Alexander E. Kel

发表

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms

T. Heinemeyer, Xin Chen, Holger Karas, 1999, Nucleic Acids Res..

BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes

Alexander E. Kel, Andrey Kechin, Evgeniy Khrapov, 2018, Comput. Biol. Chem..

Combinatorial identification of promoters induced upon immune cell activation

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 1998, German Conference on Bioinformatics.

TiProD: the Tissue-specific Promoter Database

Xin Chen, Alexander E. Kel, Edgar Wingender, 2005, Nucleic Acids Res..

MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2013, BMC Bioinformatics.

Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2005, German Conference on Bioinformatics.

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

Alexander E. Kel, Edgar Wingender, Jürgen Borlak, 2013, PLoS Comput. Biol..

Transcription Regulatory Regions Database (TRRD): its status in 1999

Alexander E. Kel, Olga V. Kel-Margoulis, Andrey N. Naumochkin, 1999, Nucleic Acids Res..

TRANSCompel®: a database on composite regulatory elements in eukaryotic genes

Alexander E. Kel, Olga V. Kel-Margoulis, Ingmar Reuter, 2002, Nucleic Acids Res..

Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and Application

Alexander E. Kel, Ilya N. Shindyalov, Nikolay A. Kolchanov, 1995, ISMB.

Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies

Alexander E. Kel, Philip Stegmaier, Denitsa Alamanova, 2010, BMC Bioinformatics.

Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates

Alexander E. Kel, Vladimir Poroikov, Alexey Lagunin, 2010, BMC Bioinformatics.

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

Alexander E. Kel, Tagir F. Valeev, Fedor A. Kolpakov, 2016, Nucleic Acids Res..

HSALBGC HSALDB 2 HSALPHA HSATPSY 1 HSC 1 A 1 HSC 4 AB HSCFVH HSERYA HSFBRGG HSFESFPS HSGHVA HSGRP 78 HSGSTPIG HSHLIC HSHSC 70 HSIG 05 HSIGJ 2 HSIL 1 B HSINT

Alexander E. Kel, Yuriy L. Orlov, Nikolay A. Kolchanov, 2005 .

CYCLONET—an integrated database on cell cycle regulation and carcinogenesis

Alexander E. Kel, Luciano Milanesi, Vladimir Poroikov, 2007, Nucleic Acids Res..

Comparative Analysis of the Secondary Structure of mRNA Encoded by High- and Low-Expression Eukaryotic Genes

Alexander E. Kel, Nikolay A. Kolchanov, Alexey V. Kochetov, 1996, German Conference on Bioinformatics.

cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing

Alexander E. Kel, Andrey Kechin, Uljana Boyarskikh, 2017, J. Comput. Biol..

FeatureScan: revealing property-dependent similarity of nucleotide sequences

Alexander E. Kel, Igor V. Deyneko, Gerhard Kauer, 2006, Nucleic Acids Res..

Application of Kernel Method to Reveal Subtypes of TF Binding Motifs

Alexander E. Kel, Edgar Wingender, Jürgen Borlak, 2004, Regulatory Genomics.

E2F composite units in promoters of cell cycle genes

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 1999, German Conference on Bioinformatics.

Modeling of Gene Regulatory Network of Cell Cycle Control. Role of E2F Feedback Loops

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2000, German Conference on Bioinformatics.

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2000, Nucleic Acids Res..

A hierarchy of databases for modeling gene regulatory mechanisms

T. Heinemeyer, Xin Chen, Alexander E. Kel, 1998, German Conference on Bioinformatics.

DATABASES ON GENE REGULATION

Alexander E. Kel, Olga V. Kel-Margoulis, Ines Liebich, 2005 .

Kernel Method for Estimation of Functional Site Local Consensi: Classification of Transcription Initiation Sites in Eukaryotic Genes

Alexander E. Kel, Yuri Tikunov, 2000, German Conference on Bioinformatics.

