Mark Borodovsky

Publication Activity (10 Years)

Years Active: 1992-2021
Publications (10 Years): 6

Top Topics

Training Algorithm

Genome Annotation

Top Venues

Briefings Bioinform.

Publications

Lars Gabriel, Katharina Jasmin Hoff, Tomás Bruna, Mark Borodovsky, Mario Stanke
TSEBRA: transcript selector for BRAKER. BMC Bioinform. 22 (1) (2021)
Karl Gemayel, Alexandre Lomsadze, Mark Borodovsky
StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. Frontiers Bioinform. 1 (2021)
Ivan V. Antonov, Evgeny Mazurov, Mark Borodovsky, Yulia A. Medvedeva
Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools. Briefings Bioinform. 20 (2) (2019)
Mark Borodovsky
New Machine Learning Algorithms for Genome Annotation. BCB (2019)
Mark Borodovsky
New automatic and effective tools for genome annotation. ICCABS (2017)
Katharina Jasmin Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinform. 32 (5) (2016)
Shiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky
Identification of protein coding regions in RNA transcripts. BCB (2014)
Ivan Antonov, Pavel V. Baranov, Mark Borodovsky
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. Nucleic Acids Res. 41 (Database-Issue) (2013)
Shiyuyun Tang, Ivan Antonov, Mark Borodovsky
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. Bioinform. 29 (1) (2013)
Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma
TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq. RECOMB (2012)
Mark Borodovsky, Teresa M. Przytycka, Sanguthevar Rajasekaran, Alexander Zelikovsky
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (4) (2011)
Jeffrey Martin, Wenhan Zhu, Karla D. Passalacqua, Nicholas H. Bergman, Mark Borodovsky
genome organization in light of whole transcriptome sequencing. BMC Bioinform. 11 (S-3) (2010)
Ivan Antonov, Mark Borodovsky
Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm. J. Bioinform. Comput. Biol. 8 (3) (2010)
Andrey Kislyuk, Alexandre Lomsadze, Alla L. Lapidus, Mark Borodovsky
Frameshift detection in prokaryotic genomic sequences. Int. J. Bioinform. Res. Appl. 5 (4) (2009)
Jeffrey Martin, Wenhan Zhu, Nicholas H. Bergman, Mark Borodovsky
Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq. BIBM (2009)
Mark Borodovsky
Decoding Novel Genomes: From Microbiomes to the Eukaryota. BIBE (2007)
Mark Borodovsky
Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood. ISBRA (2007)
Seoung Bum Kim, Kwok-Leung Tsui, Mark Borodovsky
Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets. Int. J. Bioinform. Res. Appl. 2 (2) (2006)
Zafer Aydin, Yucel Altunbasak, Mark Borodovsky
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinform. 7 (2006)
Svetlana Ekisheva, Mark Borodovsky
Probabilistic models for biological sequences: selection and Maximum Likelihood estimation. Int. J. Bioinform. Res. Appl. 2 (3) (2006)
Alexander Yu. Mitrophanov, Mark Borodovsky
Statistical significance in biological sequence analysis. Briefings Bioinform. 7 (1) (2006)
John Besemer, Mark Borodovsky
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Mark Borodovsky, Andrey Rzhetsky, Dmitrij Frishman
Biology, Computational Genomics and Evolutionary Biology. Bioinform. 21 (S3) (2005)
Jin Hong, Dong Hyun Jeong, Christopher D. Shaw, William Ribarsky, Mark Borodovsky, Chang Geun Song
GVis: A Scalable Visualization Framework for Genomic Data. EuroVis (2005)
Zafer Aydin, Yücel Altunbasak, Mark Borodovsky
Protein secondary structure prediction with semi Markov HMMs. ICASSP (5) (2004)
Rajeev K. Azad, Mark Borodovsky
Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory. Briefings Bioinform. 5 (2) (2004)
Rajeev K. Azad, Mark Borodovsky
Effects of choice of DNA sequence model structure on gene identification accuracy. Bioinform. 20 (7) (2004)
Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinform. 17 (10) (2001)
Chris Burge, Andrej Sali, Mark Borodovsky
The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA). Bioinform. 15 (11) (1999)
Anton M. Shmatkov, Arik A. Melikyan, Felix L. Chernousko, Mark Borodovsky
Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes. Bioinform. 15 (11) (1999)
Jürgen Kleffe, Klaus Hermann, Mark Borodovsky
Statistical Analysis of Genemark Performance by Cross-validation. Comput. Chem. 20 (1) (1996)
James D. McIninch, William S. Hayes, Mark Borodovsky
Applications of GeneMark in Multispecies Environments. ISMB (1996)
Mark Borodovsky, Anatoly Peresetsky
Deriving Non-homogeneous DNA Markov Chain Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy. Comput. Chem. 18 (3) (1994)
Mark Borodovsky, James D. McIninch
GENMARK: Parallel Gene Recognition for Both DNA Strands. Comput. Chem. 17 (2) (1993)
Jürgen Kleffe, Mark Borodovsky
First and second moment of counts of words in random texts generated by Markov chains. Comput. Appl. Biosci. 8 (5) (1992)