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Jan Komorowski

Research Profile

Devices

Oligonucleotide Array Sequence Analysis

Procedures

Chemicals & Drugs

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Occupations

Computational Biology

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Saccharomyces cerevisiae

Genes & Molecular Sequences

Physiology

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Protein Binding

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Publications

TOP 3
Jakub Orzechowski Westholm; Jan Komorowski; Niklas Nordberg; Ida Olsson; Susanna Tronnersjö; Hans Ronne
Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells.
Stefan Enroth; Mats G Gustafsson; Claes R Andersson; Robin Andersson; Claes Wadelius; Jan Komorowski
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.
Stefan Enroth; Jan Komorowski; Lars Påhlman; Alvaro Rada-Iglesisas; Ola Wallerman; Alkwin Wanders; Robin Andersson; Claes Wadelius
Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa.

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All Publications

2012: Jakub Orzechowski Westholm; Jan Komorowski; Niklas Nordberg; Ida Olsson; Susanna Tronnersjö; Hans Ronne
Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells.
PloS one 2012;7(2):e31577.
2012: Stefan Enroth; Mats G Gustafsson; Claes R Andersson; Robin Andersson; Claes Wadelius; Jan Komorowski
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.
Algorithms for molecular biology : AMB 2012;7(1):2.
2011: Stefan Enroth; Jan Komorowski; Lars Påhlman; Alvaro Rada-Iglesisas; Ola Wallerman; Alkwin Wanders; Robin Andersson; Claes Wadelius
Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa.
BMC cancer 2011;11():450.
2010: Johanna Sandgren; Teresita Diaz de Ståhl; Robin Andersson; Uwe Menzel; Arkadiusz Piotrowski; Helena Nord; Martin Bäckdahl; Nimrod B Kiss; Michael Brauckhoff; Jan Komorowski; Henning Dralle; Ola Hessman; Catharina Larsson; Göran Akerström; Carl Bruder; Jan P Dumanski; Gunnar Westin
Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis.
Endocrine-related cancer 2010;17(3):561-79.
2010: Johanna Sandgren; Robin Andersson; Alvaro Rada-Iglesias; Stefan Enroth; Goran Akerstrom; Jan P Dumanski; Jan Komorowski; Gunnar Westin; Claes Wadelius
Integrative epigenomic and genomic analysis of malignant pheochromocytoma.
Experimental & molecular medicine 2010;42(7):484-502.
2010: Helena Nord; Ulrika Segersten; Johanna Sandgren; Kenneth Wester; Christer Busch; Uwe Menzel; Jan Komorowski; Jan P Dumanski; Per-Uno Malmstrom; Teresita Díaz de Ståhl
Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma.
International journal of cancer. Journal international du cancer 2010;126(6):1390-402.
2010: Carolina Kristell; Jakub Orzechowski Westholm; Ida Olsson; Hans Ronne; Jan Komorowski; Pernilla Bjerling
Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes.
Genome research 2010;20(3):361-71.
2010: Marcin Kierczak; Michał Dramiński; Jacek Koronacki; Jan Komorowski
Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors.
Bioinformatics and biology insights 2010;4():137-46.
2010: Stefan Enroth; Robin Andersson; Claes Wadelius; Jan Komorowski
SICTIN: Rapid footprinting of massively parallel sequencing data.
BioData mining 2010;3(1):4.
2009: Ola Wallerman; Mehdi Motallebipour; Stefan Enroth; Kalicharan Patra; Madhu Sudhan Reddy Bysani; Jan Komorowski; Claes Wadelius
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.
Nucleic acids research 2009;37(22):7498-508.
2009: Helena Nord; Christian Hartmann; Robin Andersson; Uwe Menzel; Susan Pfeifer; Arkadiusz Piotrowski; Adam Bogdan; Wojciech Kloc; Johanna Sandgren; Tommie Olofsson; Göran Hesselager; Erik Blomquist; Jan Komorowski; Andreas von Deimling; Carl E G Bruder; Jan P Dumanski; Teresita Díaz de Ståhl
Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array.
Neuro-oncology 2009;11(6):803-18.
2009: Robin Andersson; Stefan Enroth; Alvaro Rada-Iglesias; Claes Wadelius; Jan Komorowski
Nucleosomes are well positioned in exons and carry characteristic histone modifications.
Genome research 2009;19(10):1732-41.
2009: Aleksejs Kontijevskis; Ramona Petrovska; Sviatlana Yahorava; Jan Komorowski; Jarl E S Wikberg
Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates.
Bioorganic & medicinal chemistry 2009;17(14):5229-37.
2009: Adam Ameur; Alvaro Rada-Iglesias; Jan Komorowski; Claes Wadelius
Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.
Nucleic acids research 2009;37(12):e85.
2009: Mehdi Motallebipour; Stefan Enroth; Tanel Punga; Adam Ameur; Christoph Koch; Carl Bruder; Jan Komorowski; Johan Ericsson; Claes Wadelius
Novel genes in cell cycle control and lipid metabolism with dynamically regulated binding sites for sterol regulatory element-binding protein 1 and RNA polymerase II in HepG2 cells detected by chromatin immunoprecipitation with microarray detection.
The FEBS journal 2009;276(7):1878-90.
2009: Alvaro Rada-Iglesias; Stefan Enroth; Robin Andersson; Alkwin Wanders; Lars Påhlman; Jan Komorowski; Claes Wadelius
Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation.
Epigenetics : official journal of the DNA Methylation Society 2009;4(2):107-13.
2009: Krzysztof Wabnik; Torgeir R Hvidsten; Anna Kedzierska; Jelle Van Leene; Geert De Jaeger; Gerrit T S Beemster; Jan Komorowski; Martin Kuiper
Gene expression trends and protein features effectively complement each other in gene function prediction.
Bioinformatics (Oxford, England) 2009;25(3):322-30.
2009: Marcin Kierczak; Krzysztof Ginalski; Michał Dramiński; Jacek Koronacki; Witold Rudnicki; Jan Komorowski
A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome.
Bioinformatics and biology insights 2009;3():109-27.
2009: Mehdi Motallebipour; Adam Ameur; Madhu Sudhan Reddy Bysani; Kalicharan Patra; Ola Wallerman; Jonathan Mangion; Melissa A Barker; Kevin J McKernan; Jan Komorowski; Claes Wadelius
Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.
Genome biology 2009;10(11):R129.
2009: Torgeir R Hvidsten; Astrid Laegreid; Andriy Kryshtafovych; Gunnar Andersson; Krzysztof Fidelis; Jan Komorowski
A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity.
PloS one 2009;4(7):e6266.
2008: Radha Raman Pandey; Tanmoy Mondal; Faizaan Mohammad; Stefan Enroth; Lisa Redrup; Jan Komorowski; Takashi Nagano; Debora Mancini-Dinardo; Chandrasekhar Kanduri
Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation.
Molecular cell 2008;32(2):232-46.
2008: Aleksejs Kontijevskis; Jan Komorowski; Jarl E S Wikberg
Generalized proteochemometric model of multiple cytochrome p450 enzymes and their inhibitors.
Journal of chemical information and modeling 2008;48(9):1840-50.
2008: Arkadiusz Piotrowski; Carl Bruder; Robin Andersson; Teresita Diaz de Ståhl; Uwe Menzel; Johanna Sandgren; Andrzej Poplawski; Desiree von Tell; Chiquito Crasto; Adam Bogdan; Rafal Bartoszewski; Zsuzsa Bebok; Maciej Krzyzanowski; Zbigniew Jankowski; E Christopher Partridge; Jan Komorowski; Jan P Dumanski
Somatic mosaicism for copy number variation in differentiated human tissues.
Human mutation 2008;29(9):1118-24.
2008: Robin Andersson; Carl Bruder; Arkadiusz Piotrowski; Uwe Menzel; Helena Nord; Johanna Sandgren; Torgeir R Hvidsten; Teresita Diaz de Ståhl; Jan P Dumanski; Jan Komorowski
A segmental maximum a posteriori approach to genome-wide copy number profiling.
Bioinformatics (Oxford, England) 2008;24(6):751-8.
