Research Topics
Genomes and Genes | Jan KomorowskiSummaryAffiliation: Uppsala University Country: Sweden Publications
| Collaborators
|
Detail Information
Publications
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurementsStefan 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:..- Integrative epigenomic and genomic analysis of malignant pheochromocytomaJohanna 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... - Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosaStefan 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... - Genome-scale study of the importance of binding site context for transcription factor binding and gene regulationJakub 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... - Nucleosomes are well positioned in exons and carry characteristic histone modificationsRobin 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... - Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIPAdam 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. Availability: BCRANK is available from Bioconductor (http://www.bioconductor.org/)... - Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC arrayHelena 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... 
Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysisJohanna Sandgren
Department of Surgical Sciences, Uppsala University Hospital Rudbeck Laboratory, Uppsala University, SE 751 85 Uppsala, Sweden
Endocr Relat Cancer 17:561-79. 2010....- Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seqMehdi 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... - Gis1 and Rph1 regulate glycerol and acetate metabolism in glucose depleted yeast cellsJakub 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... - Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinomaHelena 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... - Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3Jakub 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... - 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 detectionMehdi 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... - Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulationRadha 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.... 
Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylationAlvaro 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...- Combinations of histone modifications mark exon inclusion levelsStefan 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... - Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disordersAlvaro 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... - A segmental maximum a posteriori approach to genome-wide copy number profilingRobin 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... - SICTIN: Rapid footprinting of massively parallel sequencing dataStefan 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... - A comprehensive analysis of the structure-function relationship in proteins based on local structure similarityTorgeir 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... - Proteochemometrics mapping of the interaction space for retroviral proteases and their substratesAleksejs 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... - Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptorsClaes R Andersson
The Linnaeus Centre for Bioinformatics, Uppsala University and Swedish University of Agricultural Sciences, Uppsala, Sweden
BMC Syst Biol 1:45. 2007....