Alexander E. Kel

Publication Activity (10 Years)

Years Active: 1993-2022
Publications (10 Years): 8

Top Topics

Colorectal Cancer

Unsupervised Clustering

Top Venues

Nucleic Acids Res.

J. Comput. Biol.

Comput. Biol. Chem.

Publications

Fedor A. Kolpakov, Ilya R. Akberdin, Ilya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Mikhail Kulyashov, Elena Kutumova, Sergey Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Sergey Zhatchenko, Alexander E. Kel
BioUML - towards a universal research platform. Nucleic Acids Res. 50 (W1) (2022)
Semyon Kolmykov, Ivan S. Yevshin, Mikhail Kulyashov, Ruslan N. Sharipov, Yury V. Kondrakhin, Vsevolod J. Makeev, Ivan V. Kulakovskiy, Alexander E. Kel, Fedor A. Kolpakov
GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 49 (Database-Issue) (2021)
Alexander E. Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan S. Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga V. Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor A. Kolpakov, Maxim Filipenko, Edgar Wingender
Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. BMC Bioinform. (4) (2019)
Fedor A. Kolpakov, Ilya R. Akberdin, Timur A. Kashapov, llya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Elena Kutumova, Nikita Mandrik, Sergey S. Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Alexander E. Kel
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Andrey Kechin, Evgeniy Khrapov, Uljana Boyarskikh, Alexander E. Kel, Maxim Filipenko
BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes. Comput. Biol. Chem. 77 (2018)
Philip Stegmaier, Alexander E. Kel, Edgar Wingender
geneXplainR: An R interface for the geneXplain platform. J. Open Source Softw. 2 (18) (2017)
Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res. 45 (Database-Issue) (2017)
Andrey Kechin, Uljana Boyarskikh, Alexander E. Kel, Maxim Filipenko
cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. J. Comput. Biol. 24 (11) (2017)
Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander E. Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinform. 15 (S-1) (2014)
Igor V. Deyneko, Alexander E. Kel, Olga V. Kel-Margoulis, Elena V. Deineko, Edgar Wingender, Siegfried Weiss
MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters. BMC Bioinform. 14 (2013)
Eugene Kolker, Vural Özdemir, Lennart Martens, William Hancock, Gordon A. Anderson, Nathaniel Anderson, Sukru Aynacioglu, Ancha V. Baranova, Shawn R. Campagna, Rui Chen, John Choiniere, Stephen P. Dearth, Wu-Chun Feng, Lynnette Ferguson, Geoffrey C. Fox, Dmitrij Frishman, Robert Grossman, Allison P. Heath, Roger Higdon, Mara H. Hutz, Imre Janko, Lihua Jiang, Sanjay Joshi, Alexander E. Kel, Joseph W. Kemnitz, Isaac S. Kohane, Natali Kolker, Doron Lancet, Elaine Lee, Weizhong Li, Andrey Lisitsa, Adrian Llerena, Courtney MacNealy-Koch, Jean-Claude Marshall, Paola Masuzzo, Amanda May, George Mias, Matthew E. Monroe, Elizabeth Montague, Sean Mooney, Alexey I. Nesvizhskii, Santosh Noronha, Gilbert S. Omenn, Harsha Rajasimha, Preveen Ramamoorthy, Jerry Sheehan, Larry Smarr, Charles V. Smith, Todd Smith, Michael Snyder, Srikanth Rapole, Sanjeeva Srivastava, Larissa Stanberry, Elizabeth Stewart, Stefano Toppo, Peter Uetz, Kenneth Verheggen, Brynn H. Voy, Louise Warnich, Steven W. Wilhelm, Gregory Yandl
Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data 1 (4) (2013)
Philip Stegmaier, Alexander E. Kel, Edgar Wingender, Jürgen Borlak
A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs. PLoS Comput. Biol. 9 (3) (2013)
Razif R. Gabdoulline, Denitsa Eckweiler, Alexander E. Kel, Philip Stegmaier
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res. 40 (Web-Server-Issue) (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 Bioinform. 11 (2010)
Boris Sobolev, Dmitry Filimonov, Alexey Lagunin, Alexey V. 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 Bioinform. 11 (2010)
Philip Stegmaier, Mathias Krull, Nico Voss, Alexander E. Kel, Edgar Wingender
Molecular mechanistic associations of human diseases. BMC Syst. Biol. 4 (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 Bioinform. 9 (6) (2008)
Yury V. Kondrakhin, Ruslan N. Sharipov, Alexander E. Kel, Fedor A. Kolpakov
Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer. Silico Biol. 8 (5-6) (2008)
Stefan Posch, Jan Grau, André Gohr, Irad E. Ben-Gal, Alexander E. Kel, Ivo Grosse
Recognition of cis-Regulatory Elements with Vombat. J. Bioinform. Comput. Biol. 5 (2b) (2007)
Jan Grau, Jens Keilwagen, Alexander E. Kel, Ivo Grosse, Stefan Posch
Supervised Posteriors for DNA-motif Classification. German Conference on Bioinformatics (2007)
Fedor A. Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey V. Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res. 35 (Database-Issue) (2007)
Xin Chen, Jianmin Wu, Klaus Hornischer, Alexander E. Kel, Edgar Wingender
TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res. 34 (Database-Issue) (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
: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34 (Database-Issue) (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