Recognition of multiple patterns in unaligned sets of sequences. Comparison of kernel clustering method with other methods

Alexander E. Kel, Edgar Wingender, Nico Voss, 2003, German Conference on Bioinformatics.

Eukaryotic promoter recognition by binding sites for transcription factors

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1995, Comput. Appl. Biosci..

TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes

Alexander E. Kel, Olga V. Kel-Margoulis, Ines Liebich, 2005, Nucleic Acids Res..

TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations

Alexander E. Kel, Olga V. Kel-Margoulis, Ingmar Reuter, 2005, Nucleic Acids Res..

Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1996, German Conference on Bioinformatics.

TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation

T. Heinemeyer, Holger Karas, Alexander E. Kel, 1997, Nucleic Acids Res..

Identification of the significant conformational features of functional sites in B-DNA

Alexander E. Kel, Edgar Wingender, Nikolay A. Kolchanov, 1997, German Conference on Bioinformatics.

3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations

Alexander E. Kel, Razif R. Gabdoulline, Philip Stegmaier, 2012, Nucleic Acids Res..

Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer

Alexander E. Kel, Fedor A. Kolpakov, Yury V. Kondrakhin, 2008, Silico Biol..

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2019, BMC Bioinformatics.

Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods

Alexander E. Kel, Edgar Wingender, Ekaterina Shelest, 2003, Silico Biol..

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL

T. Heinemeyer, Alexander E. Kel, Olga V. Kel-Margoulis, 1998, Nucleic Acids Res..

Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals

Alexander E. Kel, Evgeny Cheremushkin, 2003, Pacific Symposium on Biocomputing.

Computer analysis and recognition of human splice sites

Alexander E. Kel, Igor B. Rogozin, Nikolay A. Kolchanov, 1991 .

Modeling the G1/S transition in mammals -Bifurcation an alysis of elementary modules

Alexander E. Kel, Szymon M. Kielbasa, Hanspeter Herzel, 2003, German Conference on Bioinformatics.

WWWTRRD: Hypertext Information System an Transcription Regulation

Alexander E. Kel, Nikolay A. Kolchanov, Elena A. Ananko, 1996, German Conference on Bioinformatics.

Transcription Regulatory Regions Database (TRRD): its status in 2000

Alexander E. Kel, Olga V. Kel-Margoulis, G. Christian Overton, 2000, Nucleic Acids Res..

A genetic algorithm for designing gene family specific oligonucleotide sets used for hybridization. The G Protein-coupled receptor Protein superfamily

Alexander E. Kel, Hans Lehrach, Vladimir N. Babenko, 1997, German Conference on Bioinformatics.

INTEGRATING THE KNOWLEDGE ON GENE REGULATION BY A FEDERATED DATABASE APPROACH : TRANSFAC, TRRD, AND COMPEL

Holger Karas, Alexander E. Kel, Nikolay A. Kolchanov, 1997 .

Data representation in the TRRD-a database of transcription regulatory regions of the eukaryotic genomes

Alexander E. Kel, Andrey N. Naumochkin, Nikolay A. Kolchanov, 1995, Proceedings of the Twenty-Eighth Annual Hawaii International Conference on System Sciences.

Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2001, Pacific Symposium on Biocomputing.

MATCHTM: a tool for searching transcription factor binding sites in DNA sequences

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2003, Nucleic Acids Res..

Building a knowledge base for systems pathology

Alexander E. Kel, Olga V. Kel-Margoulis, Frank Schacherer, 2008, Briefings Bioinform..

TRANSCompel® - a professional database on composite regulatory elements in eukaryotic genes

Alexander E. Kel, Olga V. Kel-Margoulis, Ingmar Reuter, 2001, German Conference on Bioinformatics.

TRANSFAC®: transcriptional regulation, from patterns to profiles

Alexander E. Kel, Olga V. Kel-Margoulis, Ingmar Reuter, 2003, Nucleic Acids Res..

