Mark Borodovsky | Academic Influence

Mark Borodovsky's AcademicInfluence.com Rankings

Mark Borodovsky

Biology

#2656

World Rank

#4188

Historical Rank

Bioinformatics

#53

World Rank

#54

Historical Rank

Computational Biology

#84

World Rank

#84

Historical Rank

biology Degrees

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Biology

Mark Borodovsky's Degrees

PhD Bioinformatics Stanford University
Masters Computer Science University of California, Berkeley
Bachelors Biology University of California, Berkeley

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Why Is Mark Borodovsky Influential?

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According to Wikipedia, Mark Borodovsky is a Regents' Professor at the Join Wallace H. Coulter Department of Biomedical Engineering of Georgia Institute of Technology and Emory University and Director of the Center for Bioinformatics and Computational Genomics at Georgia Tech. He has also been a Chair of the Department of Bioinformatics at the Moscow Institute of Physics and Technology in Moscow, Russia from 2012 to 2022.

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Mark Borodovsky's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

NCBI prokaryotic genome annotation pipeline (2016) (3728)
The complete genome sequence of the gastric pathogen Helicobacter pylori (1997) (3551)
cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. (1996) (1992)
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. (2001) (1808)
GeneMark.hmm: new solutions for gene finding. (1998) (1594)
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii (1996) (1149)
Ab initio gene identification in metagenomic sequences (2010) (1081)
The genome of woodland strawberry (Fragaria vesca) (2011) (1073)
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses (2005) (834)
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS (2015) (707)
GENMARK: Parallel Gene Recognition for Both DNA Strands (1993) (705)
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. (2008) (694)
Gene identification in novel eukaryotic genomes by self-training algorithm (2005) (664)
The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex[C][W] (2010) (446)
Heuristic approach to deriving models for gene finding. (1999) (416)
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) (2010) (391)
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication (2014) (373)
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database (2020) (338)
Complex history of admixture during citrus domestication revealed by genome analysis (2014) (331)
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm (2014) (312)
Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli (1996) (304)
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation (2012) (278)
Whole-Genome Annotation with BRAKER. (2019) (265)
The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle (2014) (260)
Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences. (1996) (211)
Identification of protein coding regions in RNA transcripts (2014) (204)
The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains (1996) (167)
Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES (2011) (165)
Identification of Proteins Associated with Murine Cytomegalovirus Virions (2004) (163)
Detection of new genes in a bacterial genome using Markov models for three gene classes. (1995) (150)
How to interpret an anonymous bacterial genome: machine learning approach to gene identification. (1998) (128)
GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020) (120)
The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants (2011) (112)
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models (2006) (111)
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome. (1994) (111)
Recognition of genes in DNA sequence with ambiguities. (1993) (106)
The Vfl1 Protein in Chlamydomonas Localizes in a Rotationally Asymmetric Pattern at the Distal Ends of the Basal Bodies (2001) (101)
Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes (2018) (99)
Complete Sequence and Comparative Analysis of the Genome of Herpes B Virus (Cercopithecine Herpesvirus 1) from a Rhesus Monkey (2003) (98)
Prokaryotic Gene Prediction Using GeneMark and GeneMark.hmm (2003) (94)
Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum. (2001) (94)
Statistical significance in biological sequence analysis (2006) (81)
2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research (2010) (79)
Three new isoforms of Caenorhabditis elegans UNC-89 containing MLCK-like protein kinase domains. (2004) (74)
New genes in old sequence: a strategy for finding genes in the bacterial genome. (1994) (71)
Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. (2011) (71)
A novel genetic island of meningitic Escherichia coli K1 containing the ibeA invasion gene (GimA): functional annotation and carbon-source-regulated invasion of human brain microvascular endothelial cells (2001) (62)
Bacillus anthracis genome organization in light of whole transcriptome sequencing (2010) (61)