2008: Carl Bruder; Arkadiusz Piotrowski; Antoinet A C J Gijsbers; Robin Andersson; Stephen Erickson; Teresita Diaz de Ståhl; Uwe Menzel; Johanna Sandgren; Desiree von Tell; Andrzej Poplawski; Michael Crowley; Chiquito Crasto; E Christopher Partridge; Hemant K Tiwari; David Allison; Jan Komorowski; Gert-Jan B van Ommen; Dorret I Boomsma; Nancy L Pedersen; Johan T den Dunnen; Karin Wirdefeldt; Jan P Dumanski
Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles.
American journal of human genetics 2008;82(3):763-71.
2008: Alvaro Rada-Iglesias; Adam Ameur; Philipp Kapranov; Stefan Enroth; Jan Komorowski; Thomas Gingeras; Claes Wadelius
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.
Genome research 2008;18(3):380-92.
2008: Teresita Díaz de Ståhl; Johanna Sandgren; Arkadiusz Piotrowski; Helena Nord; Robin Andersson; Uwe Menzel; Adam Bogdan; Ann-Charlotte Thuresson; A Poplawski; Desiree von Tell; Caisa M Hansson; Amir I Elshafie; Gehad Elghazali; Stefan Imreh; Magnus Nordenskjöld; Meena Upadhyaya; Jan Komorowski; Carl Bruder; Jan P Dumanski
Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array.
Human mutation 2008;29(3):398-408.
2008: Jakub Orzechowski Westholm; Niklas Nordberg; Eva Murén; Adam Ameur; Jan Komorowski; Hans Ronne
Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3.
BMC genomics 2008;9():601.
2008: Jakub Orzechowski Westholm; Feifei Xu; Hans Ronne; Jan Komorowski
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.
BMC bioinformatics 2008;9():484.
2008: Michal Draminski; Alvaro Rada-Iglesias; Stefan Enroth; Claes Wadelius; Jacek Koronacki; Jan Komorowski
Monte Carlo feature selection for supervised classification.
Bioinformatics (Oxford, England) 2008;24(1):110-7.
2007: Ulrika Bergström; Jan A Olsson; Torgeir R Hvidsten; Jan Komorowski; Ingvar Brandt
Differential gene expression in the olfactory bulb following exposure to the olfactory toxicant 2,6-dichlorophenyl methylsulphone and its 2,5-dichlorinated isomer in mice.
Neurotoxicology 2007;28(6):1120-8.
2007: Aleksejs Kontijevskis; Ramona Petrovska; Ilze Mutule; Staffan Uhlen; Jan Komorowski; Peteris Prusis; Jarl E S Wikberg
Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors.
Proteins 2007;69(1):83-96.
2007: Aleksejs Kontijevskis; Jarl E S Wikberg; Jan Komorowski
Computational proteomics analysis of HIV-1 protease interactome.
Proteins 2007;68(1):305-12.
2007: Alvaro Rada-Iglesias; Stefan Enroth; Adam Ameur; Christoph M Koch; Gayle K Clelland; Patricia Respuela-Alonso; Sarah Wilcox; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; Carl Bruder; Jan Komorowski; Claes Wadelius
Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.
Genome research 2007;17(6):708-19.
2007: Emma Rennel; Sofie Mellberg; Anna Dimberg; Ludvig Petersson; Johan Botling; Adam Ameur; Jakub Orzechowski Westholm; Jan Komorowski; Philippe Lassalle; Michael J Cross; Pär Gerwins
Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer.
Experimental cell research 2007;313(7):1285-94.
2007: Aleksejs Kontijevskis; Peteris Prusis; Ramona Petrovska; Sviatlana Yahorava; Felikss Mutulis; Ilze Mutule; Jan Komorowski; Jarl E S Wikberg
A look inside HIV resistance through retroviral protease interaction maps.
PLoS computational biology 2007;3(3):e48.
2007: Claes R Andersson; Torgeir R Hvidsten; Anders Isaksson; Mats G Gustafsson; Jan Komorowski
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors.
BMC systems biology 2007;1():45.
2006: Helena Strömbergsson; Andriy Kryshtafovych; Peteris Prusis; Krzysztof Fidelis; Jarl E S Wikberg; Jan Komorowski; Torgeir R Hvidsten
Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures.
Proteins 2006;65(3):568-79.
2006: Vidar Beisvag; Per Kristian Lehre; Herman Midelfart; Halfdan Aass; Odd Geiran; Arne K Sandvik; Astrid Laegreid; Jan Komorowski; Oyvind Ellingsen
Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data.
European journal of heart failure 2006;8(4):381-9.
2006: Adam Ameur; Vladimir Yankovski; Stefan Enroth; Ola Spjuth; Jan Komorowski
The LCB Data Warehouse.
Bioinformatics (Oxford, England) 2006;22(8):1024-6.
2006: Helena Strömbergsson; Peteris Prusis; Herman Midelfart; Maris Lapinsh; Jarl E S Wikberg; Jan Komorowski
Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions.
Proteins 2006;63(1):24-34.
2006: Bartek Wilczyński; Torgeir R Hvidsten; Andriy Kryshtafovych; Jerzy Tiuryn; Jan Komorowski; Krzysztof Fidelis
Using local gene expression similarities to discover regulatory binding site modules.
BMC bioinformatics 2006;7():505.
2005: Alvaro Rada-Iglesias; Ola Wallerman; Christoph Koch; Adam Ameur; Stefan Enroth; Gayle K Clelland; Kenneth Wester; Sarah Wilcox; Oliver M Dovey; Peter D Ellis; Vicki L Wraight; Keith James; Rob Andrews; Cordelia Langford; Pawandeep Dhami; Nigel Carter; David Vetrie; Fredrik Pontén; Jan Komorowski; Carl Bruder; Claes Wadelius
Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays.
Human molecular genetics 2005;14(22):3435-47.
2005: Torgeir R Hvidsten; Bartosz Wilczyński; Andriy Kryshtafovych; Jerzy Tiuryn; Jan Komorowski; Krzysztof Fidelis
Discovering regulatory binding-site modules using rule-based learning.
Genome research 2005;15(6):856-66.
2005: Jayne L Dennis; Torgeir R Hvidsten; Ernst Wit; Jan Komorowski; Alexandra K Bell; Ian Downie; Jacqueline Mooney; Caroline Verbeke; Christopher Bellamy; Nicol Keith; Karin A Oien
Markers of adenocarcinoma characteristic of the site of origin: development of a diagnostic algorithm.
Clinical cancer research : an official journal of the American Association for Cancer Research 2005;11(10):3766-72.
2004: Kristin G Nørsett; Astrid Laegreid; Herman Midelfart; Fekadu Yadetie; Sten Erlandsen; Sture Falkmer; Jon Erik Grønbech; Helge L Waldum; Jan Komorowski; Arne K Sandvik
Gene expression based classification of gastric carcinoma.
Cancer letters 2004;210(2):227-37.
2003: Torgeir R Hvidsten; Andriy Kryshtafovych; Jan Komorowski; Krzysztof Fidelis
A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins.
Bioinformatics (Oxford, England) 2003;19 Suppl 2():ii81-91.
2003: Fekadu Yadetie; Astrid Laegreid; Ingunn Bakke; Waclaw Kusnierczyk; Jan Komorowski; Helge L Waldum; Arne K Sandvik
Liver gene expression in rats in response to the peroxisome proliferator-activated receptor-alpha agonist ciprofibrate.
Physiological genomics 2003;15(1):9-19.
2003: Torgeir R Hvidsten; Astrid Laegreid; Jan Komorowski
Learning rule-based models of biological process from gene expression time profiles using gene ontology.
Bioinformatics (Oxford, England) 2003;19(9):1116-23.
2003: Astrid Lagreid; Torgeir R Hvidsten; Herman Midelfart; Jan Komorowski; Arne K Sandvik
Predicting gene ontology biological process from temporal gene expression patterns.
Genome research 2003;13(5):965-79.
2001: Tor-Kristian Jenssen; Astrid Laegreid; Jan Komorowski; Eivind Hovig
A literature network of human genes for high-throughput analysis of gene expression.
Nature genetics 2001;28(1):21-8.
2001: Jan Komorowski; Torgeir R Hvidsten; Tor-Kristian Jenssen; D Tjeldvoll; Eivind Hovig; Astrid Laegreid; Arne K Sandvik
[New knowledge derived from measurement of gene expression with the DNA microarray method].
Tidsskrift for den Norske lægeforening : tidsskrift for praktisk medicin, ny række 2001;121(10):1229-32.
2001: Torgeir R Hvidsten; Jan Komorowski; Arne K Sandvik; Astrid Laegreid
Predicting gene function from gene expressions and ontologies.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():299-310.