A Kel

Summary

Affiliation: BIOBASE GmbH
Country: Germany

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi ExPlain: finding upstream drug targets in disease gene regulatory networks
    A Kel
    BIOBASE GmbH, Wolfenbüttel, Germany
    SAR QSAR Environ Res 19:481-94. 2008
  9. ncbi 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
  10. ncbi 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

Collaborators

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

Detail Information

Publications11

  1. ncbi 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...
  2. ncbi 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...
  3. ncbi 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...
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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)...
  7. ncbi 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...
  8. ncbi 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...
  9. ncbi 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/...
  10. ncbi 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...
  11. ncbi 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