Steven Salzberg | Academic Influence

Steven Salzberg's AcademicInfluence.com Rankings

Steven Salzberg

Biology

#357

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#636

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#207

USA Rank

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Steven Salzberg

Computer Science

#1073

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#1112

Historical Rank

#566

USA Rank

Database

#53

World Rank

#55

Historical Rank

#30

USA Rank

computer-science Degrees

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Biology
Computer Science

Steven Salzberg's Degrees

PhD Computer Science Stanford University

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Why Is Steven Salzberg Influential?

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According to Wikipedia, Steven Lloyd Salzberg is an American computational biologist and computer scientist who is a Bloomberg Distinguished Professor of Biomedical Engineering, Computer Science, and Biostatistics at Johns Hopkins University, where he is also Director of the Center for Computational Biology.

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Steven Salzberg'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

Fast gapped-read alignment with Bowtie 2 (2012) (34760)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome (2009) (19739)
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. (2010) (11813)
HISAT: a fast spliced aligner with low memory requirements (2015) (11758)
TopHat: discovering splice junctions with RNA-Seq (2009) (11345)
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions (2013) (11019)
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (2012) (10622)
FLASH: fast length adjustment of short reads to improve genome assemblies (2011) (9165)
Programs for Machine Learning (1994) (8307)
The Sequence of the Human Genome (2001) (6572)
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads (2015) (5691)
Versatile and open software for comparing large genomes (2004) (4596)
Genome sequence of the human malaria parasite Plasmodium falciparum (2002) (4255)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype (2019) (3815)
The Transcriptional Landscape of the Mammalian Genome (2005) (3394)
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown (2016) (3385)
Kraken: ultrafast metagenomic sequence classification using exact alignments (2014) (3036)
Identifying bacterial genes and endosymbiont DNA with Glimmer (2007) (2601)
Improved microbial gene identification with GLIMMER. (1999) (2437)
Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms (2010) (2281)
The ENCODE (ENCyclopedia Of DNA Elements) Project (2004) (2194)
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi (1997) (2043)
The Genome Sequence of the Malaria Mosquito Anopheles gambiae (2002) (2020)
Evolution of genes and genomes on the Drosophila phylogeny (2007) (1992)
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007) (1798)
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae (2000) (1790)
The Genome of the African Trypanosome Trypanosoma brucei (2005) (1633)
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima (1999) (1494)
Complete Genome Sequence of a Virulent Isolate of Streptococcus pneumoniae (2001) (1380)
The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease (2005) (1341)
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus (2005) (1323)
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003) (1315)
Repetitive DNA and next-generation sequencing: computational challenges and solutions (2011) (1262)
Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. (2000) (1150)
Genome Sequence of Aedes aegypti, a Major Arbovirus Vector (2007) (1110)
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders (2004) (1090)
A whole-genome assembly of the domestic cow, Bos taurus (2009) (1080)
The genome of woodland strawberry (Fragaria vesca) (2011) (1073)
Microbial gene identification using interpolated Markov models. (1998) (1049)
Butterfly genome reveals promiscuous exchange of mimicry adaptations among species (2012) (1041)
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) (2008) (1016)
Complete genome sequence of Treponema pallidum, the syphilis spirochete. (1998) (1009)
Fast algorithms for large-scale genome alignment and comparison. (2002) (1002)
The genome of the blood fluke Schistosoma mansoni (2009) (992)
A System for Induction of Oblique Decision Trees (1994) (958)
Alignment of whole genomes. (1999) (931)
MUMmer4: A fast and versatile genome alignment system (2018) (920)
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. (1999) (919)
The MaSuRCA genome assembler (2013) (916)
On Comparing Classifiers: Pitfalls to Avoid and a Recommended Approach (1997) (897)
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria (2003) (832)
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. (2000) (796)
Comparative genomics of the neglected human malaria parasite Plasmodium vivax (2008) (787)
