Alexander E. Kel

76 papers A 3Misc 2Journal 45Unranked 25

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	BioUML - towards a universal research platform. Nucleic Acids Res. Fedor A. Kolpakov, Ilya R. Akberdin, Ilya Kiselev, Semyon Kolmykov, Yury V. Kondrakhin, Mikhail Kulyashov, Elena Kutumova, Sergey S. Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Sergey Zhatchenko, Alexander E. Kel
2021	J	`jnl`	GTRD: an integrated view of transcription regulation. Nucleic Acids Res. 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
2019	J	`jnl`	BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. Nucleic Acids Res. 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
2019	—	`ch.`	Transcription Factor Databases. Encyclopedia of Bioinformatics and Computational Biology (2) Edgar Wingender, Alexander E. Kel, Mathias Krull
2019	J	`jnl`	Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. BMC Bioinform. 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
2018	J	`jnl`	BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes. Comput. Biol. Chem. Andrey Kechin, Evgeniy Khrapov, Uljana Boyarskikh, Alexander E. Kel, Maxim Filipenko
2017	J	`jnl`	GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. Nucleic Acids Res. Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov
2017	J	`jnl`	cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing. J. Comput. Biol. Andrey Kechin, Uljana Boyarskikh, Alexander E. Kel, Maxim Filipenko
2017	J	`jnl`	geneXplainR: An R interface for the geneXplain platform. J. Open Source Softw. Philip Stegmaier, Alexander E. Kel, Edgar Wingender
2014	J	`jnl`	Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinform. Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander E. Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
2013	J	`jnl`	A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs. PLoS Comput. Biol. Philip Stegmaier, Alexander E. Kel, Edgar Wingender, Jürgen Borlak
2013	J	`jnl`	MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters. BMC Bioinform. Igor V. Deyneko, Alexander E. Kel, Olga V. Kel-Margoulis, Elena V. Deineko, Edgar Wingender, Siegfried Weiss
2013	J	`jnl`	Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications. Big Data 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 D. 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
2012	J	`jnl`	3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations. Nucleic Acids Res. Razif R. Gabdoulline, Denitsa Eckweiler, Alexander E. Kel, Philip Stegmaier
2010	J	`jnl`	Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. BMC Bioinform. Denitsa Alamanova, Philip Stegmaier, Alexander E. Kel
2010	J	`jnl`	Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. BMC Bioinform. Boris Sobolev, Dmitry Filimonov, Alexey Lagunin, Alexey V. Zakharov, Olga Koborova, Alexander E. Kel, Vladimir Poroikov
2010	J	`jnl`	Molecular mechanistic associations of human diseases. BMC Syst. Biol. Philip Stegmaier, Mathias Krull, Nico Voss, Alexander E. Kel, Edgar Wingender
2008	J	`jnl`	Building a knowledge base for systems pathology. Briefings Bioinform. Holger Michael, Jennifer Hogan, Alexander E. Kel, Olga V. Kel-Margoulis, Frank Schacherer, Nico Voss, Edgar Wingender
2008	J	`jnl`	Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer. Silico Biol. Yury V. Kondrakhin, Ruslan N. Sharipov, Alexander E. Kel, Fedor A. Kolpakov
2007	J	`jnl`	CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res. Fedor A. Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey V. Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel
2007	J	`jnl`	Recognition of cis-Regulatory Elements with Vombat. J. Bioinform. Comput. Biol. Stefan Posch, Jan Grau, André Gohr, Irad E. Ben-Gal, Alexander E. Kel, Ivo Grosse
2007	—	`conf`	Supervised Posteriors for DNA-motif Classification. German Conference on Bioinformatics Jan Grau, Jens Keilwagen, Alexander E. Kel, Ivo Grosse, Stefan Posch
2006	J	`jnl`	Beyond microarrays: Finding key transcription factors controlling signal transduction pathways. BMC Bioinform. Alexander E. Kel, Nico Voss, Ruy Jáuregui, Olga V. Kel-Margoulis, Edgar Wingender
2006	J	`jnl`	Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations. Bioinform. Alexander E. Kel, Tatiana Konovalova, T. Waleev, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender
2006	J	`jnl`	Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm. Nucleic Acids Res. T. Waleev, Dmitry Shtokalo, Tatiana Konovalova, Nico Voss, Evgeny Cheremushkin, Philip Stegmaier, Olga V. Kel-Margoulis, Edgar Wingender, Alexander E. Kel
2006	J	`jnl`	FeatureScan: revealing property-dependent similarity of nucleotide sequences. Nucleic Acids Res. Igor V. Deyneko, Björn Bredohl, Daniel Wesely, Yulia M. Kalybaeva, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer
