A. Kel

K. Hornischer, A. Kel, A. Benkahla, 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

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

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

In Silico Analysis of Regulatory Sequences in the Human Parathyroid Hormone Gene

A. Kel, Maurice Scheer, H. Mayer, 2005 .

Simulation of the Dynamics of Gene Networks Regulating the Cell Cycle in Mammalian Cells

E. Wingender, A. Kel, O. Kel-Margoulis, 2003, Russian Journal of Genetics.

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.

SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites

I. V. Ischenko, E. A. Likhachev, L. Milanesi, 1993, Comput. Appl. Biosci..

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.

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.

Advanced Computational Biology Methods Identify Molecular Switches for Malignancy in an EGF Mouse Model of Liver Cancer

J. Borlak, E. Wingender, A. Kel, 2011, PloS one.

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.

A Novel Computational Approach for the Prediction of Networked Transcription Factors of Aryl Hydrocarbon-Receptor-Regulated Genes

Edgar Wingender, Jürgen Borlak, Susanne Reymann, 2004, Molecular Pharmacology.

DATABASES ON GENE REGULATION

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

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

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

Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease

V. Poroikov, V. M. D. Martins dos Santos, A. Kel, 2020, Disease Models & Mechanisms.

Identification of a novel therapeutic agent for Inflammatory Bowel Disease guided by systems medicine

V. Poroikov, A. Kel, D. Spiller, 2019 .

Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis

V. Makeev, A. Orekhov, M. Bukrinsky, 2018, Current pharmaceutical design.

DNA methylation and gene expression profiling reveal MFAP5 as a regulatory driver of extracellular matrix remodeling in varicose vein disease.

A. Kel, M. Smetanina, A. Shevela, 2018, Epigenomics.

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

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

AUTOGENE: A COMPUTER SYSTEM FOR NUCLEOTIDE SEQUENCE ANALYSIS

L. Milanesi, A. Kel, N. Kolchanov, 1996 .

Computer analysis of the structure of transcription factor binding sites

Yury V. Kondrakhin, Ph. A. Kolpakov, E. Wingender, 1995 .

Method for Recognition of Composite Regulatory Units in Promoters . Analysis of Cell-Cycle Control Genes

E. Wingender, A. Kel, O. Kel-Margoulis, 2000 .

E2F composite units in promoters of cell cycle genes

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

Human-chimpanzee promoter comparisons: property-conserved evolution?

Yulia M. Kalybaeva, H. Blöcker, A. Kel, 2010, Genomics.

Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis

A. Kel, M. Zenkova, N. Salakhutdinov, 2019, Oncotarget.

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Lennart Martens, Stefano Toppo, Geoffrey C. Fox, 2013, Big Data.

Constructing a promoter model for antibacterial response of lung epithelial cells

E. Wingender, A. Kel, E. Shelest, 2003 .

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

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

WWWTRRD: Hypertext Information System an Transcription Regulation

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

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.

BioUML—towards a universal research platform

Yury V. Kondrakhin, F. Kolpakov, A. Kel, 2022, Nucleic Acids Res..

Using systems medicine to identify a therapeutic agent with potential for repurposing in Inflammatory Bowel Disease

V. Poroikov, A. Kel, D. Spiller, 2019, bioRxiv.

Master-regulators driving resistance of non-small cell lung cancer cells to p53 reactivator Nutlin-3

F. Kolpakov, A. Kel, S. Pintus, 2017 .

Data on master regulators and transcription factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer

A. Kel, 2016, Data in brief.

Whole genome transcriptional profiling identifies novel differentiation regulated genes in keratinocytes

J. Mandl, A. Kel, G. Schmitz, 2010, Experimental dermatology.

TRANSFAC (cid:1) and its module TRANSCompel (cid:1) : transcriptional gene regulation in eukaryotes

E. Wingender, K. Hornischer, A. Kel, 2005 .

Equal impact of diffusion and DNA binding rates on the potential spatial distribution of nuclear factor κB transcription factor inside the nucleus

A. Kel, S. Moshkovskii, A. Sycheva, 2014, Biochemistry (Moscow).

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.

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

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

TiProD: the Tissue-specific Promoter Database

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

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..

GTRD: an integrated view of transcription regulation

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

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..

Systematic DNA-binding domain classification of transcription factors.

Edgar Wingender, Philip Stegmaier, Alexander E Kel, 2004, Genome informatics. International Conference on Genome Informatics.

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL

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

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences

Inna Dubchak, Philip Stegmaier, Simon Minovitsky, 2007, BMC Genomics.