Comparative Genomics of Trypanosomatid Parasitic Protozoa (2005) (762)
Centrifuge: rapid and sensitive classification of metagenomic sequences (2016) (756)
Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana (1999) (743)
Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis (2007) (739)
Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains (2002) (731)
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii (2002) (729)
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts (2011) (716)
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006) (709)
The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans (2005) (702)
GAGE: A critical evaluation of genome assemblies and assembly algorithms. (2012) (702)
Bracken: Estimating species abundance in metagenomics data (2016) (657)
Draft Genome of the Filarial Nematode Parasite Brugia malayi (2007) (639)
The complete sequence of a human genome (2021) (622)
Quake: quality-aware detection and correction of sequencing errors (2010) (610)
GeneSplicer: a new computational method for splice site prediction. (2001) (594)
Transcriptome assembly from long-read RNA-seq alignments with StringTie2 (2019) (558)
Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster (2002) (536)
Complete genome sequence of Caulobacter crescentus (2001) (529)
Ballgown bridges the gap between transcriptome assembly and expression analysis (2015) (523)
Searching for SNPs with cloud computing (2009) (520)
Phymm and PhymmBL: Metagenomic Phylogenetic Classification with Interpolated Markov Models (2009) (501)
Bioinformatics challenges of new sequencing technology. (2008) (496)
Assembly of large genomes using second-generation sequencing. (2010) (487)
Using MUMmer to Identify Similar Regions in Large Sequence Sets (2003) (487)
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution (2005) (484)
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. (1998) (482)
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake (2007) (476)
A Weighted Nearest Neighbor Algorithm for Learning with Symbolic Features (2004) (475)
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts (2002) (474)
Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations (2015) (464)
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies (2014) (428)
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii (2017) (426)
Mugsy: fast multiple alignment of closely related whole genomes (2010) (418)
Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis (2010) (418)
Comparative Genome Sequencing for Discovery of Novel Polymorphisms in Bacillus anthracis (2002) (417)
Minimus: a fast, lightweight genome assembler (2007) (417)
C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993 (1994) (415)
Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses (2005) (397)
A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome (2002) (389)
How to map billions of short reads onto genomes (2009) (351)
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath) (2004) (341)
DAGchainer: a tool for mining segmental genome duplications and synteny (2004) (336)
Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes (2005) (327)
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. (2001) (322)
Genomic signatures of evolutionary transitions from solitary to group living (2015) (316)
Book Review: C4.5: Programs for Machine Learning by J. Ross Quinlan. Morgan Kaufmann Publishers, Inc., 1993 (1994) (315)
Repetitive DNA and next-generation sequencing: computational challenges and solutions (2012) (315)
The genomes of two key bumblebee species with primitive eusocial organization (2015) (313)
A review of methods and databases for metagenomic classification and assembly (2019) (307)
Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? (2001) (307)
Evidence for symmetric chromosomal inversions around the replication origin in bacteria (2000) (307)
Cloud Computing and the DNA Data Race (2010) (303)
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. (2003) (301)
Gene Index analysis of the human genome estimates approximately 120,000 genes (2000) (298)
Prediction of operons in microbial genomes. (2001) (289)
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A (2008) (286)
Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm (2016) (283)
Sequencing and Assembly of the 22-Gb Loblolly Pine Genome (2014) (275)
Prediction of transcription terminators in bacterial genomes. (2000) (271)
Comparative genome assembly (2004) (251)
Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana (2000) (250)
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura (2004) (249)
The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum (2017) (241)
Hierarchical scaffolding with Bambus. (2003) (238)
Finding Genes in DNA with a Hidden Markov Model (1997) (234)
Assembly of a pan-genome from deep sequencing of 910 humans of African descent (2018) (229)
Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses (2007) (228)
