Jan Komorowski

Summary

Affiliation: Uppsala University
Country: Sweden

Publications

  1. pmc Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
    Susanne Bornelöv
    Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden
    BMC Bioinformatics 15:139. 2014
  2. pmc A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    Algorithms Mol Biol 7:2. 2012
  3. doi request reprint Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates
    Aleksejs Kontijevskis
    Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, SE 75124, Uppsala, Sweden
    Bioorg Med Chem 17:5229-37. 2009
  4. pmc Integrative epigenomic and genomic analysis of malignant pheochromocytoma
    Johanna Sandgren
    Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, SE 75185 Uppsala, Sweden
    Exp Mol Med 42:484-502. 2010
  5. doi request reprint A segmental maximum a posteriori approach to genome-wide copy number profiling
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden
    Bioinformatics 24:751-8. 2008
  6. pmc Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array
    Helena Nord
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Neuro Oncol 11:803-18. 2009
  7. pmc Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden
    BMC Cancer 11:450. 2011
  8. pmc Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
    Jakub Orzechowski Westholm
    The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 9:484. 2008
  9. pmc Nucleosomes are well positioned in exons and carry characteristic histone modifications
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genome Res 19:1732-41. 2009
  10. pmc Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP
    Adam Ameur
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Nucleic Acids Res 37:e85. 2009