Exonization of the LTR transposable elements in human genome (2007) (60)
First and second moment of counts of words in random texts generated by Markov chains (1992) (57)
Reannotation of Shewanella oneidensis genome. (2003) (55)
Characteristic features of the nucleotide sequences of yeast mitochondrial ribosomal protein genes as analyzed by computer program GeneMark. (1994) (55)
Probabilistic methods of identifying genes in prokaryotic genomes: Connections to the HMM theory (2004) (54)
Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes (1999) (52)
Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi (2011) (49)
Improving gene annotation of complete viral genomes (2003) (49)
A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. (2011) (45)
Evaluating the protein coding potential of exonized transposable element sequences (2007) (45)
Eukaryotic Gene Prediction Using GeneMark.hmm (2003) (44)
TrueSight: a new algorithm for splice junction detection using RNA-seq (2012) (44)
Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm (2010) (44)
Titins in C.elegans with unusual features: coiled-coil domains, novel regulation of kinase activity and two new possible elastic regions. (2002) (43)
Identification of new human cadherin genes using a combination of protein motif search and gene finding methods. (2004) (41)
Toward unrestricted use of public genomic data (2019) (40)
The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry) (2017) (35)
Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools (2019) (35)
Identification of the nature of reading frame transitions observed in prokaryotic genomes (2013) (34)
Deriving ribosomal binding site (RBS) statistical models from unannotated DNA sequences and the use of the RBS model for N-terminal prediction. (1998) (31)
Gene Identification in Prokaryotic Genomes, Phages, Metagenomes, and EST Sequences with GeneMarkS Suite (2014) (30)
Deriving Non-homogeneous DNA Markov Chain Models by Cluster Analysis Algorithm Minimizing Multiple Alignment Entropy (1994) (27)
In silico identification of genes in bacteriophage DNA. (2009) (27)
Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system. (2007) (27)
GVis: A Scalable Visualization Framework for Genomic Data (2005) (25)
SENSITIVITY OF HIDDEN MARKOV MODELS (2005) (25)
Protein secondary structure prediction with semi Markov HMMs (2004) (25)
Problems and Solutions in Biological Sequence Analysis (2006) (24)
Comparison of Equations Describing the Ranked Frequency Distributions of Graphemes and Phonemes (1996) (21)
Frameshift detection in prokaryotic genomic sequences (2009) (19)
TSEBRA: transcript selector for BRAKER (2021) (18)
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB 2010, Niagara Falls, NY, USA, August 2-4, 2010 (2010) (17)
Effects of choice of DNA sequence model structure on gene identification accuracy (2004) (17)
GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences (2012) (16)
MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences (2012) (14)
Gene identification and classification in the Synechocystis genomic sequence by recursive gene mark analysis. (1997) (14)
Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets (2006) (13)
Computer survey for likely genes in the one megabase contiguous genomic sequence data of Synechocystis sp. strain PCC6803. (1995) (11)
Development of a workflow for identification of nuclear genotyping markers for Cyclospora cayetanensis (2020) (11)
Corrections: The complete genome sequence of the gastric pathogen Helicobacter pylori (1997) (9)
Applications of GeneMark in Multispecies Environments (1996) (9)
Statistical Predictions of Coding Regions in Prokaryotic Genomes by Using Inhomogeneous Markov Models (1999) (8)
Monitoring the partitioning of hepatic fatty acids in vivo: keeping track of control (1994) (5)
GeneMark-EP and -EP+: automatic eukaryotic gene prediction supported by spliced aligned proteins (2020) (5)
Improved Prokaryotic Gene Prediction Yields Insights into Transcription and Translation Mechanisms on Whole Genome Scale (2017) (5)
UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing (2013) (5)
Consent insufficient for data release—Response (2019) (4)
Convergence rate estimation for the TKF91 model of biological sequence length evolution. (2007) (4)
Statistical Analysis of Genemark Performance by Cross-validation (1996) (4)
Problems and Solutions in Biological Sequence Analysis: RNA structure analysis (2006) (3)
GeneMark-HM: improving gene prediction in DNA sequences of human microbiome (2021) (3)
Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii (2020) (3)
Prediction of gene locations using DNA Markov chain models (1993) (3)
TSEBRA: transcript selector for BRAKER (2021) (3)
A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. “Hillquist”) (2022) (2)
Assessment of Gene Annotation Accuracy by Inferring Transcripts from RNA-Seq (2009) (2)
errata: The yeast genome directory (1997) (2)
Bioinformatics Pipeline for Human Papillomavirus Short Read Genomic Sequences Classification Using Support Vector Machine (2020) (2)