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise (2018) (225)
What are decision trees? (2008) (224)
A weighted nearest neighbor algorithm for learning with symbolic features (2004) (219)
A Nearest Hyperrectangle Learning Method (1991) (215)
Interpolated Markov models for eukaryotic gene finding. (1999) (211)
A probabilistic method for identifying start codons in bacterial genomes (2001) (205)
INSTANCE-BASED LEARNING : Nearest Neighbour with Generalisation (1995) (205)
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts (2018) (203)
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues (2013) (200)
Full-length messenger RNA sequences greatly improve genome annotation (2002) (198)
Induction of Oblique Decision Trees (1993) (196)
Computational methods in molecular biology (1998) (195)
Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. (2013) (193)
Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation (2014) (187)
Microbial genome sequencing (2000) (176)
Skewed oligomers and origins of replication. (1998) (174)
Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp (2011) (173)
Beware of mis-assembled genomes (2005) (172)
OC1: A Randomized Induction of Oblique Decision Trees (1993) (172)
The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. (2016) (166)
JIGSAW: integration of multiple sources of evidence for gene prediction (2005) (165)
GAGE-B: an evaluation of genome assemblers for bacterial organisms (2013) (162)
Next-generation genome annotation: we still struggle to get it right (2019) (160)
The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications (2005) (160)
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation (2011) (160)
An optimized protocol for analysis of EST sequences. (2000) (155)
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering (2011) (154)
A new rhesus macaque assembly and annotation for next-generation sequencing analyses (2014) (153)
Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification (2019) (147)
Computational gene prediction using multiple sources of evidence. (2003) (146)
On growing better decision trees from data (1996) (146)
Liftoff: accurate mapping of gene annotations (2020) (144)
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005) (143)
Between a chicken and a grape: estimating the number of human genes (2010) (140)
A method for identifying splice sites and translational start sites in eukaryotic mRNA (1997) (139)
The COMBREX Project: Design, Methodology, and Initial Results (2013) (137)
Genome re-annotation: a wiki solution? (2007) (137)
Sequence of the Sugar Pine Megagenome (2016) (137)
Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. (1999) (134)
Pan-genomics in the human genome era (2020) (134)
DNA uptake signal sequences in naturally transformable bacteria. (1999) (134)
Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system (2016) (131)
Lin, X. et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768 (1999) (126)
A Decision Tree System for Finding Genes in DNA (1998) (125)
The Value of Complete Microbial Genome Sequencing (You Get What You Pay For) (2002) (124)
Unexpected cross-species contamination in genome sequencing projects (2014) (123)
Lookahead and Pathology in Decision Tree Induction (1995) (121)
Genome Sequence Assembly: Algorithms and Issues (2002) (120)
Clustering metagenomic sequences with interpolated Markov models (2010) (119)
PhymmBL expanded: confidence scores, custom databases, parallelization and more (2011) (118)
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. (2000) (114)
Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 (2002) (111)
Non-classical receptive field mediates switch in a sensory neuron ’ s frequency tuning (111)
Gene synteny and evolution of genome architecture in trypanosomatids. (2004) (110)
OperonDB: a comprehensive database of predicted operons in microbial genomes (2008) (109)
Between a chicken and a grape: estimating the number of human genes (2010) (108)
The age of the Arabidopsis thaliana genome duplication (2003) (108)
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes (2013) (107)
Acquisition and Evolution of Plant Pathogenesis–Associated Gene Clusters and Candidate Determinants of Tissue-Specificity in Xanthomonas (2008) (105)
The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies (2019) (100)
A clustering method for repeat analysis in DNA sequences (2001) (100)
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv . oryzae PXO 99 A (2008) (99)
Open questions: How many genes do we have? (2018) (98)
Genome Sequence of the Dioxin-Mineralizing Bacterium Sphingomonas wittichii RW1 (2010) (98)
Hawkeye: an interactive visual analytics tool for genome assemblies (2007) (97)
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank (2020) (96)
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana (2007) (93)
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole genome sequencing studies at scale (2020) (93)