Search for Master Regulators in Walking Cancer Pathways.

Alexander E Kel, A. Kel, 2017, Methods in molecular biology.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

Lennart Martens, Doron Lancet, Dmitrij Frishman, 2014, Omics : a journal of integrative biology.

TOWARD MORE TRANSPARENT AND REPRODUCIBLE

Robert L. Grossman, Lennart Martens, Doron Lancet, 2013 .

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..

Mild mitochondrial uncoupling does not affect mitochondrial biogenesis but downregulates pyruvate carboxylase in adipocytes: role for triglyceride content reduction.

A. Kel, T. Arnould, P. Renard, 2012, American journal of physiology. Endocrinology and metabolism.

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

E. Wingender, A. Kel, O. Kel-Margoulis, 2013, BMC Bioinformatics.

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: identification of transcription factor binding site combinations using genetic algorithm

E. Wingender, A. Kel, E. Cheremushkin, 2006, Nucleic Acids Res..

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

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

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

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

Molecular mechanistic associations of human diseases

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

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..

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.

Genome wide prediction of HNF4α functional binding sites by the use of local and global sequence context

Alexander E Kel, A. Kel, V. Matys, 2008, Genome Biology.

Eukaryotic promoter recognition by binding sites for transcription factors

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

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.

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.

P-Match: transcription factor binding site search by combining patterns and weight matrices

D. S. Chekmenev, C. Haid, A. E. Kel, 2005, Nucleic Acids Res..

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.

Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories

A. Kel, E. Cheremushkin, M. Mukerji, 2007, Molecular Genetics and Genomics.

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

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

Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response—What is First?

A. Orekhov, A. Kel, S. Pintus, 2020, International journal of molecular sciences.

Role of Phagocytosis in the Pro-Inflammatory Response in LDL-Induced Foam Cell Formation; a Transcriptome Analysis

A. Orekhov, A. Kel, S. Pintus, 2020, International journal of molecular sciences.

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.

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

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

[Computer system "AutoGene" for automatic analysis of nucleotide sequences].

N A Kolchanov, D A Grigorovich, A A Ptitsyn, 1996, Molekuliarnaia biologiia.

Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences

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

In silico method for identification of promising anticancer drug targets

V V Poroikov, A A Lagunin, D A Filimonov, 2009, SAR and QSAR in environmental research.

Beyond microarrays: Finding key transcription factors controlling signal transduction pathways

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

Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods.

A Srivastava, G Mazzocco, A Kel, 2016, Molecular bioSystems.

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

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

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information

Barend Mons, Marco Masseroli, Stefano Ceri, 2014, BMC Bioinformatics.

Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3

F. Kolpakov, A. Kel, S. Pintus, 2018, BMC Medical Genomics.

Building a knowledge base for systems pathology

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

CYCLONET—an integrated database on cell cycle regulation and carcinogenesis

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

Cyclonet - a database on cell cycle regulation ?

Sb Ras, A E Kel, I Deineko, 2004 .

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..

A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs

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

geneXplainR: An R interface for the geneXplain platform

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

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis

T Kivioja, C. Tonelli, A. Kel, 2012, Cell Death and Differentiation.

Prediction of EVT6-NTRK3-Dependent Papillary Thyroid Cancer Using Minor Expression Profile

A. A. Ivanov, A. Kel, N. Kushlinskii, 2022, Bulletin of Experimental Biology and Medicine.

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.

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

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

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

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

Recognition of cis-Regulatory Elements with Vombat

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

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

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

TRANSFAC®: transcriptional regulation, from patterns to profiles

E. Wingender, R. Geffers, K. Hornischer, 2003, Nucleic Acids Res..

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

E. Wingender, A. Kel, E. Cheremushkin, 2006, Bioinform..

Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm

A. Kel, E. Cheremushkin, O. Kel-Margoulis, 2006, Nucleic Acids Res..

Composite Module Analyst: a Fitness-based Tool for Identification of Transcription Factor Binding Site Combinations

A. Kel, E. Cheremushkin, O. Kel-Margoulis, 2022 .

TRANSPATH®: a high quality database focused on signal transduction : Data integration in functional genomics and proteomics: application to biological pathways

Edgar Wingender, Mathias Krull, Anatolij Potapov, 2004 .

Molecular mechanistic associations of human diseases

E. Wingender, A. Kel, N. Voss, 2010, BMC Systems Biology.

FeatureScan: revealing property-dependent similarity of nucleotide sequences

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