Publications by authors named "Mikhail Pachkov"

19Publications

Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs.

Genome Res 2019 07 28;29(7):1164-1177. Epub 2019 May 28.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.239319.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6633267PMC
July 2019

The ISMARA client.

F1000Res 2016 15;5. Epub 2016 Dec 15.

SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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https://f1000research.com/articles/5-2851/v1
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http://dx.doi.org/10.12688/f1000research.9794.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5302150PMC
December 2016

ARMADA: Using motif activity dynamics to infer gene regulatory networks from gene expression data.

Methods 2015 Sep 8;85:62-74. Epub 2015 Jul 8.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Basel, Switzerland. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10462023153000
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http://dx.doi.org/10.1016/j.ymeth.2015.06.024DOI Listing
September 2015

Automated reconstruction of whole-genome phylogenies from short-sequence reads.

Mol Biol Evol 2014 May 5;31(5):1077-88. Epub 2014 Mar 5.

Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msu088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995342PMC
May 2014

ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs.

Genome Res 2014 May 10;24(5):869-84. Epub 2014 Feb 10.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.169508.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009616PMC
May 2014

SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates.

Nucleic Acids Res 2013 Jan 24;41(Database issue):D214-20. Epub 2012 Nov 24.

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.

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http://dx.doi.org/10.1093/nar/gks1145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531101PMC
January 2013

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.

Genome Res 2013 Jan 10;23(1):60-73. Epub 2012 Sep 10.

Biozentrum of the University of Basel and Swiss Institute of Bioinformatics, CH 4056 Basel, Switzerland.

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http://dx.doi.org/10.1101/gr.142661.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530684PMC
January 2013

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.

Bioinformatics 2012 Feb;28(4):487-94

Biozentrum, University of Basel, Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btr695DOI Listing
February 2012

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

Authors:
Harukazu Suzuki Alistair R R Forrest Erik van Nimwegen Carsten O Daub Piotr J Balwierz Katharine M Irvine Timo Lassmann Timothy Ravasi Yuki Hasegawa Michiel J L de Hoon Shintaro Katayama Kate Schroder Piero Carninci Yasuhiro Tomaru Mutsumi Kanamori-Katayama Atsutaka Kubosaki Altuna Akalin Yoshinari Ando Erik Arner Maki Asada Hiroshi Asahara Timothy Bailey Vladimir B Bajic Denis Bauer Anthony G Beckhouse Nicolas Bertin Johan Björkegren Frank Brombacher Erika Bulger Alistair M Chalk Joe Chiba Nicole Cloonan Adam Dawe Josee Dostie Pär G Engström Magbubah Essack Geoffrey J Faulkner J Lynn Fink David Fredman Ko Fujimori Masaaki Furuno Takashi Gojobori Julian Gough Sean M Grimmond Mika Gustafsson Megumi Hashimoto Takehiro Hashimoto Mariko Hatakeyama Susanne Heinzel Winston Hide Oliver Hofmann Michael Hörnquist Lukasz Huminiecki Kazuho Ikeo Naoko Imamoto Satoshi Inoue Yusuke Inoue Ryoko Ishihara Takao Iwayanagi Anders Jacobsen Mandeep Kaur Hideya Kawaji Markus C Kerr Ryuichiro Kimura Syuhei Kimura Yasumasa Kimura Hiroaki Kitano Hisashi Koga Toshio Kojima Shinji Kondo Takeshi Konno Anders Krogh Adele Kruger Ajit Kumar Boris Lenhard Andreas Lennartsson Morten Lindow Marina Lizio Cameron Macpherson Norihiro Maeda Christopher A Maher Monique Maqungo Jessica Mar Nicholas A Matigian Hideo Matsuda John S Mattick Stuart Meier Sei Miyamoto Etsuko Miyamoto-Sato Kazuhiko Nakabayashi Yutaka Nakachi Mika Nakano Sanne Nygaard Toshitsugu Okayama Yasushi Okazaki Haruka Okuda-Yabukami Valerio Orlando Jun Otomo Mikhail Pachkov Nikolai Petrovsky Charles Plessy John Quackenbush Aleksandar Radovanovic Michael Rehli Rintaro Saito Albin Sandelin Sebastian Schmeier Christian Schönbach Ariel S Schwartz Colin A Semple Miho Sera Jessica Severin Katsuhiko Shirahige Cas Simons George St Laurent Masanori Suzuki Takahiro Suzuki Matthew J Sweet Ryan J Taft Shizu Takeda Yoichi Takenaka Kai Tan Martin S Taylor Rohan D Teasdale Jesper Tegnér Sarah Teichmann Eivind Valen Claes Wahlestedt Kazunori Waki Andrew Waterhouse Christine A Wells Ole Winther Linda Wu Kazumi Yamaguchi Hiroshi Yanagawa Jun Yasuda Mihaela Zavolan David A Hume Takahiro Arakawa Shiro Fukuda Kengo Imamura Chikatoshi Kai Ai Kaiho Tsugumi Kawashima Chika Kawazu Yayoi Kitazume Miki Kojima Hisashi Miura Kayoko Murakami Mitsuyoshi Murata Noriko Ninomiya Hiromi Nishiyori Shohei Noma Chihiro Ogawa Takuma Sano Christophe Simon Michihira Tagami Yukari Takahashi Jun Kawai Yoshihide Hayashizaki

Nat Genet 2009 May 19;41(5):553-62. Epub 2009 Apr 19.

RIKEN Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ng.375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711855PMC
May 2009

MicroRNA-221-222 regulate the cell cycle in mast cells.

J Immunol 2009 Jan;182(1):433-45

Institute for Research in Biomedicine, Bellinzona, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2610349PMC
http://dx.doi.org/10.4049/jimmunol.182.1.433DOI Listing
January 2009

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.

Gene 2007 Jul 24;396(2):215-25. Epub 2007 Mar 24.

Department of Bioinformatics, Faculty of Biology and Pharmaceutics, Friedrich-Schiller University Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany.

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http://linkinghub.elsevier.com/retrieve/pii/S037811190700112
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http://dx.doi.org/10.1016/j.gene.2007.02.033DOI Listing
July 2007

SwissRegulon: a database of genome-wide annotations of regulatory sites.

Nucleic Acids Res 2007 Jan 27;35(Database issue):D127-31. Epub 2006 Nov 27.

Biozentrum, The University of Basel, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland.

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http://dx.doi.org/10.1093/nar/gkl857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716717PMC
January 2007

Understanding the roadmap of metabolism by pathway analysis.

Methods Mol Biol 2007 ;358:199-226

Department of Bioinformatics, Friedrich-Schiller University of Jena, Germany.

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http://dx.doi.org/10.1007/978-1-59745-244-1_12DOI Listing
January 2007