Collaborators

Detail Information

Publications35

  1. pmc Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
    Susanne Bornelöv
    Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden
    BMC Bioinformatics 15:139. 2014
    ..This interpretation may be eased if interacting elements can be identified and visualized, something that requires appropriate tools and methods...
  2. pmc A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    Algorithms Mol Biol 7:2. 2012
    ..abstract:..
  3. doi request reprint Proteochemometrics mapping of the interaction space for retroviral proteases and their substrates
    Aleksejs Kontijevskis
    Department of Pharmaceutical Biosciences, Uppsala University, Husargatan 3, SE 75124, Uppsala, Sweden
    Bioorg Med Chem 17:5229-37. 2009
    ..Our results demonstrate the feasibility of using the developed general strategy in the design of inhibitory peptides that can potentially serve as templates for drug resistance-improved HIV retardants...
  4. pmc Integrative epigenomic and genomic analysis of malignant pheochromocytoma
    Johanna Sandgren
    Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, SE 75185 Uppsala, Sweden
    Exp Mol Med 42:484-502. 2010
    ..Our approach to associate histone methylations and DNA copy number changes to gene expression revealed apparent impact on global gene transcription, and enabled the identification of candidate tumor genes for further exploration...
  5. doi request reprint A segmental maximum a posteriori approach to genome-wide copy number profiling
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden
    Bioinformatics 24:751-8. 2008
    ..Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis...
  6. pmc Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array
    Helena Nord
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Neuro Oncol 11:803-18. 2009
    ..The large individual variation observed between the samples demonstrates the underlying complexity of the disease and strengthens the demand for an individualized therapy based on the genetic profile of the patient...
  7. pmc Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden
    BMC Cancer 11:450. 2011
    ..In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples...
  8. pmc Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
    Jakub Orzechowski Westholm
    The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    BMC Bioinformatics 9:484. 2008
    ..Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence) is important for gene regulation...
  9. pmc Nucleosomes are well positioned in exons and carry characteristic histone modifications
    Robin Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genome Res 19:1732-41. 2009
    ..Thus, exons are not only characterized by their coding capacity, but also by their nucleosome organization, which seems evolutionarily conserved since it is present in both primates and nematodes...
  10. pmc Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP
    Adam Ameur
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Nucleic Acids Res 37:e85. 2009
    ..Overall, this approach can help to pinpoint the causative SNPs in complex disorders where the associated haplotypes are located in regulatory regions...
  11. ncbi request reprint Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma
    Helena Nord
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Int J Cancer 126:1390-402. 2010
    ..The observed overrepresentation of amplicons within high-grade and recurrent cases may be clinically useful for the identification of patients who will benefit from a more aggressive therapy...
  12. pmc 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
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE 75185 Uppsala, Sweden
    Genome Res 18:380-92. 2008
    ..This expands our understanding about the transcriptional control of metabolic processes and its alteration in metabolic disorders...
  13. ncbi request reprint Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis
    Johanna Sandgren
    Department of Surgical Sciences, Uppsala University Hospital Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
    Endocr Relat Cancer 17:561-79. 2010
    ....
  14. pmc Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq
    Mehdi Motallebipour
    Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, Uppsala SE 75185, Sweden
    Genome Biol 10:R129. 2009
    ..The forkhead box/winged helix family members FOXA1, FOXA2, and FOXA3 are of high importance in development and specification of the hepatic linage and the continued expression of liver-specific genes...
  15. doi request reprint 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
    Mehdi Motallebipour
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    FEBS J 276:1878-90. 2009
    ..Furthermore, we found evidence of sterol-regulated binding of SREBP-1 and RNA polymerase II to HCFC1 and FLNA. From the results of this work, we infer that SREBP-1 may be involved in processes other than lipid metabolism...
  16. pmc Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3
    Jakub Orzechowski Westholm
    The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 751 24 Uppsala, Sweden
    BMC Genomics 9:601. 2008
    ..We have used microarrays to study global gene expression in all possible combinations of mig1, mig2 and mig3 deletion mutants...
  17. ncbi request reprint Proteochemometric analysis of small cyclic peptides' interaction with wild-type and chimeric melanocortin receptors
    Aleksejs Kontijevskis
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    Proteins 69:83-96. 2007
    ..The analysis also revealed important amino acids that explain the selectivity of the HS-129 peptide for the MC4 receptor...
  18. pmc Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cells
    Jakub Orzechowski Westholm
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS ONE 7:e31577. 2012
    ..Significantly, Gis1 and Rph1 control a number of genes involved in acetate and glycerol formation, metabolites that have been implicated in aging. Furthermore, several genes involved in acetyl-CoA metabolism are downregulated by Gis1...
  19. ncbi request reprint Computational proteomics analysis of HIV-1 protease interactome
    Aleksejs Kontijevskis
    The Linnaeus Centre for Bioinformatics, Uppsala University, S 75124 Uppsala, Sweden
    Proteins 68:305-12. 2007
    ..Our study is an example how computational biology methods can advance the understanding of the viral interactomes...
  20. pmc ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer
    Madhusudhan Bysani
    Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, PO Box 815, Uppsala, SE 751 08, Sweden
    BMC Med Genomics 6:50. 2013
    ..Many transcription factors (TFs) are crucial for the control of the genes involved in metabolism, and abnormality in their function may lead to disease...
  21. pmc Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
    Marcin Kruczyk
    Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, Sweden
    BMC Bioinformatics 14:280. 2013
    ..We present the first meta-server called Peak Finder MetaServer (PFMS) that collects results from several peak finders and produces consensus peaks. Our application accepts three standard ChIP-seq data formats: BED, BAM, and SAM...
  22. doi request reprint Generalized proteochemometric model of multiple cytochrome p450 enzymes and their inhibitors
    Aleksejs Kontijevskis
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    J Chem Inf Model 48:1840-50. 2008
    ..This approach may aid in the selection of novel drug candidates that are unlikely to inhibit multiple CYP subtypes...
  23. pmc A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity
    Torgeir R Hvidsten
    The Linnaeus Centre for Bioinformatics, Uppsala University and The Swedish University for Agricultural Sciences, Uppsala, Sweden
    PLoS ONE 4:e6266. 2009
    ..With structural genomics it is believed that structural similarities may give functional hypotheses for many of the remaining proteins...
  24. pmc Combinations of histone modifications mark exon inclusion levels
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Center, Uppsala University, Uppsala, Sweden
    PLoS ONE 7:e29911. 2012
    ..The resulting model was evaluated with cross validation and had an average accuracy of 72% for 27% of the exons, which demonstrates that epigenetic signals substantially mark alternative splicing...
  25. ncbi request reprint Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation
    Alvaro Rada-Iglesias
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Epigenetics 4:107-13. 2009
    ..Therefore, the suggested polycomb pre-marking of genes for cancer DNA hypermethylation is not necessarily limited to ES or early precursor cells but can occur later in differentiated tissues...
  26. ncbi request reprint Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
    Radha Raman Pandey
    Department of Genetics and Pathology, Dag Hammarskjölds väg 20, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
    Mol Cell 32:232-46. 2008
    ....
  27. pmc A look inside HIV resistance through retroviral protease interaction maps
    Aleksejs Kontijevskis
    Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
    PLoS Comput Biol 3:e48. 2007
    ..The approach allowed a detailed analysis of the molecular-chemical mechanisms involved in substrate cleavage by retroviral proteases...
  28. pmc Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
    Claes R Andersson
    The Linnaeus Centre for Bioinformatics, Uppsala University and Swedish University of Agricultural Sciences, Uppsala, Sweden
    BMC Syst Biol 1:45. 2007
    ....
  29. pmc Nucleosome regulatory dynamics in response to TGFβ
    Stefan Enroth
    The Linnaeus Centre for Bioinformatics, Biomedical Center, Uppsala University, SE 75124 Uppsala, Sweden
    Nucleic Acids Res 42:6921-34. 2014
    ..Changes in binding affinity were verified for HNF4α by qPCR. Strikingly many of these loci were associated with expression changes, as measured by RNA sequencing. ..
  30. pmc Rule-based models of the interplay between genetic and environmental factors in childhood allergy
    Susanne Bornelöv
    Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    PLoS ONE 8:e80080. 2013
    ..Interactions identified with this approach could provide useful hints for further in-depth studies of etiological mechanisms and may also strengthen the basis for risk assessment and prevention. ..
  31. pmc SICTIN: Rapid footprinting of massively parallel sequencing data
    Stefan Enroth
    Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    BioData Min 3:4. 2010
    ..The construction of these footprints is however a time consuming task...
  32. ncbi request reprint Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer
    Emma Rennel
    Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, S 751 85 Uppsala, Sweden
    Exp Cell Res 313:1285-94. 2007
    ..Increased endocan protein expression in human renal cancer suggests a role in tumor growth...
  33. ncbi request reprint Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array
    Teresita Díaz de Ståhl
    Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
    Hum Mutat 29:398-408. 2008
    ..This report contributes to the establishment of the common baseline for CNV, which is an important resource in human genetics...
  34. ncbi request reprint Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures
    Helena Strömbergsson
    The Linnaeus Centre for Bioinformatics, Uppsala University, SE 751 24, Uppsala, Sweden
    Proteins 65:568-79. 2006
    ..Current approaches are limited to families of closely related proteins. families of closely related proteins...
  35. ncbi request reprint The LCB Data Warehouse
    Adam Ameur
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Bioinformatics 22:1024-6. 2006
    ..lcb.uu.se/index.phtml?i_login=test. User accounts are created upon request. Additional facilities including plug-ins, user documentation and a password protected data storage system are available from http://www.lcb.uu.se/lcbdw.php..