2006	J	`jnl`	TRANSFAC Nucleic Acids Res. 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
2006	J	`jnl`	TRANSPATH Nucleic Acids Res. 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
2006	J	`jnl`	TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res. Xin Chen, Jianmin Wu, Klaus Hornischer, Alexander E. Kel, Edgar Wingender
2005	—	`conf`	Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation. German Conference on Bioinformatics Alexander E. Kel, Tatiana Konovalova, Tagir F. Valeev, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender
2005	—	`conf`	Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data. ICNC (2) Tatiana Konovalova, Tagir F. Valeev, Evgeny Cheremushkin, Alexander E. Kel
2005	J	`jnl`	Signal-Theoretical DNA Similarity Measure Revealing Unexpected Similarities of E. coli Promoters. Silico Biol. Igor V. Deyneko, Alexander E. Kel, Helmut Blöcker, Gerhard Kauer
2004	—	`conf`	Application of Kernel Method to Reveal Subtypes of TF Binding Motifs. Regulatory Genomics Alexander E. Kel, Yuri Tikunov, Nico Voss, Jürgen Borlak, Edgar Wingender
2004	J	`jnl`	Bifurcation analysis of the regulatory modules of the mammalian G1/S transition. Bioinform. Maciej Swat, Alexander E. Kel, Hanspeter Herzel
2004	—	`conf`	From Composite Patters to Pathways - Prediction of Key Regulators of Gene Expression. German Conference on Bioinformatics Alexander E. Kel, Nico Voss, Tatiana Konovalova, Dmitri Tchekmenev, P. Wabnitz, Olga V. Kel-Margoulis, Edgar Wingender
2004	J	`jnl`	Large-scale collection and characterization of promoters of human and mouse genes. Silico Biol. 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
2004	J	`jnl`	Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods. Bioinform. Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender
2003	J	`jnl`	Composition-sensitive analysis of the human genome for regulatory signals. Silico Biol. Olga V. Kel-Margoulis, Dmitri Tchekmenev, Alexander E. Kel, Ellen Gößling, Klaus Hornischer, Birgit Lewicki-Potapov, Edgar Wingender
2003	J	`jnl`	MATCHTM: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. Alexander E. Kel, Ellen Gößling, Ingmar Reuter, Evgeny Cheremushkin, Olga V. Kel-Margoulis, Edgar Wingender
2003	—	`conf`	Modeling the G1/S transition in mammals -Bifurcation an alysis of elementary modules. German Conference on Bioinformatics Maciej Swat, Alexander E. Kel, Szymon M. Kielbasa, Hanspeter Herzel
2003	J	`jnl`	Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods. Silico Biol. Ekaterina Shelest, Alexander E. Kel, Ellen Gößling, Edgar Wingender
2003	—	`conf`	Recognition of multiple patterns in unaligned sets of sequences. Comparison of kernel clustering method with other methods. German Conference on Bioinformatics Alexander E. Kel, Yuri Tikunov, Nico Voss, Edgar Wingender
2003	J	`jnl`	TRANSFAC®: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 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
2003	Misc	`conf`	Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals. Pacific Symposium on Biocomputing Evgeny Cheremushkin, Alexander E. Kel
2002	Misc	`conf`	Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters. Pacific Symposium on Biocomputing Olga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender, Alexander E. Kel
2002	J	`jnl`	TRANSCompel®: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res. Olga V. Kel-Margoulis, Alexander E. Kel, Ingmar Reuter, Igor Deineko, Edgar Wingender
2001	—	`conf`	ClusterScan: A Tool for Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters. German Conference on Bioinformatics Alexander E. Kel, Olga V. Kel-Margoulis, T. G. Ivanova, Edgar Wingender
2001	—	`conf`	MATCH German Conference on Bioinformatics Ellen Gößling, Olga V. Kel-Margoulis, Alexander E. Kel, Edgar Wingender
2001	—	`conf`	TRANSCompel® - a professional database on composite regulatory elements in eukaryotic genes. German Conference on Bioinformatics Olga V. Kel-Margoulis, Igor Deineko, Ingmar Reuter, Edgar Wingender, Alexander E. Kel
2000	J	`jnl`	COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res. Olga V. Kel-Margoulis, Aida G. Romashchenko, Nikolay A. Kolchanov, Edgar Wingender, Alexander E. Kel
2000	—	`conf`	Kernel Method for Estimation of Functional Site Local Consensi: Classification of Transcription Initiation Sites in Eukaryotic Genes. German Conference on Bioinformatics Yuri Tikunov, Alexander E. Kel
2000	—	`conf`	Modeling of Gene Regulatory Network of Cell Cycle Control. Role of E2F Feedback Loops. German Conference on Bioinformatics Alexander E. Kel, Igor Deineko, Olga V. Kel-Margoulis, Edgar Wingender, Vadim Ratner
2000	J	`jnl`	Transcription Regulatory Regions Database (TRRD): its status in 2000. Nucleic Acids Res. 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
