Mark Borodovsky

According to our database, Mark Borodovsky authored at least 35 papers between 1992 and 2021.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2021

StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.

Karl Gemayel, Alexandre Lomsadze, Mark Borodovsky

Frontiers Bioinform., 2021

TSEBRA: transcript selector for BRAKER.

Lars Gabriel, Katharina Jasmin Hoff, Tomás Bruna, Mark Borodovsky, Mario Stanke

BMC Bioinform., 2021

2019

Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.

Ivan V. Antonov, Evgeny Mazurov, Mark Borodovsky, Yulia A. Medvedeva

Briefings Bioinform., 2019

New Machine Learning Algorithms for Genome Annotation.

Mark Borodovsky

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2017

New automatic and effective tools for genome annotation.

Mark Borodovsky

Proceedings of the 7th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2017

2016

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.

Katharina Jasmin Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke

Bioinform., 2016

2014

Identification of protein coding regions in RNA transcripts.

Shiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013

GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences.

Ivan Antonov, Pavel V. Baranov, Mark Borodovsky

Nucleic Acids Res., 2013

MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences.

Shiyuyun Tang, Ivan Antonov, Mark Borodovsky

Bioinform., 2013

2012

TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq.

Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma

Proceedings of the Research in Computational Molecular Biology, 2012

2011

Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications.

Mark Borodovsky, Teresa M. Przytycka, Sanguthevar Rajasekaran, Alexander Zelikovsky

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

2010

Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm.

Ivan Antonov, Mark Borodovsky

J. Bioinform. Comput. Biol., 2010

<i>Bacillus anthracis </i>genome organization in light of whole transcriptome sequencing.

Jeffrey Martin, Wenhan Zhu, Karla D. Passalacqua, Nicholas H. Bergman, Mark Borodovsky

BMC Bioinform., 2010

2009

Frameshift detection in prokaryotic genomic sequences.

Andrey Kislyuk, Alexandre Lomsadze, Alla L. Lapidus, Mark Borodovsky

Int. J. Bioinform. Res. Appl., 2009

Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq.

Jeffrey Martin, Wenhan Zhu, Nicholas H. Bergman, Mark Borodovsky

Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009

2007

Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood.

Mark Borodovsky

Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

Decoding Novel Genomes: From Microbiomes to the Eukaryota.

Mark Borodovsky

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets.

Seoung Bum Kim, Kwok-Leung Tsui, Mark Borodovsky

Int. J. Bioinform. Res. Appl., 2006

Probabilistic models for biological sequences: selection and Maximum Likelihood estimation.

Svetlana Ekisheva, Mark Borodovsky

Int. J. Bioinform. Res. Appl., 2006

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.

Zafer Aydin, Yucel Altunbasak, Mark Borodovsky

BMC Bioinform., 2006

Statistical significance in biological sequence analysis.

Alexander Yu. Mitrophanov, Mark Borodovsky

Briefings Bioinform., 2006

2005

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

John Besemer, Mark Borodovsky

Nucleic Acids Res., 2005

The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: <i>in silico</i> Biology, Computational Genomics and Evolutionary Biology.

Mark Borodovsky, Andrey Rzhetsky, Dmitrij Frishman

Bioinform., 2005

GVis: A Scalable Visualization Framework for Genomic Data.

Jin Hong, Dong Hyun Jeong, Christopher D. Shaw, William Ribarsky, Mark Borodovsky, Chang Geun Song

Proceedings of the 7th Joint Eurographics, 2005

2004

Effects of choice of DNA sequence model structure on gene identification accuracy.

Rajeev K. Azad, Mark Borodovsky

Bioinform., 2004

Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory.

Rajeev K. Azad, Mark Borodovsky

Briefings Bioinform., 2004

Protein secondary structure prediction with semi Markov HMMs.

Zafer Aydin, Yücel Altunbasak, Mark Borodovsky

Proceedings of the 2004 IEEE International Conference on Acoustics, 2004

2001

The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA).

Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin

Bioinform., 2001

1999

Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes.

Anton M. Shmatkov, Arik A. Melikyan, Felix L. Chernousko, Mark Borodovsky

Bioinform., 1999

The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA).

Chris Burge, Andrej Sali, Mark Borodovsky

Bioinform., 1999

1996

Statistical Analysis of Genemark Performance by Cross-validation.

Jürgen Kleffe, Klaus Hermann, Mark Borodovsky

Comput. Chem., 1996

Applications of GeneMark in Multispecies Environments.

James D. McIninch, William S. Hayes, Mark Borodovsky

Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, 1996

1994

Deriving Non-homogeneous DNA Markov Chain Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy.

Mark Borodovsky, Anatoly Peresetsky

Comput. Chem., 1994

1993

GENMARK: Parallel Gene Recognition for Both DNA Strands.

Mark Borodovsky, James D. McIninch

Comput. Chem., 1993

1992

First and second moment of counts of words in random texts generated by Markov chains.

Jürgen Kleffe, Mark Borodovsky

Comput. Appl. Biosci., 1992