First and second moment of counts of words in random texts generated by Markov chains. - Jürgen Kleffe; Mark Borodovsky (Comput. Appl. Biosci., 1992)

GENMARK: Parallel Gene Recognition for Both DNA Strands. - Mark Borodovsky; James D. McIninch (Comput. Chem., 1993)

Deriving Non-homogeneous DNA Markov Chain Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy. - Mark Borodovsky; Anatoly Peresetsky (Comput. Chem., 1994)

Applications of GeneMark in Multispecies Environments. - James D. McIninch; William S. Hayes; Mark Borodovsky (ISMB, 1996)

Statistical Analysis of Genemark Performance by Cross-validation. - Jürgen Kleffe; Klaus Hermann; Mark Borodovsky (Comput. Chem., 1996)

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)

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 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)

Protein secondary structure prediction with semi Markov HMMs. - Zafer Aydin; Yücel Altunbasak; Mark Borodovsky (ICASSP (5), 2004)

Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory. - Rajeev K. Azad; Mark Borodovsky (Briefings Bioinform., 2004)

Effects of choice of DNA sequence model structure on gene identification accuracy. - Rajeev K. Azad; Mark Borodovsky (Bioinform., 2004)

GVis: A Scalable Visualization Framework for Genomic Data. - Jin Hong 003; Dong Hyun Jeong; Christopher D. Shaw; William Ribarsky; Mark Borodovsky; Chang Geun Song (EuroVis, 2005)

The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology. - Mark Borodovsky; Andrey Rzhetsky; Dmitrij Frishman (Bioinform., 2005)

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. - John Besemer; Mark Borodovsky (Nucleic Acids Res., 2005)

Statistical significance in biological sequence analysis. - Alexander Yu. Mitrophanov; Mark Borodovsky (Briefings Bioinform., 2006)

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. - Zafer Aydin; Yucel Altunbasak; Mark Borodovsky (BMC Bioinform., 2006)

Probabilistic models for biological sequences: selection and Maximum Likelihood estimation. - Svetlana Ekisheva; Mark Borodovsky (Int. J. Bioinform. Res. Appl., 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)

Decoding Novel Genomes: From Microbiomes to the Eukaryota. - Mark Borodovsky (BIBE, 2007)

Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood. - Mark Borodovsky (ISBRA, 2007)

Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq. - Jeffrey Martin; Wenhan Zhu; Nicholas H. Bergman; Mark Borodovsky (BIBM, 2009)

Frameshift detection in prokaryotic genomic sequences. - Andrey Kislyuk; Alexandre Lomsadze; Alla L. Lapidus; Mark Borodovsky (Int. J. Bioinform. Res. Appl., 2009)

Bacillus anthracis genome organization in light of whole transcriptome sequencing. - Jeffrey Martin; Wenhan Zhu; Karla D. Passalacqua; Nicholas H. Bergman; Mark Borodovsky (BMC Bioinform., 2010)

Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm. - Ivan Antonov; Mark Borodovsky (J. Bioinform. Comput. Biol., 2010)

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)

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 004 (RECOMB, 2012)

MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. - Shiyuyun Tang; Ivan Antonov; Mark Borodovsky (Bioinform., 2013)

GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. - Ivan Antonov; Pavel V. Baranov; Mark Borodovsky (Nucleic Acids Res., 2013)

Identification of protein coding regions in RNA transcripts. - Shiyuyun Tang; Alexandre Lomsadze; Mark Borodovsky (BCB, 2014)

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)

New automatic and effective tools for genome annotation. - Mark Borodovsky (ICCABS, 2017)

New Machine Learning Algorithms for Genome Annotation. - Mark Borodovsky (BCB, 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)

TSEBRA: transcript selector for BRAKER. - Lars Gabriel; Katharina Jasmin Hoff; Tomás Bruna; Mark Borodovsky; Mario Stanke (BMC Bioinform., 2021)

StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. - Karl Gemayel; Alexandre Lomsadze; Mark Borodovsky (Frontiers Bioinform., 2021)