Alexander E. Kel

Razif R. Gabdoulline, D. Eckweiler, Alexander E. Kel, Philip Stegmaier: 3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Research 40(Web-Server-Issue): 180-185 (2012)

Denitsa Alamanova, Philip Stegmaier, Alexander E. Kel: Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. BMC Bioinformatics 11: 225 (2010)

Boris Sobolev, Dmitry Filimonov, Alexey Lagunin, Alexey Zakharov, Olga Koborova, Alexander E. Kel, Vladimir Poroikov: Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. BMC Bioinformatics 11: 313 (2010)

Holger Michael, Jennifer Hogan, Alexander E. Kel, Olga V. Kel-Margoulis, Frank Schacherer, Nico Voss, Edgar Wingender: Building a knowledge base for systems pathology. Briefings in Bioinformatics 9(6): 518-531 (2008)

Stefan Posch, Jan Grau, André Gohr, Irad E. Ben-Gal, Alexander E. Kel, Ivo Grosse: Recognition of cis-Regulatory Elements with Vombat. J. Bioinformatics and Computational Biology 5(2b): 561-577 (2007)

Fedor Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel: CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Research 35(Database-Issue): 550-556 (2007)

Jan Grau, Jens Keilwagen, Alexander E. Kel, Ivo Grosse, Stefan Posch: Supervised Posteriors for DNA-motif Classification. German Conference on Bioinformatics 2007: 123-134

Alexander E. Kel, Tatiana Konovalova, T. Waleev, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender: Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinformatics 22(10): 1190-1197 (2006)

Alexander E. Kel, Nico Voss, Ruy Jauregui, Olga V. Kel-Margoulis, Edgar Wingender: Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. BMC Bioinformatics 7(S-2) (2006)

Xin Chen, Jian-min Wu, Klaus Hornischer, Alexander E. Kel, Edgar Wingender: TiProD: the Tissue-specific Promoter Database. Nucleic Acids Research 34(Database-Issue): 104-107 (2006)

V. Matys, Olga V. Kel-Margoulis, Ellen Fricke, Ines Liebich, Sigrid Land, A. Barre-Dirrie, Ingmar Reuter, D. Chekmenev, Mathias Krull, Klaus Hornischer, Nico Voss, Philip Stegmaier, Birgit Lewicki-Potapov, H. Saxel, Alexander E. Kel, Edgar Wingender: TRANSFAC^® and its module TRANSCompel^®: transcriptional gene regulation in eukaryotes. Nucleic Acids Research 34(Database-Issue): 108-110 (2006)

Mathias Krull, Susanne Pistor, Nico Voss, Alexander E. Kel, Ingmar Reuter, Deborah Kronenberg, Holger Michael, Knut Schwarzer, Anatolij Potapov, Claudia Choi, Olga V. Kel-Margoulis, Edgar Wingender: TRANSPATH^®: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Research 34(Database-Issue): 546-551 (2006)

T. Waleev, D. Shtokalo, Tatiana Konovalova, Nico Voss, Evgeny Cheremushkin, Philip Stegmaier, Olga V. Kel-Margoulis, Edgar Wingender, Alexander E. Kel: Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. Nucleic Acids Research 34(Web-Server-Issue): 541-545 (2006)

Igor V. Deyneko, Björn Bredohl, Daniel Wesely, Yulia M. Kalybaeva, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer: FeatureScan: revealing property-dependent similarity of nucleotide sequences. Nucleic Acids Research 34(Web-Server-Issue): 591-595 (2006)

Alexander E. Kel, Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender: Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation. German Conference on Bioinformatics 2005: 63-75

Tatiana Konovalova, Tagir Valeev, Evgeny Cheremushkin, Alexander E. Kel: Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data. ICNC (2) 2005: 1202-1205

Maciej Swat, Alexander E. Kel, Hanspeter Herzel: Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. Bioinformatics 20(10): 1506-1511 (2004)

Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender: Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods. Bioinformatics 20(10): 1512-1516 (2004)

Yutaka Suzuki, Riu Yamashita, Matsuyuki Shirota, Yuta Sakakibara, Joe Chiba, Junko Mizushima-Sugano, Alexander E. Kel, Takahiro Arakawa, Piero Carninci, Jun Kawai, Yoshihide Hayashizaki, Toshihisa Takagi, Kenta Nakai, Sumio Sugano: Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biology 4 (2004)

Alexander E. Kel, Nico Voss, Tatiana Konovalova, Dmitri Tchekmenev, P. Wabnitz, Olga V. Kel-Margoulis, Edgar Wingender: From Composite Patters to Pathways - Prediction of Key Regulators of Gene Expression. German Conference on Bioinformatics 2004: 189-198

Alexander E. Kel, Yuri Tikunov, Nico Voss, Jürgen Borlak, Edgar Wingender: Application of Kernel Method to Reveal Subtypes of TF Binding Motifs. Regulatory Genomics 2004: 42-51

Ekaterina Shelest, Alexander E. Kel, Ellen Gößling, Edgar Wingender: Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods. In Silico Biology 3: 7 (2003)