Annotation of Phage Genomes with Multiple Genetic Codes (2022) (2)
`Small genomics' on a large scale (1998) (2)
UBM: Quantitative systems biology (2009) (1)
StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes (2021) (1)
GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistence with Extrinsic Data (2023) (1)
Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences (2011) (1)
algorithm with unsupervised training Gene prediction in novel fungal genomes using an ab initio Material Supplemental (2008) (1)
'Small genomics' on a large scale. E. coli and small genomes, American Society for Microbiology, Snowbird, UT, USA, 12-15 October 1997. (1998) (1)
Probabilistic models for biological sequences: selection and Maximum Likelihood estimation (2006) (1)
New Machine Learning Algorithms for Genome Annotation (2019) (1)
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications (2011) (0)
2 K 09 and Thereafter : The Coming Era of Integrative Bioinformatics (2010) (0)
StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence (2020) (0)
Gene Structure Prediction – Chasing the Horizon (2014) (0)
Dynamic Systems Models (2016) (0)
Multiple sequence alignment methods (2006) (0)
Prediction of protein coding regions in unannotated dna sequences using an inhomogeneous markov model of genetic information encoding (1997) (0)
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications (2007) (0)
Corrigendum to “Identification of New Human Cadherin Genes Using a Combination of Protein Motif Search and Gene Finding Methods” [J. Mol. Biol.337 (2004) 307–317] (2014) (0)
Building phylogenetic trees (2006) (0)
GeneMarkS-2 : Raising Standards of Accuracy in Gene Recognition (2017) (0)
Invited Talk: Ab Initio Gene Finding Engines: What Is Under the Hood (2007) (0)
The 2010 ACM International Conference on Bioinformatics and Computational Biology : ACM-BCB 2010 : Niagara Falls, New York, U.S.A., August 2-4, 2010 (2010) (0)
Problems and Solutions in Biological Sequence Analysis: Probabilistic approaches to phylogeny (2006) (0)
New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes (2013) (0)
What Gene Prediction in Transcriptomes, Metatranscrptomes, Metagenomes, and Microbial Genomes has in Common (2015) (0)
Problems and Solutions in Biological Sequence Analysis: Transformational grammars (2006) (0)
Bioinformatics: in silico biology, biological networks, from genomics to epidemiology (2003) (0)
Gene Prediction with Integration of DNA, RNA and Protein Sequence Information (2012) (0)
Novel Genomes: From Microbiomes to the Eukaryota (2007) (0)
Rhesus Monkey ) from a Cercopithecine Herpesvirus 1 ( Analysis of the Genome of Herpes B Virus Complete Sequence and Comparative (2003) (0)
MetaGeneMark-2: Improved Gene Prediction in Metagenomes (2022) (0)
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation (2012) (0)
Problems and Solutions in Biological Sequence Analysis: Preface (2006) (0)
Problems and Solutions in Biological Sequence Analysis: Introduction (2006) (0)
Transcriptome based annotation for new version of C. sativus genome (2016) (0)
Problems and Solutions in Biological Sequence Analysis: Pairwise alignment (2006) (0)
Problems and Solutions in Biological Sequence Analysis: Profile HMMs for sequence families (2006) (0)
Problems and Solutions in Biological Sequence Analysis: Background on probability (2006) (0)
The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function (November 11-14, 1999, Atlanta, Georgia, USA) (1999) (0)
Bioinformatics Research and Applications, 6th International Symposium, ISBRA 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings (2010) (0)
Improving accuracy of gene prediction programs of the genemark family by means of genome segmentation (2007) (0)
IEEE 7th BIBE Research Tutorial Lecture: Decoding Novel Genomes: From Microbiomes to the Eukaryota (2007) (0)
TrueSight: Self-training Algorithm for Splice Junction Detection Using RNA-seq (2012) (0)
Finding Genes in Compositionally Heterogeneous Plants (2013) (0)
Proceedings of the 6th International Conference on Bioinformatics Research and Applications (2010) (0)
New automatic and effective tools for genome annotation (2017) (0)
The Third Georgia Tech-Emory International Conference on Bioinformatics: In Silico Biology; Bioinformatics After Human Genome (November 15-18, 2001, Atlanta, Georgia, USA) (2001) (0)
GeneMark Family of Gene Prediction Tools for Prokaryotic and Eukaryotic Genomes (2016) (0)
Current Techniques and Approaches for Metagenomic Exploration of Phage Diversity (2021) (0)
The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology (2005) (0)
Prokaryotic gene identification in silico (2004) (0)
GeneMark-EP and -EP+: eukaryotic gene prediction with self-training in the space of genes and proteins (2020) (0)
Markov chains and hidden Markov models (2006) (0)
Problems and Solutions in Biological Sequence Analysis: Pairwise alignment using HMMs (2006) (0)

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