An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing (2017) (90)
A nearest hyperrectangle learning method (2004) (88)
Predicting protein secondary structure with a nearest-neighbor algorithm. (1992) (85)
Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm (1995) (84)
First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae) (2016) (84)
The Complete Genome Sequence of Bacillus anthracis Ames “Ancestor” (2008) (84)
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification (2010) (82)
Comprehensive DNA Signature Discovery and Validation (2007) (82)
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. (2005) (82)
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions (2006) (81)
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 (2020) (81)
Detection and correction of false segmental duplications caused by genome mis-assembly (2010) (81)
Finding a Majority Among N Votes. (1982) (78)
The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae (2017) (76)
Human contamination in bacterial genomes has created thousands of spurious proteins (2019) (76)
Computational discovery of internal micro-exons. (2003) (76)
Sequence analysis TopHat : discovering splice junctions with RNA-Seq (2009) (75)
DECISION TREES FOR AUTOMATED IDENTIFICATION OF COSMIC-RAY HITS IN HUBBLE SPACE TELESCOPE IMAGES (1995) (74)
The tuatara genome reveals ancient features of amniote evolution (2020) (74)
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms (2015) (74)
The sequence and analysis of Trypanosoma brucei chromosome II. (2003) (72)
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads (2008) (72)
Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification (2016) (71)
Short Read Mapping: An Algorithmic Tour (2017) (70)
Learning with Nested Generalized Exemplars (1990) (70)
On Comparing Classifiers: A Critique of Current Research and Methods (1999) (69)
Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries (2017) (68)
Sequence and analysis of the Arabidopsis genome. (2001) (67)
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders (2003) (67)
Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies (2011) (66)
Efficient Algorithms for Finding Multi-way Splits for Decision Trees (1995) (64)
Towards a Better Understanding of Memory-based Reasoning Systems (1994) (62)
Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths (2011) (62)
Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster. (2004) (61)
Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships (2015) (61)
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes (2010) (61)
Removing contaminants from databases of draft genomes (2018) (61)
Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data (2022) (60)
Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics (2018) (56)
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A (2008) (56)
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations (2019) (55)
Physiogenomic resources for rat models of heart, lung and blood disorders (2006) (52)
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome (2019) (52)
Faculty Opinions recommendation of SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. (2013) (52)
Horizontal gene transfer is not a hallmark of the human genome (2017) (50)
Computational gene finding in plants (2004) (50)
Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species. (2001) (49)
Automated correction of genome sequence errors. (2004) (49)
The contents of the syringe (2008) (48)
Corrigendum: Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus (2006) (48)
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies (2013) (47)
Genome Sequence of the Wolbachia Endosymbiont of Culex quinquefasciatus JHB (2008) (47)
Decision Tree Induction: How Effective is the Greedy Heuristic? (1995) (46)
Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences (2013) (46)
Open access to tree genomes: the path to a better forest (2013) (46)
Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing (2019) (46)
Learning with a Helpful Teacher (1991) (45)
Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing (2018) (45)
Efficient decoding algorithms for generalized hidden Markov model gene finders (2005) (45)
A Probabilistic Framework for Memory-Based Reasoning (1998) (44)
Genomic architecture of complex traits in loblolly pine. (2018) (44)
Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise (2018) (44)
Insignia: a DNA signature search web server for diagnostic assay development (2009) (41)
Statement on the consideration of biodefence and biosecurity (2003) (41)
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding (2005) (41)
Genomic Variation Among and Within Six Juglans Species (2018) (41)
Flexible isoform-level differential expression analysis with Ballgown (2014) (40)
Finding Genes in Human DNA with a Hidden Markov Model (1996) (40)
Distance Metrics for Instance-Bsed Learning (1991) (40)
Use and mis-use of supplementary material in science publications (2015) (39)