Olga V. Kel-Margoulis, Dmitri Tchekmenev, Alexander E. Kel, Ellen Gößling, Klaus Hornischer, Birgit Lewicki-Potapov, Edgar Wingender: Composition-sensitive analysis of the human genome for regulatory signals. In Silico Biology 3: 13 (2003)

V. Matys, Ellen Fricke, R. Geffers, Ellen Gößling, Martin Haubrock, R. Hehl, Klaus Hornischer, Dagmar Karas, Alexander E. Kel, Olga V. Kel-Margoulis, Dorothee-U. Kloos, Sigrid Land, Birgit Lewicki-Potapov, Holger Michael, Richard Münch, Ingmar Reuter, Stella Rotert, H. Saxel, Maurice Scheer, S. Thiele, Edgar Wingender: TRANSFAC®: transcriptional regulation, from patterns to profiles. Nucleic Acids Research 31(1): 374-378 (2003)

Alexander E. Kel, Ellen Gößling, Ingmar Reuter, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender: MATCHTM: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Research 31(13): 3576-3579 (2003)

Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender: Recognition of multiple patterns in unaligned sets of sequences. Comparison of kernel clustering method with other methods. German Conference on Bioinformatics 2003: 63-68

Maciej Swat, Alexander E. Kel, Szymon M. Kielbasa, Hanspeter Herzel: Modeling the G1/S transition in mammals -Bifurcation an alysis of elementary modules. German Conference on Bioinformatics 2003: 147-152

Evgeny Cheremushkin, Alexander E. Kel: Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals. Pacific Symposium on Biocomputing 2003: 291-302

Olga V. Kel-Margoulis, Alexander E. Kel, Ingmar Reuter, Igor Deineko, Edgar Wingender: TRANSCompel®: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Research 30(1): 332-334 (2002)

Olga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender, Alexander E. Kel: Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters. Pacific Symposium on Biocomputing 2002: 187-198

Alexander E. Kel, Olga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender: ClusterScan: A Tool for Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters. German Conference on Bioinformatics 2001: 96-101

Ellen Gößling, Olga V. Kel-Margoulis, Alexander E. Kel, Edgar Wingender: MATCH^TM - a tool for searching transcription factor binding sites in DNA sequences. Application for the analysis of human chromosomes. German Conference on Bioinformatics 2001: 158-161

Olga V. Kel-Margoulis, Igor Deineko, Ingmar Reuter, Edgar Wingender, Alexander E. Kel: TRANSCompel® - a professional database on composite regulatory elements in eukaryotic genes. German Conference on Bioinformatics 2001: 185-187

Nikolay A. Kolchanov, Olga A. Podkolodnaya, Elena A. Ananko, Elena V. Ignatieva, Irina L. Stepanenko, Olga V. Kel-Margoulis, Alexander E. Kel, Tatyana I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, I. M. Korostishevskaya, Aida G. Romashchenko, G. Christian Overton: Transcription Regulatory Regions Database (TRRD): its status in 2000. Nucleic Acids Research 28(1): 298-301 (2000)

Olga V. Kel-Margoulis, Aida G. Romashchenko, Nikolay A. Kolchanov, Edgar Wingender, Alexander E. Kel: COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Research 28(1): 311-315 (2000)

Yuri Tikunov, Alexander E. Kel: Kernel Method for Estimation of Functional Site Local Consensi: Classification of Transcription Initiation Sites in Eukaryotic Genes. German Conference on Bioinformatics 2000: 83-88

Alexander E. Kel, Igor Deineko, Olga V. Kel-Margoulis, Edgar Wingender, Vadim Ratner: Modeling of Gene Regulatory Network of Cell Cycle Control. Role of E2F Feedback Loops. German Conference on Bioinformatics 2000: 107-114

Nikolay A. Kolchanov, Elena A. Ananko, Olga A. Podkolodnaya, Elena V. Ignatieva, Irina L. Stepanenko, Olga V. Kel-Margoulis, Alexander E. Kel, Tatyana I. Merkulova, T. N. Goryachkovskaya, T. V. Busygina, F. A. Kolpakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, Aida G. Romashchenko: Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Research 27(1): 303-306 (1999)

T. Heinemeyer, Xin Chen, Holger Karas, Alexander E. Kel, Olga V. Kel-Margoulis, Ines Liebich, T. Meinhardt, Ingmar Reuter, Frank Schacherer, Edgar Wingender: Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Research 27(1): 318-322 (1999)

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender: E2F composite units in promoters of cell cycle genes. German Conference on Bioinformatics 1999: 148-154

Alexander E. Kel, Andrey A. Ptitsyn, Vladimir N. Babenko, Sebastian Meier-Ewert, Hans Lehrach: A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily. Bioinformatics 14(3): 259-270 (1998)

T. Heinemeyer, Edgar Wingender, Ingmar Reuter, Henning Hermjakob, Alexander E. Kel, Olga V. Kel-Margoulis, Elena V. Ignatieva, Elena A. Ananko, Olga A. Podkolodnaya, F. A. Kolpakov, Nikolay L. Podkolodny, Nikolay A. Kolchanov: Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Research 26(1): 362-367 (1998)

