Selected Publications

  • Diamanti K., Cavalli M., Pan G., Pereira M. J., Kumar C., Skrtic S., Grabherr M., Risérus U., Eriksson J. W., Komorowski J. and Wadelius C. (2019). "Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes". Scientific Reports 9(1):9653 [link]
  • Umer H. M., Cavalli M., Dabrowski M. J., Diamanti K., Kruczyk M., Pan G., Komorowski J. and Wadelius C. (2016). "A Significant Regulatory Mutation Burden at a High Affinity Position of the Ctcf Motif in Gastrointestinal Cancers". Human Mutation 37(9):904–913 [link]
  • Diamanti K., Umer H. M. , Kruczyk M., Dąbrowski M. J. , Cavalli M., Wadelius C. and Komorowski J. (2016). "Maps of context-dependent putative regulatory regions and genomic signal interactions". Nucleic Acids Res 44(19):9110-9120 [link]
  • Enroth S., Bornelov S., Wadelius C., Komorowski J. (2012). "Combinations of histone modifications mark exon inclusion levels". PLoS One 7(1): e29911 [link]
  • Andersson R., Enroth S., Rada-Iglesias A., Wadelius C. and Komorowski J. (2009). "Nucleosomes are well positioned in exons and carry characteristic histone modifications". Genome Research 19(10):1732-1741 [link]

All Publications

  1. Esther Rheinbay, Morten Muhlig Nielsen, […]PCAWG Consortium (2020). "Analyses of non-coding somatic drivers in 2,658 cancer whole genomes". Nature 578(7793):102-111 [link]
  2. The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (2020). "Pan-cancer analysis of whole genomes". Nature 578(7793):82–93 [link]
  3. Fredrik Barrenas, Kevin Raehtz, Cuiling Xu, Lynn Law, Richard R. Green, Guido Silvestri, Steven E. Bosinger, Andrew Nishida, Qingsheng Li, Wuxun Lu, Jianshui Zhang, Matthew J. Thomas, Jean Chang, Elise Smith, Jeffrey M. Weiss, Reem A. Dawoud, George H. Richter, Anita Trichel, Dongzhu Ma, Xinxia Peng, Jan Komorowski, Cristian Apetrei, Ivona Pandrea & Michael Gale Jr (2019). "Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control". Nature Communications 10(5101):15 [link]
  4. Diamanti K., Cavalli M., Pan G., Pereira M. J., Kumar C., Skrtic S., Grabherr M., Risérus U., Eriksson J. W., Komorowski J. and Wadelius C. (2019). "Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes". Scientific Reports 9(1):9653 [link]
  5. Moghadam B.T., Etemadikhah M., Rajkowska G., Stockmeier C., Grabherr M., Komorowski J., Feuk L., Lindholm-Carlström E. (2019). "Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods". Journal of Psychiatric Research 114(1):41-47 [link]
  6. Cavalli M., Baltzer N., Pan G., Bárcenas-Walls J.R., Smolinska-Garbulowska K., Kumar C., Skrtic S., Komorowski J. and Wadelius C. (2019). "Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases". Human Genomics 13(1):20 [link]
  7. Cavalli M., Baltzer N., Umer H.M., Grau J., Lemnian I., Pan G., Wallerman O., Spalinskas R., Sahlén P., Grosse I., Komorowski J. and Wadelius C. (2019). "Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases". Scientific Reports 9(1):2695 [link]
  8. Grabherr M.G., Kaminska B. and Komorowski J. (2018). "Special Issue Introduction: The Wonders and Mysteries Next Generation Sequencing Technologies Help Reveal". Genes 9(10):505 [link]
  9. Baltzer N., Nygård M., Sundström K., Dillner J., Nygård J., Komorowski J. (2018). "Stratifying Cervical Cancer Risk with Registry Data". IEEE 14th International Conference on e-Science (e-Science) 14(1):288-289 [link]