1999	—	`conf`	E2F composite units in promoters of cell cycle genes. German Conference on Bioinformatics Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender
1999	J	`jnl`	Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res. T. Heinemeyer, Xin Chen, Holger Karas, Alexander E. Kel, Olga V. Kel-Margoulis, Ines Liebich, T. Meinhardt, Ingmar Reuter, Frank Schacherer, Edgar Wingender
1999	J	`jnl`	Transcription Regulatory Regions Database (TRRD): its status in 1999. Nucleic Acids Res. 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
1998	J	`jnl`	A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily. Bioinform. Alexander E. Kel, Andrey A. Ptitsyn, Vladimir N. Babenko, Sebastian Meier-Ewert, Hans Lehrach
1998	—	`conf`	A hierarchy of databases for modeling gene regulatory mechanisms. German Conference on Bioinformatics Edgar Wingender, Xin Chen, T. Heinemeyer, Alexander E. Kel, Ines Liebich, T. Meinhardt
1998	—	`conf`	Combinatorial identification of promoters induced upon immune cell activation. German Conference on Bioinformatics Alexander E. Kel, Olga V. Kel-Margoulis, Vladimir N. Babenko, Nikolay A. Kolchanov, Edgar Wingender
1998	J	`jnl`	Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 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
1998	A	`conf`	GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. ISMB 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
1997	—	`conf`	A genetic algorithm for designing gene family specific oligonucleotide sets used for hybridization. The G Protein-coupled receptor Protein superfamily.. German Conference on Bioinformatics Alexander E. Kel, Andrey A. Ptitsyn, Vladimir N. Babenko, Sebastian Meier-Ewert, Hans Lehrach
1997	—	`conf`	Identification of the significant conformational features of functional sites in B-DNA. German Conference on Bioinformatics Mikhail P. Ponomarenko, Julia V. Ponomarenko, Alexander E. Kel, Nikolay A. Kolchanov, N. Karas, Edgar Wingender, Heinz Sklenar
1997	—	`conf`	Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD). German Conference on Bioinformatics Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov
1997	J	`jnl`	TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res. Edgar Wingender, Alexander E. Kel, Olga V. Kel-Margoulis, Holger Karas, T. Heinemeyer, P. Dietze, Rainer Knüppel, Aida G. Romashchenko, Nikolay A. Kolchanov
1996	—	`conf`	Comparative Analysis of the Secondary Structure of mRNA Encoded by High- and Low-Expression Eukaryotic Genes. German Conference on Bioinformatics I. V. Ischenko, Alexey V. Kochetov, Alexander E. Kel, Nikolay A. Kolchanov, L. L. Kisselev
1996	—	`conf`	Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. German Conference on Bioinformatics Yury V. Kondrakhin, Fedor A. Kolpakov, Alexander E. Kel, Nikolay A. Kolchanov, Luciano Milanesi
1996	—	`conf`	Genetic Algorithm for Selection of Oligonucleotides for Identification by Hybridisation of Genomic DNA Fragments Possessing Gene Potential. German Conference on Bioinformatics Alexander E. Kel, M. Philipenko, Vladimir N. Babenko, Nikolay A. Kolchanov
1996	—	`conf`	TRRD and COMPEL Databases an Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences. German Conference on Bioinformatics Alexander E. Kel, O. V. Kel, I. V. Ischenko, Nikolay A. Kolchanov, Holger Karas, Edgar Wingender, Heinz Sklenar
1996	—	`conf`	TRRD and COMPEL Databases on Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences. German Conference on Bioinformatics - Selected Papers Alexander E. Kel, O. V. Kel, Oleg V. Vishnevsky, Mikhail P. Ponomarenko, I. V. Ischenko, Holger Karas, Edgar Wingender, Nikolay A. Kolchanov, Heinz Sklenar
1996	—	`conf`	WWWTRRD: Hypertext Information System an Transcription Regulation. German Conference on Bioinformatics Elena A. Ananko, Elena V. Ignatieva, Alexander E. Kel, Nikolay A. Kolchanov
1995	A	`conf`	Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences. ISMB Alexander E. Kel, Yury V. Kondrakhin, Ph. A. Kolpakov, O. V. Kel, Aida G. Romashchenko, Edgar Wingender, Luciano Milanesi, Nikolay A. Kolchanov
1995	—	`conf`	Data representation in the TRRD-a database of transcription regulatory regions of the eukaryotic genomes. HICSS (5) O. V. Kel, A. G. Romachenko, Alexander E. Kel, Andrey N. Naumochkin, Nikolay A. Kolchanov
1995	J	`jnl`	Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. Yury V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi
1995	A	`conf`	Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and Application. ISMB Nikolay A. Kolchanov, Oleg V. Vishnevsky, Vladimir N. Babenko, Alexander E. Kel, Ilya N. Shindyalov
1993	J	`jnl`	SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput. Appl. Biosci. Alexander E. Kel, Mikhail P. Ponomarenko, E. A. Likhachev, Yuri L. Orlov, I. V. Ischenko, Luciano Milanesi, Nikolay A. Kolchanov