Alexander E. Kel, Olga V. Kel-Margoulis, Vladimir N. Babenko, Nikolay A. Kolchanov, Edgar Wingender: Combinatorial identification of promoters induced upon immune cell activation. German Conference on Bioinformatics 1998

Edgar Wingender, Xin Chen, T. Heinemeyer, Alexander E. Kel, Ines Liebich, T. Meinhardt: A hierarchy of databases for modeling gene regulatory mechanisms. German Conference on Bioinformatics 1998

Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Alexander E. Kel, Y. V. Kondrakhin, Anatoly S. Frolov, F. A. Kolpakov, T. N. Goryachkovskaya, O. V. Kel, Elena A. Ananko, Elena V. Ignatieva, Olga A. Podkolodnaya, Vladimir N. Babenko, Irina L. Stepanenko, Aida G. Romashchenko, Tatyana I. Merkulova, Denis G. Vorobiev, Sergey V. Lavryushev, Y. V. Ponomarenko, Alexey V. Kochetov, G. B. Kolesov, Victor V. Solovyev, Luciano Milanesi, Nikolay L. Podkolodny, Edgar Wingender, T. Heinemeyer: GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. ISMB 1998: 95-104

Edgar Wingender, Alexander E. Kel, Olga V. Kel-Margoulis, Holger Karas, T. Heinemeyer, P. Dietze, R. Knüppel, Aida G. Romashchenko, Nikolay A. Kolchanov: TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Research 25(1): 265-268 (1997)

Alexander E. Kel, Andrey A. Ptitsyn, Vladimir N. Babenko, Sebastian Meier-Ewert, Hans Lehrach: A genetic algorithm for designing gene family specific oligonucleotide sets used for hybridization. The G Protein-coupled receptor Protein superfamily.. German Conference on Bioinformatics 1997: 53-55

Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov: Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD). German Conference on Bioinformatics 1997: 153-154

Mikhail P. Ponomarenko, Julia V. Ponomarenko, Alexander E. Kel, Nikolay A. Kolchanov, N. Karas, Edgar Wingender, Heinz Sklenar: Identification of the significant conformational features of functional sites in B-DNA. German Conference on Bioinformatics 1997: 171

Alexander E. Kel, O. V. Kel, Oleg V. Vishnevsky, Mikhail P. Ponomarenko, I. V. Ischenko, Holger Karas, Edgar Wingender, Nikolay A. Kolchanov, Heinz Sklenar: TRRD and COMPEL Databases on Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences. German Conference on Bioinformatics - Selected Papers 1996: 99-105

Alexander E. Kel, O. V. Kel, I. V. Ischenko, Nikolay A. Kolchanov, Holger Karas, Edgar Wingender, Heinz Sklenar: TRRD and COMPEL Databases an Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences. German Conference on Bioinformatics 1996: 113-117

I. V. Ischenko, Alexey V. Kochetov, Alexander E. Kel, Nikolay A. Kolchanov, L. L. Kisselev: Comparative Analysis of the Secondary Structure of mRNA Encoded by High- and Low-Expression Eukaryotic Genes. German Conference on Bioinformatics 1996: 124-129

Elena A. Ananko, Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov: WWWTRRD: Hypertext Information System an Transcription Regulation. German Conference on Bioinformatics 1996: 153-155

Alexander E. Kel, M. Philipenko, Vladimir N. Babenko, Nikolay A. Kolchanov: Genetic Algorithm for Selection of Oligonucleotides for Identification by Hybridisation of Genomic DNA Fragments Possessing Gene Potential. German Conference on Bioinformatics 1996: 238-240

Y. V. Kondrakhin, F. A. Kolpakov, Alexander E. Kel, Nikolay A. Kolchanov, Luciano Milanesi: Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. German Conference on Bioinformatics 1996: 247-250

Y. V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi: Eukaryotic promoter recognition by binding sites for transcription factors. Computer Applications in the Biosciences 11(5): 477-488 (1995)

O. V. Kel, A. G. Romachenko, Alexander E. Kel, Andrey N. Naumochkin, Nikolay A. Kolchanov: Data representation in the TRRD-a database of transcription regulatory regions of the eukaryotic genomes. HICSS (5) 1995: 42-51

Alexander E. Kel, Y. V. Kondrakhin, Ph. A. Kolpakov, O. V. Kel, Aida G. Romashchenko, Edgar Wingender, Luciano Milanesi, Nikolay A. Kolchanov: Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences. ISMB 1995: 197-205

Nikolay A. Kolchanov, Oleg V. Vishnevsky, Vladimir N. Babenko, Alexander E. Kel, Ilya N. Shindyalov: Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and Application. ISMB 1995: 206-214

Alexander E. Kel, Mikhail P. Ponomarenko, E. A. Likhachev, Yuri L. Orlov, I. V. Ischenko, Luciano Milanesi, Nikolay A. Kolchanov: SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Computer Applications in the Biosciences 9(6): 617-627 (1993)