  10. Dabrowski M. J., Draminski M., Diamanti K., Stepniak K., Mozolewska M. A., Teisseyre P., Koronacki J., Komorowski J., Kaminska B. and Wojtas B. (2018). "Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival". Scientific Reports 8(1):4390 [link]
  11. Rheinbay E., Nielsen M. M., Abascal F., Tiao G., Hornshøj H., Hess J. M., Pedersen R. I., Feuerbach L., Sabarinathan R., Madsen H. T., Kim J., Mularoni L., Shuai S., Camaioni A. S. L., Herrmann C., Maruvka Y. E., Shen C., Amin S. B., Bertl J., Dhingra P., Diamanti K., Gonzalez-Perez A., Guo Q., Haradhvala N. J., Isaev K., Juul M., Komorowski J., Lee D., Lochovsky L., Liu E. M., Pich O., Umer H. M., Uusküla-Reimand L., Wadelius C., Wadi L., Zhang J., Boroevich K. A., Carlevaro-Fita J., Chakravarty D., Chan C. W. Y., Fonseca N. A., Hamilton M. P., Hong C., Kahles A., Kim Y., Lehmann K-V., Johnson T. A., Kahraman A., Park K., Saksena G., Sieverling L., Sinnott-Armstrong N. A., Campbell P. J., Hobolth A., Kellis M., Lawrence M. S., Raphael B., Rubin M. A., Sander C., Stein L., Stuart J., Tsunoda T., Wheeler D. A., Johnson R., Reimand J., Gerstein M. B., Khurana E., Lopez-Bigas N., Martincorena I., Pedersen J. S., Getz G. (2017). "Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes". bioRxiv 237313(1):1-101 [link]
  12. Baltzer N., Sundström K., Nygård J. F., Dillner J. and Komorowski J. (2017). "Risk stratification in cervical cancer screening by complete screening history: Applying bioinformatics to a general screening population". International Journal of Cancer 141(1):200-209 [link]
  13. Torabi B. M., Zamani N., Komorowski J. and Grabherr M. (2017). "PiiL: visualization of DNA methylation and gene expression data in gene pathways". BMC Genomics 18(1):571-583 [link]
  14. Umer H. M., Cavalli M., Dabrowski M. J., Diamanti K., Kruczyk M., Pan G., Komorowski J. and Wadelius C. (2016). "A Significant Regulatory Mutation Burden at a High Affinity Position of the Ctcf Motif in Gastrointestinal Cancers". Human Mutation 37(9):904–913 [link]
  15. Diamanti K., Umer H. M. , Kruczyk M., Dąbrowski M. J. , Cavalli M., Wadelius C. and Komorowski J. (2016). "Maps of context-dependent putative regulatory regions and genomic signal interactions". Nucleic Acids Res 44(19):9110-9120 [link]
  16. Torabi B. M., Dabrowski M., Kaminska B., Grabherr M. G. and Komorowski J. (2016). "Combinatorial identification of DNA methylation patterns over age in the human brain". BMC Bioinformatics 17(393):1-10 [link]
  17. Khaliq Z., Leijon M., Belák S. and Komorowski J. (2016). "Identification of combinatorial host-specific signatures with a potential to affect host adaptation in influenza A H1N1 and H3N2 subtypes". BMC Genomics 17(529): [link]
  18. Barrenas F., Green R. R., Thomas M. J., Law G. L., Proll S. C., Engelmann F., Messaoudi I., Marzi A., Feldmann H. and Katze M. G. (2015). "Next-Generation Sequencing Reveals a Controlled Immune Response to Zaire Ebola Virus Challenge in Cynomolgus Macaques Immunized with Vesicular Stomatitis Virus Expressing Zaire Ebola Virus Glycoprotein (VSVΔG/EBOVgp)". Clinical and Vaccine Immunology 22(3):354-356 [link]
  19. Khaliq Z., Leijon M., Belák S. and Komorowski J. (2015). "A complete map of potential pathogenicity markers of avian influenza virus subtype H5 predicted from 11 expressed proteins". BMC Microbiology 15(0):128 [link]