A Reference Genome Sequence for Giant Sequoia (2020) (39)
Improving pan-genome annotation using whole genome multiple alignment (2011) (39)
Flexible analysis of transcriptome assemblies with Ballgown (2014) (39)
Managing information for concurrent engineering: Challenges and barriers (1990) (38)
Online Supplementary Material (2015) (38)
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie (2020) (38)
Semi-automated assembly of high-quality diploid human reference genomes (2022) (37)
Best-Case Results for Nearest-Neighbor Learning (1995) (37)
Learning to Catch: Applying Nearest Neighbor Algorithms to Dynamic Control Tasks (1994) (36)
2009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates (2009) (36)
Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space (2015) (36)
The complete sequence of a human Y chromosome (2022) (35)
Genomic Features of a Bumble Bee Symbiont Reflect Its Host Environment (2014) (35)
The Genome Assembly Archive: A New Public Resource (2004) (35)
Liftoff: an accurate gene annotation mapping tool (2020) (33)
Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs (2018) (33)
Assembly and annotation of an Ashkenazi human reference genome (2020) (32)
BMC Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99 A (2008) (32)
Genome-Wide Analysis of Repetitive Elements in Papaya (2008) (31)
Next-generation sequencing: insights to advance clinical investigations of the microbiome (2022) (31)
Closure of the NCBI SRA and implications for the long-term future of genomics data storage (2011) (31)
Erratum: Repetitive DNA and next-generation sequencing: Computational challenges and solutions (Nature Reviews Genetics (2012) 13 (36-46)) (2012) (31)
Analysis of power spectral densities of electrocardiograms (1971) (30)
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX (2012) (30)
Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities (2019) (30)
Uncensored exchange of scientific results (2003) (29)
Heuristics for Inductive Learning (1985) (29)
A Teaching Strategy for Memory-Based Control (1997) (29)
Efficient oligonucleotide probe selection for pan-genomic tiling arrays (2009) (27)
Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome (2012) (26)
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species (2005) (26)
Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop (2008) (25)
Combining Genetic Algorithms with Memory Based Reasoning (1995) (24)
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes (2020) (24)
Inherited causes of clonal haematopoiesis in 97,691 whole genomes (2020) (21)
Analysis of Carica papaya Telomeres and Telomere-Associated Proteins: Insights into the Evolution of Telomere Maintenance in Brassicales (2008) (20)
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie (2021) (20)
Do-it-yourself genetic testing (2010) (20)
Reminder to deposit DNA sequences (2016) (19)
Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. (2020) (19)
Bioinformatics: Finding genes in Plasmodium falciparum (2000) (18)
Local Induction of Decision Trees: Towards Interactive Data Mining (1996) (18)
Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing (2013) (18)
Detection of lineage-specific evolutionary changes among primate species (2011) (18)
Genome sequencing unveils a regulatory landscape of platelet reactivity (2019) (18)
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks (2021) (17)
16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model (2017) (17)
HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer (2018) (17)
Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin (2021) (16)
Guillain-Barré Syndrome Outbreak in Peru 2019 Associated With Campylobacter jejuni Infection (2021) (16)
An empirical analysis of training protocols for probabilistic gene finders (2005) (16)
Finding Genes in DNA Using Decision Trees and Dynamic Programming (1996) (16)
Contamination in the Draft of the Human Genome Masquerades As Lateral Gene Transfer (2002) (16)
A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes. (2007) (16)
Improving Classification Methods via Feature Selection (1992) (15)
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons (2006) (14)
Gene discovery in DNA sequences (1999) (14)
Cryptococcus neoformans The Genome of the Basidiomycetous Yeast and Human Pathogen (2012) (14)
Metagenome analysis using the Kraken software suite (2022) (14)
Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies (2020) (13)
Genomics: Yeast rises again (2003) (12)
Using GlimmerM to Find Genes in Eukaryotic Genomes (2003) (12)
Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. (2020) (11)
An empirical analysis of training protocols for probabilistic gene finders (2004) (11)
Induction of shallow decision trees (2007) (11)
Chapter 10 - Decision trees and Markov chains for gene finding (1998) (11)
Nested Hyper-Rectangles for Exemplar-Based Learning (1989) (11)
Testing Simple Polygons (1997) (10)
Testing Orthogonal Shapes (1995) (10)
