Alexander E. Kel

According to our database1, Alexander E. Kel authored at least 69 papers between 1993 and 2019.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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PhD thesis 
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Bibliography

2019
Transcription Factor Databases.
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer.
BMC Bioinform., 2019

2018
BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes.
Comput. Biol. Chem., 2018

2017
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.
Nucleic Acids Res., 2017

geneXplainR: An R interface for the geneXplain platform.
J. Open Source Softw., 2017

cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing.
J. Comput. Biol., 2017

2013
A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs.
PLoS Comput. Biol., 2013

MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters.
BMC Bioinform., 2013

2012
3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations.
Nucleic Acids Res., 2012

2010
Molecular mechanistic associations of human diseases.
BMC Syst. Biol., 2010

Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates.
BMC Bioinform., 2010

Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies.
BMC Bioinform., 2010

2008
Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer.
Silico Biol., 2008

Building a knowledge base for systems pathology.
Briefings Bioinform., 2008

2007
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis.
Nucleic Acids Res., 2007

Recognition of cis-Regulatory Elements with Vombat.
J. Bioinform. Comput. Biol., 2007

Supervised Posteriors for DNA-motif Classification.
Proceedings of the German Conference on Bioinformatics, 2007

2006
Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm.
Nucleic Acids Res., 2006

TRANSFAC<sup>®</sup> and its module TRANSCompel<sup>®</sup>: transcriptional gene regulation in eukaryotes.
Nucleic Acids Res., 2006

TRANSPATH<sup>®</sup>: an information resource for storing and visualizing signaling pathways and their pathological aberrations.
Nucleic Acids Res., 2006

FeatureScan: revealing property-dependent similarity of nucleotide sequences.
Nucleic Acids Res., 2006

TiProD: the Tissue-specific Promoter Database.
Nucleic Acids Res., 2006

Beyond microarrays: Finding key transcription factors controlling signal transduction pathways.
BMC Bioinform., 2006

Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations.
Bioinform., 2006

2005
Signal-Theoretical DNA Similarity Measure Revealing Unexpected Similarities of E. coli Promoters.
Silico Biol., 2005

Composite Module Analyst: Tool for Prediction of DNA Transcription Regulation. Testing on Simulated Data.
Proceedings of the Advances in Natural Computation, First International Conference, 2005

Composite Module Analyst: A Fitness-Based Tool for Prediction of Transcription Regulation.
Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, 2005

2004
Large-scale collection and characterization of promoters of human and mouse genes.
Silico Biol., 2004

Bifurcation analysis of the regulatory modules of the mammalian G1/S transition.
Bioinform., 2004

Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods.
Bioinform., 2004

Application of Kernel Method to Reveal Subtypes of TF Binding Motifs.
Proceedings of the Regulatory Genomics, 2004

From Composite Patters to Pathways - Prediction of Key Regulators of Gene Expression.
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

2003
TRANSFAC®: transcriptional regulation, from patterns to profiles.
Nucleic Acids Res., 2003

MATCHTM: a tool for searching transcription factor binding sites in DNA sequences.
Nucleic Acids Res., 2003

Prediction of potential C/EBP/NF-kappaB composite elements using matrix-based search methods.
Silico Biol., 2003

Composition-sensitive analysis of the human genome for regulatory signals.
Silico Biol., 2003

Whole Genome Human/Mouse Phylogenetic Footprinting of Potential Transcription Regulatory Signals.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Modeling the G1/S transition in mammals -Bifurcation an alysis of elementary modules.
Proceedings of the German Conference on Bioinformatics, 2003

2002
TRANSCompel®: a database on composite regulatory elements in eukaryotic genes.
Nucleic Acids Res., 2002

Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
ClusterScan: A Tool for Automatic Annotation of Genomic Regulatory Sequences by Searching for Composite Clusters.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

TRANSCompel® - a professional database on composite regulatory elements in eukaryotic genes.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

MATCH<sup>TM</sup> - a tool for searching transcription factor binding sites in DNA sequences. Application for the analysis of human chromosomes.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

2000
Transcription Regulatory Regions Database (TRRD): its status in 2000.
Nucleic Acids Res., 2000

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.
Nucleic Acids Res., 2000

Kernel Method for Estimation of Functional Site Local Consensi: Classification of Transcription Initiation Sites in Eukaryotic Genes.
Proceedings of the German Conference on Bioinformatics (GCB 2000), 2000

Modeling of Gene Regulatory Network of Cell Cycle Control. Role of E2F Feedback Loops.
Proceedings of the German Conference on Bioinformatics (GCB 2000), 2000

1999
Transcription Regulatory Regions Database (TRRD): its status in 1999.
Nucleic Acids Res., 1999

Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms.
Nucleic Acids Res., 1999

E2F composite units in promoters of cell cycle genes.
Proceedings of the German Conference on Bioinformatics, 1999

1998
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Nucleic Acids Res., 1998

A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily.
Bioinform., 1998

GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome.
Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

A hierarchy of databases for modeling gene regulatory mechanisms.
Proceedings of the German Conference on Bioinformatics, 1998

Combinatorial identification of promoters induced upon immune cell activation.
Proceedings of the German Conference on Bioinformatics, 1998

1997
TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation.
Nucleic Acids Res., 1997

Identification of the significant conformational features of functional sites in B-DNA.
Proceedings of the German Conference on Bioinformatics, 1997

Lipid Metabolism Transcription Regulatory Regions Database (LM-TRRD).
Proceedings of the German Conference on Bioinformatics, 1997

1996
Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes.
Proceedings of the German Conference on Bioinformatics, 1996

Genetic Algorithm for Selection of Oligonucleotides for Identification by Hybridisation of Genomic DNA Fragments Possessing Gene Potential.
Proceedings of the German Conference on Bioinformatics, 1996

TRRD and COMPEL Databases on Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences.
Proceedings of the Bioinformatics, German Conference on Bioinformatics, Leipzig, 1996

TRRD and COMPEL Databases an Transcription Linked to TRANSFAC as Tools for Analysis and Recognition of Regulatory Sequences.
Proceedings of the German Conference on Bioinformatics, 1996

Comparative Analysis of the Secondary Structure of mRNA Encoded by High- and Low-Expression Eukaryotic Genes.
Proceedings of the German Conference on Bioinformatics, 1996

WWWTRRD: Hypertext Information System an Transcription Regulation.
Proceedings of the German Conference on Bioinformatics, 1996

1995
Eukaryotic promoter recognition by binding sites for transcription factors.
Comput. Appl. Biosci., 1995

Identification of CDNA Sequences by Specific Oligonucleotide Sets - A Computer Tool and Application.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences.
Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, 1995

Data representation in the TRRD-a database of transcription regulatory regions of the eukaryotic genomes.
Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995

1993
SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites.
Comput. Appl. Biosci., 1993


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