  20. Bornelöv S. and Komorowski J. (2015). "Selection of Significant Features using Monte Carlo Feature Selection". Challenges in Computational Statistics and Data Mining 0(0):25-38 [link]
  21. Enroth S., Andersson R., Bysani M., Wallerman O., Termén S., Tuch B., De La Vega F., Heldin C.H., Moustakas A., Komorowski J. and Wadelius C. (2014). "Nucleosome regulatory dynamics in response to TGFβ". Nucleic Acids Research 42(11):6921-6934 [link]
  22. Barrenas F., Palermo R.E., Agricola B., Agy M.B., Aicher L., Carter V., Flanary L., Green R.R., McLain R., Li Q., Lu W., Murnane R., Peng X., Thomas M.J., Weiss J.M., Anderson D.M., Katze M.G. (2014). "Deep transcriptional sequencing of mucosal challenge compartment from rhesus macaques acutely infected with simian immunodeficiency virus implicates loss of cell adhesion preceding immune activation". Journal of Virology 88(14): 7962-7972 [link]
  23. Bornelöv S., Marillet S. and Komorowski J. (2014). "Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers". BMC Bioinformatics 15(0):139 [link]
  24. Kruczyk M., Przanowski P., Dabrowski M., Swiatek-Machado K., Mieczkowski J., Wallerman O., Ronowicz A., Piotrowski A., Wadelius C., Kaminska B. and Komorowski J. (2014). "Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells". BBA - Gene Regulatory Mechanisms 1839(11):1341–1350 [link]
  25. Diamanti K., Kanavos A., Makris C. and Tokis T. (2014). "Handling Weighted Sequences Employing Inverted Files and Suffix Trees". International Conference on Web Information Systems and Technologies (WEBIST 2014) 0(0):231-238 [link]
  26. Przanowski P., Dabrowski M., Ellert-Miklaszewska A., Kloss M., Mieczkowski J., Kaza B., Ronowicz A., Hu F., Piotrowski A., Kettenmann H., Komorowski J., Kaminska B. (2014). "The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia". Journal of Molecular Medicine 92(3):239-254 [link]
  27. Dąbrowski M.J., Pilot M., Kruczyk M., Zmihorski M., Umer H.M., Gliwicz J. (2014). "Reliability assessment of null allele detection: inconsistencies between and within different methods". Mol Ecol Resour. 14(2):361-373 [link]
  28. Kruczyk M., Umer H. M. , Enroth S., Komorowski J. (2013). "Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data". BMC bioinformatics 14(1):208 [link]
  29. Enroth S., Andersson C., Andersson R., Wadelius C., Gustafsson M. G., Komorowski J. (2012). "A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements". Algorithms for Molecular Biology 7(1):1748-1758 [link]
  30. Kruczyk M., Zetterberg H., Hansson O., Rolstad S., Minthon L., Wallin A., Blennow K., Komorowski J., Andersson M. G. (2012). "Monte Carlo feature selection and rule-based models to predict Alzheimer's disease in mild cognitive impairment". Journal of Neural Transmission 119(7):821-831 [link]
  31. Enroth S., Bornelov S., Wadelius C., Komorowski J. (2012). "Combinations of histone modifications mark exon inclusion levels". PLoS One 7(1): e29911 [link]
  32. J. Orzechowski Westholm, S. Tronnersj, N. Nordberg, I. Olsson, J. Komorowski, H. Ronne (2012). "Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells". PLoS One 7(2):e31577 [link]
  33. Susanne Bornelov, Stefan Enroth, Jan Komorowski (2012). "Visualization of Rules in Rule-Based Classifiers". Intelligent Decision Technologies Smart Innovation 15(1):329-338 [link]
