Mark Borodovsky

37 papers A 1B 2C 1Journal 25Unranked 6

Year	Rank	Type	Title / Venue / Authors
2021	J	`jnl`	StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. Frontiers Bioinform. Karl Gemayel, Alexandre Lomsadze, Mark Borodovsky
2021	J	`jnl`	TSEBRA: transcript selector for BRAKER. BMC Bioinform. Lars Gabriel, Katharina Jasmin Hoff, Tomás Bruna, Mark Borodovsky, Mario Stanke
2019	—	`conf`	New Machine Learning Algorithms for Genome Annotation. BCB Mark Borodovsky
2019	J	`jnl`	Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools. Briefings Bioinform. Ivan V. Antonov, Evgeny Mazurov, Mark Borodovsky, Yulia A. Medvedeva
2017	—	`conf`	New automatic and effective tools for genome annotation. ICCABS Mark Borodovsky
2016	J	`jnl`	BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. Bioinform. Katharina Jasmin Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
2014	—	`conf`	Identification of protein coding regions in RNA transcripts. BCB Shiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky
2013	J	`jnl`	GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. Nucleic Acids Res. Ivan Antonov, Pavel V. Baranov, Mark Borodovsky
2013	J	`jnl`	MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences. Bioinform. Shiyuyun Tang, Ivan Antonov, Mark Borodovsky
2012	B	`conf`	TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq. RECOMB Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene E. Robinson, Jian Ma
2011	J	`jnl`	Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. Mark Borodovsky, Teresa M. Przytycka, Sanguthevar Rajasekaran, Alexander Zelikovsky
2010	—	`ed.`	Bioinformatics Research and Applications, 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings ISBRA Mark Borodovsky, Johann Peter Gogarten, Teresa M. Przytycka, Sanguthevar Rajasekaran
2010	J	`jnl`	Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm. J. Bioinform. Comput. Biol. Ivan Antonov, Mark Borodovsky
2010	—	`ed.`	Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB 2010, Niagara Falls, NY, USA, August 2-4, 2010 BCB Aidong Zhang, Mark Borodovsky, Gultekin Özsoyoglu, Armin R. Mikler
2009	—	`conf`	Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq. BIBM Jeffrey Martin, Wenhan Zhu, Nicholas H. Bergman, Mark Borodovsky
2009	J	`jnl`	Frameshift detection in prokaryotic genomic sequences. Int. J. Bioinform. Res. Appl. Andrey Kislyuk, Alexandre Lomsadze, Alla L. Lapidus, Mark Borodovsky
2007	C	`conf`	Decoding Novel Genomes: From Microbiomes to the Eukaryota. BIBE Mark Borodovsky
2007	—	`conf`	Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood. ISBRA Mark Borodovsky
2006	J	`jnl`	Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets. Int. J. Bioinform. Res. Appl. Seoung Bum Kim, Kwok-Leung Tsui, Mark Borodovsky
2006	J	`jnl`	Probabilistic models for biological sequences: selection and Maximum Likelihood estimation. Int. J. Bioinform. Res. Appl. Svetlana Ekisheva, Mark Borodovsky
2006	J	`jnl`	Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinform. Zafer Aydin, Yucel Altunbasak, Mark Borodovsky
2006	J	`jnl`	Statistical significance in biological sequence analysis. Briefings Bioinform. Alexander Yu. Mitrophanov, Mark Borodovsky
2005	B	`conf`	GVis: A Scalable Visualization Framework for Genomic Data. EuroVis Jin Hong, Dong Hyun Jeong, Christopher D. Shaw, William Ribarsky, Mark Borodovsky, Chang Geun Song
2005	J	`jnl`	GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. John Besemer, Mark Borodovsky
2005	J	`jnl`	The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: Bioinform. Mark Borodovsky, Andrey Rzhetsky, Dmitrij Frishman
2004	J	`jnl`	Effects of choice of DNA sequence model structure on gene identification accuracy. Bioinform. Rajeev K. Azad, Mark Borodovsky
2004	J	`jnl`	Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory. Briefings Bioinform. Rajeev K. Azad, Mark Borodovsky
2004	—	`conf`	Protein secondary structure prediction with semi Markov HMMs. ICASSP (5) Zafer Aydin, Yücel Altunbasak, Mark Borodovsky
2001	J	`jnl`	The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA). Bioinform. Mark Borodovsky, Eugene V. Koonin, Chris Burge, James W. Fickett, John Logsdon, Andrej Sali, Gary D. Stormo, Igor B. Zhulin
1999	J	`jnl`	Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes. Bioinform. Anton M. Shmatkov, Arik A. Melikyan, Felix L. Chernousko, Mark Borodovsky
1999	J	`jnl`	The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA). Bioinform. Chris Burge, Andrej Sali, Mark Borodovsky
1996	A	`conf`	Applications of GeneMark in Multispecies Environments. ISMB James D. McIninch, William S. Hayes, Mark Borodovsky
1996	J	`jnl`	Comparison of Equations Describing the Ranked Frequency Distributions of Graphemes and Phonemes. J. Quant. Linguistics Colin Martindale, S. M. Gusein-Zade, Dean McKenzie, Mark Borodovsky
1996	J	`jnl`	Statistical Analysis of Genemark Performance by Cross-validation. Comput. Chem. Jürgen Kleffe, Klaus Hermann, Mark Borodovsky
1994	J	`jnl`	Deriving Non-homogeneous DNA Markov Chain Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy. Comput. Chem. Mark Borodovsky, Anatoly Peresetsky
1993	J	`jnl`	GENMARK: Parallel Gene Recognition for Both DNA Strands. Comput. Chem. Mark Borodovsky, James D. McIninch
1992	J	`jnl`	First and second moment of counts of words in random texts generated by Markov chains. Comput. Appl. Biosci. Jürgen Kleffe, Mark Borodovsky