A Kel

Summary

Affiliation: BIOBASE GmbH
Country: Germany

Publications

  1. pmc P-Match: transcription factor binding site search by combining patterns and weight matrices
    D S Chekmenev
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 33:W432-7. 2005
  2. pmc Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context
    Alexander E Kel
    BIOBASE GmbH, Halchtersche Str, 38304 Wolfenbüttel, Germany
    Genome Biol 9:R36. 2008
  3. ncbi request reprint Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors
    A E Kel
    Institute of Cytology and Genetics, Novosibirsk, Russia
    J Mol Biol 309:99-120. 2001
  4. pmc MATCH: A tool for searching transcription factor binding sites in DNA sequences
    A E Kel
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:3576-9. 2003
  5. ncbi request reprint Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
    A Kel
    Institute of Cytology and Genetics SB RAN, Lavrentyev pr, 10, 630090, Novosibirsk, Russia
    Bioinformatics 20:1512-6. 2004
  6. ncbi request reprint Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
    A Kel
    BIOBASE GmbH Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Bioinformatics 22:1190-7. 2006
  7. ncbi request reprint A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily
    A Kel
    Institute of Cytology and Genetics, pr Lavrentyeva 10, 630090, Novosibirsk, Russia
    Bioinformatics 14:259-70. 1998
  8. ncbi request reprint Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells
    A Kel
    Institute of Cytology and Genetics, pr Lavrentyeva 10, 630090, Novosibirsk, Russia
    J Mol Biol 288:353-76. 1999
  9. doi request reprint ExPlain: finding upstream drug targets in disease gene regulatory networks
    A Kel
    BIOBASE GmbH, Wolfenbüttel, Germany
    SAR QSAR Environ Res 19:481-94. 2008
  10. pmc 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations
    R Gabdoulline
    Heinrich Heine University of Duesseldorf, Universitaetstr 1, 40225 Duesseldorf, Germany
    Nucleic Acids Res 40:W180-5. 2012

Collaborators

  • E Wingender
  • M Q Zhang
  • Monika Niehof
  • Z Jay Chen
  • A Fujiyama
  • Si Hyen Cho
  • J Borlak
  • R Gabdoulline
  • P Stegmaier
  • T Waleev
  • D S Chekmenev
  • Y Sakaki
  • D Eckweiler
  • T Konovalova
  • N Voss
  • O Kel-Margoulis
  • D Shtokalo
  • E Cheremushkin
  • C Haid
  • R Reinhardt
  • K Wu
  • S F Tsai
  • A Toyoda
  • I Hellmann
  • M L Yaspo
  • P Galgoczy
  • S Paabo
  • H Bloecker
  • G P Zhao
  • M Hattori
  • T Kitano
  • S H Choi
  • K J Hsiao
  • M Kube
  • T Taylor
  • Y S Lee
  • G F Zhu
  • H S Park
  • A Kahla
  • P Khaitovich
  • S Y Wang
  • Y Kuroki
  • B F Wang
  • T T Liu
  • S Taenzer
  • H J Zheng
  • M Scharfe
  • T Itoh
  • R Sudbrak
  • H Lehrach
  • J E Cheong
  • S Oota
  • C G Kim
  • G Nordsiek
  • H Watanabe
  • S X Ren
  • M Platzer
  • X L Zhang
  • N Saitou

Detail Information

Publications12

  1. pmc P-Match: transcription factor binding site search by combining patterns and weight matrices
    D S Chekmenev
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 33:W432-7. 2005
    ..Furthermore, a number of tissue-specific profiles are provided that were compiled by the TRANSFAC team. A public version of the P-Match tool is available at http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi...
  2. pmc Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context
    Alexander E Kel
    BIOBASE GmbH, Halchtersche Str, 38304 Wolfenbüttel, Germany
    Genome Biol 9:R36. 2008
    ..When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor...
  3. ncbi request reprint Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors
    A E Kel
    Institute of Cytology and Genetics, Novosibirsk, Russia
    J Mol Biol 309:99-120. 2001
    ..The tools described are available at http://compel.bionet.nsc.ru/FunSite/SiteScan.html...
  4. pmc MATCH: A tool for searching transcription factor binding sites in DNA sequences
    A E Kel
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:3576-9. 2003
    ..com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called Match Professional is available at http://www.biobase.de...
  5. ncbi request reprint Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
    A Kel
    Institute of Cytology and Genetics SB RAN, Lavrentyev pr, 10, 630090, Novosibirsk, Russia
    Bioinformatics 20:1512-6. 2004
    ..Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences...
  6. ncbi request reprint Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
    A Kel
    BIOBASE GmbH Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Bioinformatics 22:1190-7. 2006
    ..Cis-element combinations provide a structural basis for the generation of unique patterns of gene expression...
  7. ncbi request reprint A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily
    A Kel
    Institute of Cytology and Genetics, pr Lavrentyeva 10, 630090, Novosibirsk, Russia
    Bioinformatics 14:259-70. 1998
    ..The critical point is to design appropriate sets of oligonucleotides that can be used effectively in identification by hybridization...
  8. ncbi request reprint Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells
    A Kel
    Institute of Cytology and Genetics, pr Lavrentyeva 10, 630090, Novosibirsk, Russia
    J Mol Biol 288:353-76. 1999
    ..The program for recognition NFAT composite elements is available through the World Wide Web (http://compel.bionet.nsc.ru/FunSite/CompelScan. html and http://transfac.gbf.de/dbsearch/funsitep/s _comp.html)...
  9. doi request reprint ExPlain: finding upstream drug targets in disease gene regulatory networks
    A Kel
    BIOBASE GmbH, Wolfenbüttel, Germany
    SAR QSAR Environ Res 19:481-94. 2008
    ..ExPlain system was applied to microarray data on inflammatory bowel diseases (IBD). The results obtained suggest a number of highly interesting biological hypotheses about molecular mechanisms of pathological genetic disregulation...
  10. pmc 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations
    R Gabdoulline
    Heinrich Heine University of Duesseldorf, Universitaetstr 1, 40225 Duesseldorf, Germany
    Nucleic Acids Res 40:W180-5. 2012
    ..The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/...
  11. pmc Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm
    T Waleev
    A P Ershov s Institute of Informatics Systems 6, Lavrentiev Avenue, 630090 Novosibirsk, Russia
    Nucleic Acids Res 34:W541-5. 2006
    ..gene-regulation.com/pub/programs/cma/CMA.html. An advanced version of CMA is also a part of the commercial system ExPlaintrade mark (www.biobase.de) designed for causal analysis of gene expression data...
  12. ncbi request reprint Human versus chimpanzee chromosome-wide sequence comparison and its evolutionary implication
    Y Sakaki
    RIKEN, Genomic Sciences Center, Yokohama 230 0045, Japan
    Cold Spring Harb Symp Quant Biol 68:455-60. 2003