  34. Stefan Enroth, Alvaro Rada-Iglesisas, Robin Andersson, Ola Wallerman, Alkwin Wanders, Lars Pahlman, Jan Komorowski, Claes Wadelius (2011). "Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa". BMC Cancer 11(0):450 [link]
  35. Kristell C, Westholm JO, Olsson I, Ronne H, Komorowski J, Bjerling P. (2010). "Nitrogen depletion in the fission yeast Schizosaccharomyces pombe causes nucleosome loss in both promoters and coding regions of activated genes". Genome Research 20(3):361-371 [link]
  36. Sandgren J, Diaz de Stohl T, Andersson R, Menzel U, Piotrowski A, Nord H, Bockdahl M, Kiss NB, Brauckhoff M, Komorowski J, Dralle H, Hessman O, Larsson C, Akerstrom G, Bruder C, Dumanski JP, Westin G. (2010). "Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis". Endocrine-Related Cancer 17(3):561-579 [link]
  37. Sandgren J, Andersson R, Rada-Iglesias A, Enroth S, Akerstrom G, Dumanski JP, Komorowski J, Westin G, Wadelius C. (2010). "Integrative epigenomic and genomic analysis of malignant pheochromocytoma". Experimental & Molecular Medicine 42(7):484-502 [link]
  38. Stefan Enroth, Robin Andersson, Claes Wadelius, Jan Komorowski (2010). "SICTIN: Rapid footprinting of massively parallel sequencing data". BioData Mining 3(1):4 [link]
  39. Marcin Kierczak, Michal Draminski, Jacek Koronacki, Jan Komorowski (2010). "Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors". Bioinformatics and Biology Insights 4(0):137-146 [link]
  40. Andersson R., Enroth S., Rada-Iglesias A., Wadelius C. and Komorowski J. (2009). "Nucleosomes are well positioned in exons and carry characteristic histone modifications". Genome Research 19(10):1732-1741 [link]
  41. Torgeir R. Hvidsten, Astrid Laegreid, Andriy Kryshtafovych, Gunnar Andersson, Krzysztof Fidelis, Jan Komorowski (2009). "A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity". PLoS One 4(7):e6266 [link]
  42. Nord H, Hartmann C, Andersson R, Menzel U, Pfeifer S, Piotrowski A, Bogdan A, Kloc W, Sandgren J, Olofsson T, Hesselager G, Blomquist E, Komorowski J, von Deimling A, Bruder CE, Dumanski JP, Diaz de Stohl (2009). "Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array". Neuro-Oncology 11(6):803-818 [link]
  43. Nord H, Segersten U, Sandgren J, Wester K, Busch C, Menzel U, Komorowski J, Dumanski JP, Malmstrom PU, de Stohl TD. (2009). "Focal amplifications are associated with high-grade and recurrences in stage Ta bladder carcinoma". International Journal of Cancer 126(6):1390-1402 [link]
  44. Marcin Kierczak, Krzysztof Ginalski, Michal Draminski, Jacek Koronacki, Witold R Rudnicki, Jan Komorowski (2009). "A Rough Set-Based Model of HIV-1 Reverse Transcriptase Resistome". Bioinformatics and Biology Insights 3(0):109-127 [link]
  45. Ola Wallerman, Mehdi Motallebipour, Stefan Enroth, Kalicharan Patra, Madhu Sudhan Reddy Bysani, Jan Komorowski, Claes Wadelius (2009). "Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing". Nucleic Acids Research 37(22):7498-7508 [link]
  46. Aleksejs Kontijevskis, Ramona Petrovska, Sviatlana Yahorava, Jan Komorowski (2009). "Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates". Bioorganic & Medicinal Chemistry 17(14):5229-5237 [link]
  47. Mehdi Motallebipour, Stefan Enroth, Tanel Punga, Adam Ameur, Christoph Koch, Ian Dunham, Jan Komorowski, Johan Ericsson, Claes Wadelius (2009). "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 276(7):1878-1890 [link]