The SAMBA tool uses long reads to improve the contiguity of genome assemblies (2021) (10)
Chapter 3 - An introduction to biological sequence analysis (1998) (10)
Lateral gene transfer or viral colonization? (2001) (10)
Learning Nested Concept Classes with Limited Storage (1991) (10)
Chapter 18 Committees of decision trees (1996) (10)
Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments (2020) (10)
Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir (2021) (9)
HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts (2014) (9)
Removing Contaminants from Metagenomic Databases (2018) (9)
Shared data are key to beating threat from flu (2006) (9)
Pinpointing good hypotheses with heuristics (1986) (9)
Faculty Opinions recommendation of Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. (2014) (9)
Balrog: A universal protein model for prokaryotic gene prediction (2020) (9)
Ultrafast and accurate 16S microbial community analysis using Kraken 2 (2020) (8)
Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space (2014) (8)
First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans) (2017) (8)
Next-generation genome annotation: we still struggle to get it right (2019) (8)
DIAMUND: Direct Comparison of Genomes to Detect Mutations (2013) (8)
Recent advances in RNA sequence analysis (2010) (8)
The Perils of Gene Patents (2012) (8)
Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection (2015) (8)
Algorithms in Bioinformatics, 9th International Workshop, WABI 2009, Philadelphia, PA, USA, September 12-13, 2009. Proceedings (2009) (7)
An APOO Pseudogene on Chromosome 5q Is Associated With Low-Density Lipoprotein Cholesterol Levels (2018) (7)
Unrestricted free access works and must continue (2003) (7)
Genomic characterization of chromosome translocations in patients with T/myeloid mixed-phenotype acute leukemia (2018) (7)
Generating Hypotheses to Explain Prediction Failures (1983) (7)
The giant sequoia genome and proliferation of disease resistance genes (2020) (7)
Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia. (2021) (6)
Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children with asthma. (2019) (6)
Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18 (2008) (6)
A Method to Improve the Performance of Translation Start Site Detection and Its Application for Gene Finding (2002) (6)
Exemplar-Based Learning to Predict Protein Folding (1990) (6)
High performance computing for dna sequence alignment and assembly (2010) (5)
PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools (2021) (5)
Genome-wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia (2021) (5)
Finding Repeats in Genome Sequences (2008) (5)
Serum interferon as a biological marker in malignant tumors. (1985) (5)
Databases: Reminder to deposit DNA sequences (2016) (5)
Bootstrapping Memory-Based Learning with Genetic Algorithms (1994) (4)
The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order (2019) (4)
Erratum to: An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing (2017) (4)
A reference-quality, fully annotated genome from a Puerto Rican individual (2021) (4)
Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent (2019) (4)
Sequestration: inadvertently killing biomedical research to score political points (2013) (4)
Gemina: A Web-Based Epidemiology and Genomic Metadata System Designed to Identify Infectious Agents (2007) (4)
The novel fusion transcript NR5A2‐KLHL29FT is generated by an insertion at the KLHL29 locus (2017) (4)
The Terabase Search Engine: a large‐scale relational database of short‐read sequences (2018) (4)
Metagenomic classification with KrakenUniq on low-memory computers (2022) (4)
Lateral gene transfer or viral colonization? [3] (multiple letters) (2001) (4)
Releasing the Kraken (2021) (4)
Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies (2022) (4)
The genome of the American groundhog, Marmota monax (2020) (3)
Machine learning moves out of the lab (1988) (3)
Faculty Opinions recommendation of Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. (2018) (3)
Genes and genomes, an imperfect world: comparison of gene annotations of two Bos taurus draft assemblies (2010) (3)
Life Inside a Dinosaur Bone: a Thriving Microbiome (2018) (3)
Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals (2022) (3)
Genomics of Theileria parva (2002) (3)
Mind the gaps (2010) (3)
Author ' s personal copy Bioinformatics challenges of new sequencing technology (2008) (3)
Author Correction: Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations (2019) (3)
LEARNING BY BUILDING CAUSAL EXPLANATIONS. (1984) (3)
Structure-guided isoform identification for the human transcriptome (2022) (3)
The Human "Contaminome" and Understanding Infectious Disease. (2022) (2)
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources (2022) (2)
Highly accurate isoform identification for the human transcriptome (2022) (2)
Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection. (2015) (2)