: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34 (Database-Issue) (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 Res. 34 (Web-Server-Issue) (2006)
Alexander E. Kel, Nico Voss, Ruy Jáuregui, Olga V. Kel-Margoulis, Edgar Wingender
Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. BMC Bioinform. 7 (S-2) (2006)
T. Waleev, Dmitry 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 Res. 34 (Web-Server-Issue) (2006)
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. Bioinform. 22 (10) (2006)
Igor V. Deyneko, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer
Signal-Theoretical DNA Similarity Measure Revealing Unexpected Similarities of E. coli Promoters. Silico Biol. 5 (5-6) (2005)
Tatiana Konovalova, Tagir F. Valeev, Evgeny Cheremushkin, Alexander E. Kel
Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data. ICNC (2) (2005)
Alexander E. Kel, Tatiana Konovalova, Tagir F. 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)
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)
Maciej Swat, Alexander E. Kel, Hanspeter Herzel
Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. Bioinform. 20 (10) (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. Silico Biol. 4 (4) (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. Bioinform. 20 (10) (2004)
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)
Ekaterina Shelest, Alexander E. Kel, Ellen Gößling, Edgar Wingender
Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods. Silico Biol. 3 (1-2) (2003)
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)
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. Silico Biol. 3 (1-2) (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)
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 Res. 31 (13) (2003)
Evgeny Cheremushkin, Alexander E. Kel
Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals. Pacific Symposium on Biocomputing (2003)
V. Matys, Ellen Fricke, R. Geffers, Ellen Gößling, Martin Haubrock, Reinhard 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 Res. 31 (1) (2003)
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 Res. 30 (1) (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)
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)
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)
Ellen Gößling, Olga V. Kel-Margoulis, Alexander E. Kel, Edgar Wingender
- a tool for searching transcription factor binding sites in DNA sequences. Application for the analysis of human chromosomes. German Conference on Bioinformatics (2001)
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)
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 Res. 28 (1) (2000)
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, Fedor 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 Res. 28 (1) (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)
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 Res. 27 (1) (1999)
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, Fedor A. Kolpakov, Nikolay L. Podkolodny, Andrey N. Naumochkin, Aida G. Romashchenko
Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res. 27 (1) (1999)
Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender
E2F composite units in promoters of cell cycle genes. German Conference on Bioinformatics (1999)
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, Yury V. Kondrakhin, Anatoly S. Frolov, Fedor 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)
T. Heinemeyer, Edgar Wingender, Ingmar Reuter, Henning Hermjakob, Alexander E. Kel, Olga V. Kel-Margoulis, Elena V. Ignatieva, Elena A. Ananko, Olga A. Podkolodnaya, Fedor A. Kolpakov, Nikolay L. Podkolodny, Nikolay A. Kolchanov
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 26 (1) (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)
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. Bioinform. 14 (3) (1998)
Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov
Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD). German Conference on Bioinformatics (1997)
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)
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)
Edgar Wingender, Alexander E. Kel, Olga V. Kel-Margoulis, Holger Karas, T. Heinemeyer, P. Dietze, Rainer Knüppel, Aida G. Romashchenko, Nikolay A. Kolchanov
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res. 25 (1) (1997)
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)
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)
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)
Yury V. Kondrakhin, Fedor 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)
Elena A. Ananko, Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov
WWWTRRD: Hypertext Information System an Transcription Regulation. German Conference on Bioinformatics (1996)
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)
Yury V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi
Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11 (5) (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)
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)
Alexander E. Kel, Yury 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)
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. Comput. Appl. Biosci. 9 (6) (1993)