  48. Alvaro Rada-Iglesias, Stefan Enroth, Robin Andersson, Alkwin Wanders, Lars Pahlman, Jan Komorowski, Claes Wadelius (2009). "Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation". Epigenetics 4(2):107-113 [link]
  49. Krzysztof Wabnik, Torgeir R. Hvidsten, Anna Kedzierska, Jelle Van Leene, Geert De Jaeger, Gerrit T.S. Beemster, Jan Komorowski, Martin T.R. Kuiper (2009). "Gene expression trends and protein features effectively complement each other in gene function prediction". Bioinformatics 25(3):322-330 [link]
  50. Adam Ameur, Alvaro Rada-Iglesias, Jan Komorowski, Claes Wadelius (2009). "Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP". Nucleic Acids Research 37(12):e85 [link]
  51. Mehdi Motallebipour, Adam Ameur, Madhu Sudhan Reddy Bysani, Kalicharan Patra, Ola Wallerman, Jonathan Mangion, Melissa A. Barker, Kevin J. McKernan, Jan Komorowski, Claes Wadelius (2009). "Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq". Genome Biology 10(11):R129 [link]
  52. Marcin Kierczak, Witold R. Rudnicki, Jan Komorowski (2008). "Construction of Rough Set-Based Classifiers for Predicting HIV Resistance to Nucleoside Reverse Transcriptase Inhibitors". Studies in Fuzziness and Soft Computing 224(0):249-258 [link]
  53. T. D. de Ståhl, J. Sandgren, A. Piotrowski, H. Nord, R. Andersson, U. Menzel, A. Bogdan, A. C. Thuresson, A. Poplawski, D. von Tell, C. M. Hansson, A. I. Elshafie, G. Elghazali, S. Imreh, M. Nordenskjöld, M. Upadhyaya, J. Komorowski, C. E. Bruder, J. P. Dumanski (2008). "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 29(3):398-408 [link]
  54. R. R. Pandey, T. Mondal,F. Mohammad, S. Enroth, L. Redrup, J. Komorowski, D. Mancini-DiNardo, C. Kanduri (2008). "Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation". Molecular Cell 32(2):232-246 [link]
  55. Westholm JO, Nordberg N, MurΟ©n E, Ameur A, Komorowski J, Ronne H. (2008). "Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3". BMC Genomics 0(0):601 [link]
  56. Michal Draminski, Alvaro Rada-Iglesias, Stefan Enroth, Claes Wadelius, Jacek Koronacki, Jan Komorowski (2008). "Monte Carlo feature selection for supervised classification". Bioinformatics 24(1):110-117 [link]
  57. Robin Andersson, Carl E.G. Bruder, Arkadiusz Piotrowski, Uwe Menzel, Helena Nord, Johanna Sandgren, Torgeir R. Hvidsten, Teresita Diaz de Stahl, Jan P. Dumanski, Jan Komorowski (2008). "A segmental maximum a posteriori approach to genome-wide copy number profiling". Bioinformatics 24(6):751-758 [link]
  58. Alvaro Rada-Iglesias, Adam Ameur, Philipp Kapranov, Stefan Enroth, Jan Komorowski, Thomas R. Gingeras, Claes Wadelius (2008). "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 18(3):380-392 [link]
  59. Aleksejs Kontijevskis, Jan Komorowski, Jarl E.S. Wikberg (2008). "Generalized proteochemometric model of multiple cytochrome p450 enzymes and their inhibitors". Journal of Chemical Information and Modeling 48(9):1840-1850 [link]
  60. Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne, Jan Komorowski (2008). "Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation". BMC bioinformatics 9(0):484 [link]
  61. F. M. Mikhail, A. Sathienkijkanchai, N. H. Robin, S. Prucka, J. S. Biggerstaff, J. Komorowski, R. Andersson, C. E. Bruder, A. Piotrowski, T. D. de Ståhl, J. P. Dumanski, A. J. Carroll (2007). "Overlapping phenotype of Wolf-Hirschhorn and Beckwith-Wiedemann syndromes in a girl with der(4)t(4;11)(pter;pter)". American Journal of Medical Genetics Part A 143A(15):1760-1766 [link]