Composition-sensitive analysis of the human genome for regulatory signals

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2003, Silico Biol..

Molecular mechanistic associations of human diseases

Alexander E. Kel, Edgar Wingender, Mathias Krull, 2010, BMC Systems Biology.

GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome

T. Heinemeyer, Alexander E. Kel, Edgar Wingender, 1998, ISMB.

Large-scale collection and characterization of promoters of human and mouse genes

Alexander E. Kel, Kenta Nakai, Toshihisa Takagi, 2004, Silico Biol..

Beyond microarrays: Finding key transcription factors controlling signal transduction pathways

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2006, BMC Bioinformatics.

Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD)

Alexander E. Kel, Nikolay A. Kolchanov, Elena V. Ignatieva, 1997, German Conference on Bioinformatics.

Recognition of cis-Regulatory Elements with Vombat

Alexander E. Kel, Ivo Grosse, Stefan Posch, 2007, J. Bioinform. Comput. Biol..

Genetic Algorithm for Selection of Oligonucleotides for Identification by Hybridisation of Genomic DNA Fragments Possessing Gene Potential

Alexander E. Kel, Nikolay A. Kolchanov, Vladimir N. Babenko, 1996, German Conference on Bioinformatics.

Bifurcation analysis of the regulatory modules of the mammalian G1/S transition

Alexander E. Kel, Hanspeter Herzel, Maciej Swat, 2004, Bioinform..

Supervised Posteriors for DNA-motif Classification

Alexander E. Kel, Jens Keilwagen, Ivo Grosse, 2007, German Conference on Bioinformatics.

Transcription Factor Databases

Alexander E. Kel, Mathias Krull, Edgar Wingender, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences

Alexander E. Kel, Edgar Wingender, Luciano Milanesi, 1995, ISMB.

TRANSCRIPTION REGULATORY REGIONS DATABASE (TRRD)

Alexander E. Kel, Olga V. Kel-Margoulis, O. A. Podkolodnaya, 2000 .

Signal-Theoretical DNA Similarity Measure Revealing Unexpected Similarities of E. coli Promoters

Alexander E. Kel, Igor V. Deyneko, Gerhard Kauer, 2005, Silico Biol..

From Composite Patters to Pathways - Prediction of Key Regulators of Gene Expression

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2004, German Conference on Bioinformatics.

geneXplainR: An R interface for the geneXplain platform

Alexander E. Kel, Edgar Wingender, Philip Stegmaier, 2017, J. Open Source Softw..

Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data

Alexander E. Kel, Tatiana Konovalova, Tagir F. Valeev, 2005, ICNC.

Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2006, Bioinform..

GTRD: an integrated view of transcription regulation

Alexander E. Kel, Vsevolod J. Makeev, Fedor A. Kolpakov, 2020, Nucleic Acids Res..

Databases and Tools for in silico Analysis of Regulation of Gene Expression

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2005 .

GeneXplain — Identification of Causal Biomarkers and Drug Targets in Personalized Cancer Pathways

Alexander E. Kel, F. A. Kolpakov, Galina Selivanova, 2011 .

“Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data

Alexander E. Kel, Edgar Wingender, Philip Stegmaier, 2015, Microarrays.

GenViewer: A computing tool for protein-coding regions prediction in nucleotide sequences

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1993 .

REGULATION OF TRANSCRIPTION OF LIPID METABOLISM GENES : DESCRIPTION IN THETRRD DATABASE

Alexander E. Kel, Tatyana I. Merkulova, Ignat'eva Ev, 1997 .

Multi-omics “upstream analysis” of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer

Alexander E. Kel, Olga V. Kel-Margoulis, Edgar Wingender, 2016, EuPA open proteomics.

COMPUTER ANALYSIS AND RECOGNITION OF FUNCTIONAL SITES VIA OLIGONUCLEOTIDE PATTERN DISTRIBUTIONS

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1993 .