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Resources for regulatory genomics



ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs.
Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan and Erik van Nimwegen
Genome Research, 2014
DOI: 10.1101/gr.169508.113


Crunch: Integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.
Severin M Berger, Mikhail Pachkov, Phil Arnold, Saeed Omidi, Nicholas Kelley, Silvia Salatino and Erik van Nimwegen
Genome Research, 2019
DOI: 10.1101/gr.239319.118


Automated reconstruction of whole genome phylogenies from short sequence reads.
Frederic Bertels, Olin K. Silander, Mikhail Pachkov, Paul B. Rainey and Erik van Nimwegen
Molecular Biology and Evolution, 2014, 31(5), 1077-88
DOI: 10.1093/molbev/msu088


Whole genome phylogenies reflect the distributions of recombination rates for many bacterial species.
Thomas Sakoparnig, Chris Field and Erik van Nimwegen
eLife, 2021
DOI: 10.7554/eLife.65366


Bayesian inference of gene expression states from single-cell RNA-seq data.
Jérémie Breda, Mihaela Zavolan and Erik van Nimwegen
Nature Biotechnology, 2021, 39, 1008-1016
DOI: 10.1038/s41587-021-00875-x


SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.
M. Pachkov, P. Balwierz, P. Arnold, E. Ozonov and E. van Nimwegen
Nucleic acids research, 2013, 41(D1), D214-D220
DOI: 10.1093/nar/gks1145

SwissRegulon: a database of genome-wide annotations of regulatory sites.
M. Pachkov, I. Erb, N. Molina and E. Van Nimwegen
Nucleic acids research, 2007, 35(suppl 1), D127-D131
DOI: 10.1093/nar/g


MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.
Phil Arnold, Ionas Erb, Mikhail Pachkov, Nacho Molina and Erik van Nimwegen
Bioinformatics, 2012, 28(4), 487-494
DOI: 10.1093/bioinformatics/btr695


PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny.
Rahul Siddharthan, Eric D Siggia, Erik van Nimwegen
PLOS CompBio, 2005
DOI: 10.1371/journal.pcbi.0010067


Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.
Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen
PLOS CompBio, 2017
DOI: 10.1371/journal.pcbi.1005176


Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method.
Lukas Burger and Erik van Nimwegen
Molecular Systems Biology, 2008, 4:165
DOI: 10.1038/msb4100203

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