  62. F. M. Mikhail, M. Descartes, A. Piotrowski, R. Andersson, T. D. de Ståhl, J. Komorowski, C. E. Bruder, J. P. Dumanski, A. J. Carroll (2007). "A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene". American Journal of Medical Genetics Part A 143(18):2178-2184 [link]
  63. T. R. Hvidsten and J. Komorowski (edited by E. Orlowska, J. F. Peters and A. Skowron) (2007). "Rough Sets in Bioinformatics". Transactions on Rough Sets VII 4400(0):225-243 [link]
  64. Emma Rennel, Sofie Mellberg, Anna Dimberg, Ludvig Petersson, Johan Botling, Adam Ameur, Jakub Orzechowski Westholm, Jan Komorowski, Philippe Lassalle, Michael J. Cross, Par Gerwins (2007). "Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer". Experimental Cell Research 313(7):1285-1294 [link]
  65. Aleksejs Kontijevskis, Peteris Prusis, Ramona Petrovska, Sviatlana Yahorava, Felikss Mutulis, Ilze Mutule, Jan Komorowski, Jarl E.S. Wikberg (2007). "A look inside HIV resistance through retroviral protease interaction maps". PLoS Computational Biology 3(3):e48 [link]
  66. Aleksejs Kontijevskis, Jarl E.S. Wikberg, Jan Komorowski (2007). "Computational proteomics analysis of HIV-1 protease interactome". Proteins 68(1):305-312 [link]
  67. Aleksejs Kontijevskis, Ramona Petrovska, Ilze Mutule, Staffan Uhlen, Jan Komorowski, Peteris Prusis, Jarl E.S. Wikberg (2007). "Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors". Proteins 69(1):83-96 [link]
  68. Alvaro Rada-Iglesias, Stefan Enroth, Adam Ameur, Christoph Koch, Gayle K. Clelland, Patricia Respuela-Alonso, Sarah Wilcox, Oliver M. Dovey, Peter D. Ellis, Cordelia F. Langford, Ian Dunham, Jan Komorowski, Claes Wadelius (2007). "Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes". Genome Research 17(6):708-719 [link]
  69. Ewan Birney, John A. Stamatoyannopoulos, Anindya Dutta, Roderic Guigo, Thomas R. Gingeras, Elliott H. Margulies, Zhiping Weng, Michael Snyder, Emmanouil T. Dermitzakis, Robert E. Thurman, Michael S. Kuehn, Christopher M. Taylor, Shane Neph, Christoph M. Koch, ... (178) ..., Adam Ameur, Stefan Enroth, Alvaro Rada-Iglesias, Ola Wallerman, Jan Komorowski, ... (95) ..., Yuko Yoshinaga, Baoli Zhu, Pieter J. de Jong (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447(7146):799-816 [link]
  70. Ulrika Bergstrom, J. A. Olsson, Torgeir R. Hvidsten, Jan Komorowski, Brandt I. (2007). "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 28(6):1120-1128 [link]
  71. Claes R. Andersson, Torgeir R. Hvidsten, Anders Isaksson, Mats G. Gustafsson, Jan Komorowski (2007). "Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors". BMC Systems Biology 1(0):45 [link]
  72. Witold R. Rudnicki, Marcin Kierczak, Jacek Koronacki, Jan Komorowski (2006). "A Statistical Method for Determining Importance of Variables in an Information System". Lecture Notes in Computer Science 4259(0):557-566 [link]
  73. Vidar Beisvag, Per Kristian Lehre, Herman Midelfart, Halfdan Aass, Odd Geiran, Arne Kristian Sandvik, Astrid Lægreid, Jan Komorowski, Øyvind Ellingsen (2006). "Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data". The European Journal of Heart Failure 8(4):381-389 [link]
