havas, Kristina M; Milchevskaya, Vladislava; Radic, Ksenija; Alladin, Ashna; Kafkia, Eleni; Garcia, Marta; Stolte, Jens; Klaus, Bernd; Rotmensz, Nicole; Gibson, Toby J; Burwinkel, Barbara; Schneeweiss, Andreas; Pruneri, Giancarlo; Patil, Kiran R; Sotillo, Rocio; Jechlinger, Martin (2017) — The Journal of Clinical Investigation, 15 May 2017EMBL newspieceVideo Interview

  • Functional Outcomes and Quality of Life After Radical Prostatectomy Only Versus a Combination of Prostatectomy with Radiation and Hormonal Therapy. – Adam M, Tennstedt P, Lanwehr D, Tilki D, Steuber T, Beyer B, Thederan I, Heinzer H, Haese A, Salomon G, Budäus L, Michl U, Pehrke D, Stattin P, Bernard J, Klaus B, Pompe RS, Petersen C, Huland H, Graefen M, Schwarz R, Huber W, Loeb S, Schlomm T. (2017) — Eur. Urol. 71(3):330-336

  • miR-16 and miR-125b are involved in barrier function dysregulation through the modulation of claudin-2 and cingulin expression in the jejunum in IBS with diarrhoea. — Martínez C, Rodiño-Janeiro BK, Lobo B, Stanifer ML, Klaus B, Granzow M, González-Castro AM, Salvo-Romero E, Alonso-Cotoner C, Pigrau M, Roeth R, Rappold G, Huber W, González-Silos R, Lorenzo J, de Torres I, Azpiroz F, Boulant S, Vicario M, Niesler B, Santos J. (2017) — Gut


  • Statistical relevance—relevant statistics, part IIBernd Klaus, 2016 — EMBO J

  • An end to end workflow for differential gene expression using Affymetrix microarraysBernd Klaus — version 1 , 2016 — F1000Research 2016, 5:1384

  • Data-driven hypothesis weighting increases detection power in genome-scale multiple testing — Nikolaos Ignatiadis, Bernd Klaus, Judith Zaugg, Wolfgang Huber, 2016 — Nature Methods — earlier BioRxiv Preprint — Software package IHW on Github and Bioconductor.

  • DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies — Christophe D Chabbert, Lars M Steinmetz, Bernd Klaus, 2016 — PeerJ — Software package DChIPRep on Bioconductor. — Omic Tools website

  • Landscape and dynamics of transcription initiation in the malaria parasite Plasmodium falciparum — Sophie Adjalley, Christophe Chabbert, Bernd Klaus, Vicent Pelechano, Lars Steinmetz, 2016.— Cell Reports, Volume 14, Issue 10, p2463–2475 — earlier BioRxiv PreprintEMBL newspiece.

  • CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma — Elisa M Noll, Christian Eisen, Albrecht Stenzinger, Elisa Espinet, Alexander Muckenhuber, Corinna Klein, Vanessa Vogel, Bernd Klaus, Wiebke Nadler, Christoph Rösli, Christian Lutz, Michael Kulke, Jan Engelhardt, Franziska M Zickgraf, Octavio Espinosa, Matthias Schlesner, Xiaoqi Jiang, Annette Kopp-Schneider, Peter Neuhaus, Marcus Bahra, Bruno V Sinn, Roland Eils, Nathalia A Giese, Thilo Hackert, Oliver Strobel, Jens Werner, Markus W Büchler, Wilko Weichert, Andreas Trumpp & Martin R Sprick, 2016 — Nature Medicine, 22, 278–287.


  • Statistical relevance—relevant statistics, part IBernd Klaus, 2015 — EMBO J (2015) 34, 2727-2730

  • A high-throughput ChIP Seq for large-scale chromatin studies — Christophe D Chabbert, Sophie H Adjalley, Bernd Klaus, Emilie S Fritsch, Ishaan Gupta, Vicent Pelechano, Lars M Steinmetz, 2015.— Mol Syst Biol.; 11(1):777EMBL newspiece


  • A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast — Fritsch, E.S., Chabbert, C.D., Klaus, B. & Steinmetz, L.M., 2014 — Genetics — also issue highlight in Genetics 10/2014

  • Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization — Aleksandra Pekowska, Bernd Klaus, Felix Alexander Klein, Simon Anders, Malgorzata Oles, Lars Michael Steinmetz, Paul Bertone, Wolfgang Huber, 2014. — BioRxiv Preprint

  • Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions — Gupta, I., Clauder-Munster, S., Klaus, B., Jarvelin, A.I., Aiyar, R.S., Benes, V., Wilkening, S., Huber, W., Pelechano, V. & Steinmetz, L.M., 2014.— Mol Syst Biol. 2014; 10(2):719Research highlight in Nature Reviews Genetics

2009 — 2013



Chromium is a work–in–progress R package for the comprehensive analysis of Hi–C data developed by Annika Gable, Aleksandra Pekowska and myself. You can find it on github.


The DChIPRep DChIPRep implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al. and is available from Bioconductor.

PhD Thesis

  • Script files related to my PhD thesis can be downloaded here.

  • Script files implementing the effect sizes variable selection methods presented in the article “Effect Size Estimation and Misclassification Rate Based Variable Selection in Linear Discriminant Analysis” can be downloaded here.


concaveFDR is a an FDR estimation package, similar in spirit to fdrtool and locfdr. It will be submitted to Bioconductor at some point and extensive documentation will be become available.

  • The R package (beta status!) via github like so:

You can download some introductory slides from MAS Toulouse 2014. Most of the methodology is also treated in my PhD thesis.

Simulation Studies and a re-analysis of exon usage conservation

There are two simulation studies and one real data analysis of exon usage conservation. For the background on the exon usage analysis see the original paper: Reyes et. al. — Drift and conservation of differential exon usage across tissues in primate species. All of the files can obtained via github:

  • Simulation Study with normal mixture models: Rmd

  • Simulation Study with the half normal decay model: Rmd

  • Exon Usage Analysis: Rmd