  74. Helena Strombergsson, Peteris Prusis, Herman Midelfart, Maris Lapinsh, Jarl E.S. Wikberg, Jan Komorowski (2006). "Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions". Proteins 63(1):24-34 [link]
  75. Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, Jan Komorowski (2006). "The LCB Data Warehouse". Bioinformatics 22(8):1024-1026 [link]
  76. Helena Strombergsson, Andriy Kryshtafovych, Peteris Prusis, Krzysztof Fidelis, Jarl E.S. Wikberg, Jan Komorowski, Torgeir R. Hvidsten (2006). "Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures". Proteins 65(3):568-579 [link]
  77. Bartek Wilczynski, Torgeir R. Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski, Krzysztof Fidelis (2006). "Using local gene expression similarities to discover regulatory binding site modules". BMC Bioinformatics 7(0):505 [link]
  78. Michal Draminski, Jacek Koronacki, Jan Komorowski (2005). "A study on Monte Carlo Gene Screening". Intelligent Information Systems 31(0):349-356 [link]
  79. Witold R. Rudnicki, Jan Komorowski (2005). "Soft Computing Approach to the Analysis of the Amino Acid Similarity Matrices". Intelligent Information Systems 31(0):663-670 [link]
  80. Jayne L. Dennis, Torgeir R. Hvidsten, Ernst C. Wit, Jan Komorowski, Alexandra K. Bell, Ian Downie, Jacqueline Mooney, Caroline Verbeke, Christopher Bellamy, W. Nicol Keith, Karin A. Oien (2005). "Markers of Adenocarcinoma Characteristic of the Site of Origin: Development of a Diagnostic Algorithm". Clinical Cancer Research 11(10):3766-3772 [link]
  81. Hung Son Nguyen, Marta Luksza, Ewa Makosa, Jan Komorowski (2005). "An Approach to Mining Data with Continuous Decision Values". Intelligent Information Systems 31(0):653-661 [link]
  82. Robin Andersson, Aida Vittoria, Jan Maluszynski, Jan Komorowski (2005). "RoSy: A Rough Knowledge Base System". Rough Sets, Fuzzy Sets, Data Mining, and Granular-Soft Computing (RSFDGrC) 3642(0):48-58 [link]
  83. Torgeir R. Hvidsten, Bartosz Wilczynski, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski, Krzysztof Fidelis (2005). "Discovering regulatory binding-site modules using rule-based learning". Genome Research 15(6):856-866 [link]
  84. Alvaro Rada-Iglesias, Ola Wallerman, Christoph Koch, Adam Ameur, Stefan Enroth, Gayle 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 Ponten, Jan Komorowski, Ian Dunham, Claes Wadelius (2005). "Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays". Human Molecular Genetics 14(22):3435-3447 [link]
  85. Witold R. Rudnicki, Jan Komorowski (2004). "Feature Synthesis and Extraction for the Construction of Generalized Properties of Amino Acids". Proceedings of Rough Sets and Current Trends in Computing 3066(0):786-791 [link]
  86. K. G. Norsett, A. Laegreid, H. Midelfart, F. Yadetie, S. E. Erlandsen, S. Falkmer, J. E. Gronbech, H. L. Waldum, J. Komorowski, A. K. Sandvik (2004). "Gene expression based classification of gastric carcinoma". Cancer Letters 210(2):227-237 [link]
  87. B.Wilczynski, T.Hvidsten, A.Kryshtafovych, L.Stubbs, J.Komorowski, K. Fidelis (2003). "A rule-based framework for gene regulation pathways discovery". IEEE Computer Society Bioinformatics Conference 0(0):435-436 [link]
  88. A.Kryshtafovych, T.R. Hvidsten, J. Komorowski, K. Fidelis (2003). "Fold Recognition Using Sequence Fingerprints of Protein Local Substructures". IEEE Computer Society Bioinformatics Conference 0(0):517-518 [link]
  89. Astrid Lagreid, Torgeir R. Hvidsten, Herman Midelfart, Jan Komorowski, Arne K. Sandvik (2003). "Predicting gene ontology biological process from temporal gene expression patterns". Genome Research 13(5):965-979 [link]
  90. Torgeir R. Hvidsten, Astrid Laegreid, Jan Komorowski (2003). "Learning rule-based models of biological process from gene expression time profiles using gene ontology". Bioinformatics 19(9):1116-1123 [link]
  91. Fekadu Yadetie, Astrid Laegreid, Ingunn Bakke, Waclaw Kusnierczyk, Jan Komorowski, Helge L. Waldum, Arne K. Sandvik (2003). "Liver gene expression in rats in response to the peroxisome proliferator-activated receptor-alpha agonist ciprofibrate". Physiological Genomics 15(1):9-19 [link]
  92. Torgeir R. Hvidsten, Andriy Kryshtafovych, Jan Komorowski, Krzysztof Fidelis (2003). "A novel approach to fold recognition using sequence-derived properties from sets of structurally similar local fragments of proteins". Bioinformatics 19 Suppl 2(0):ii81-91 [link]
  93. H. Midelfart, J. Komorowski, K. Nørsett, F. Yadetie, A.K. Sandvik, A. Lægreid (2002). "Learning Rough Set Classifiers from Gene Expression and Clinical Data". Fundamenta Informaticae 53(2):155-183 [link]
  94. Herman Midelfart, Astrid Lægreid, Jan Komorowski (2001). "Classification of Gene Expression Data in an Ontology". Proceedings of the Second International Symposium on Medical Data Analysis 2199(0):186-194 [link]
  95. Tor-Kristian Jenssen, Lisa M.J. Öberg, Magnus L. Andersson, Jan Komorowski (2001). "Methods for Large-Scale Mining of Networks of Human Genes". Proceedings of The First SIAM Conference on Datamining 0(0):1-16 [link]
  96. T. R. Hvidsten, J. Komorowski, A. K. Sandvik, A. Laegreid (2001). "Predicting gene function from gene expressions and ontologies". Pacific Symposium on Biocomputing 0(0):299-310 [link]
  97. T. K. Jenssen, A. Laegreid, J. Komorowski, E. Hovig (2001). "A literature network of human genes for high-throughput analysis of gene expression". Nature Genetics 28(1):21-28 [link]
  98. J. Komorowski, T. R. Hvidsten, T. K. Jenssen, D. Tjeldvoll, E. Hovig, A. Laegreid, A. K. Sandvik (2001). "[New knowledge derived from measurement of gene expression with the DNA microarray method]". Tidsskrift for den Norske laegeforening : tidsskrift for praktisk medicin, ny raekke 121(10):1229-1232 [link]
  99. Jan Komorowski, Zdzislaw Pawlak, Lech Polkowski, Andrzej Skowron (2000). "Rough Sets: A Tutorial". Rough Fuzzy Hybridization – A New Trend in Decision Making 0(0):3-98 [link]
  100. Jan Komorowski, Torgeir R. Hvidsten, Tor-Kristian Jenssen, Dyre Tjeldvoll, Eivind Hovig, Arne K. Sandvik, Astrid Lægreid (2000). "Towards Knowledge Discovery from cDNA Microarray Gene Expression Data". Principles and Practice of Knowledge Discovery in Databases 1910(0):470-475 [link]
  101. Komorowski J, Öhrn A. (1999). "Modelling prognostic power of cardiac tests using rough sets". Artificial Intelligence in Medicine 15(2):167-191 [link]
  102. Tor-Kristian Jenssen, Jan Komorowski and Aleksander Øhrn (1998). "Some Heuristics for Default Knowledge Discovery". Lecture Notes in Computer Science 1424(0):373-380 [link]
  103. A. Ohrn, S. Vinterbo, P. Szymanski, J. Komorowski (1997). "Modelling cardiac patient set residuals using rough sets". American Medical Informatics Association Fall Symposium 0(0):203-207 [link]