Hervé Tettelin pneumoniae Streptococcus Complete Genome Sequence of a Virulent Isolate of (2013) (2)
Data from: The genomes of two key bumblebee species with primitive eusocial organisation (2015) (2)
Assembly and annotation of an Ashkenazi human reference genome (2020) (2)
Next-Generation Sequencing in Neuropathologic Diagnosis of Infections of the Nervous System (Open Access) (2016) (2)
Efforts to deregulate Rainbow papaya in Japan: Molecular characterization of transgene and vector inserts (2010) (2)
Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes (2020) (2)
Investigations of the Greedy Heuristic for Classiication Tree Induction (2007) (2)
It is time to end the patenting of software (2006) (2)
Gene finding in eukaryotes (2002) (2)
A new rhesus macaque assembly and annotation for next-generation sequencing analyses (2014) (2)
A reference-quality, fully annotated genome from a Puerto Rican individual. (2021) (2)
A preliminary comparison of the mouse and human genomes (2002) (2)
CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure (2022) (2)
Microbial infection & immune defence (2000) (1)
Bioinformatics Methods for Microbial Detection and Forensic Diagnostic Design (2005) (1)
Real world knowledge representation (1987) (1)
Erosion and Redeposition of Reservoir Sediment in Response to Removal of Marmot Dam, Sandy River, Oregon (2008) (1)
Balrog: A universal protein model for prokaryotic gene prediction. (2021) (1)
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions (2013) (1)
Faculty Opinions recommendation of The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome. (2008) (1)
Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet. (2020) (1)
LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies (2022) (1)
Trypanosoma brucei The Genome of the African Trypanosome (2007) (1)
Resources and Opportunities Rice Bioinformatics . Analysis of Rice Sequence Data and Leveraging the Data to Other Plant Species 1 (2001) (1)
Erratum: Uncensored exchange of scientific results (Proceedings of the National Academy of Sciences (2003) 100, 4, (1464) DOI: 10.1073/pnas.0630491100) (2012) (1)
NIH funding: It does support innovators (2013) (1)
Proceedings of the 9th international conference on Algorithms in bioinformatics (2009) (1)
Rapidly fatal infection with Bacillus cereus/thuringiensis: genome assembly of the responsible pathogen and consideration of possibly contributing toxins. (2021) (1)
Kraken: ultrafast metagenomic sequence classification using exact alignments (2014) (1)
Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries (2018) (1)
JASPER: a fast genome polishing tool that improves accuracy and creates population-specific reference genomes (2022) (1)
Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies (2014) (1)
The 15th Genomic Standards Consortium meeting (2013) (1)
Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries (2018) (1)
The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual (2022) (1)
Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program (2021) (1)
Open access to tree genomes: the path to a better forest (2013) (1)
Variant-specific inflation factors for assessing population stratification at the phenotypic variance level (2021) (0)
Transcriptome assembly from long-read RNA-seq alignments with StringTie2 (2019) (0)
[Clinical and laboratory aspects of Kahler's disease. Considerations on 19 cases]. (1966) (0)
Faculty Opinions recommendation of A high-coverage genome sequence from an archaic Denisovan individual. (2012) (0)
Using Protein Domains to Improve the Accuracy of Ab Initio Gene Finding (2007) (0)
Laboratory Strains Clinical and Mycobacterium tuberculosis Whole-Genome Comparison of (2002) (0)
SkewIT: Skew Index Test for detecting mis-assembled bacterial genomes (2020) (0)
Addtional files-2 (2015) (0)
Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries (2020) (0)
Book Review: Contesting the Market: Pay Equity and the Politics of Economic Restructuring (2002) (0)
Algorithms for whole genome analysis (2001) (0)
Author Correction: Inherited causes of clonal haematopoiesis in 97,691 whole genomes (2021) (0)
Identifying mis-assembled bacterial genomes using GC Skew (2019) (0)
Publisher Correction: The tuatara genome reveals ancient features of amniote evolution (2020) (0)
A tutorial introduction to computation for biologists (1998) (0)
Faculty Opinions recommendation of Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. (2019) (0)
Bioinformatics : Finding genes in Plasmodium falciparum. Authors' reply (2000) (0)
Artificial Intelligence A probabilistic framework for memory-based reasoning (1997) (0)
Supplementary Material 24 (2010) (0)
Book Review:Computational Molecular Biology: An Algorithmic Approach Pavel A. Pevzner (2001) (0)
Genome interpretation and assembly-recent progress and next steps. (2012) (0)
Improving Genome Assembly without Sequencing (2005) (0)
Genome-wide association study of asthma in individuals of African ancestry reveals novel asthma susceptibility loci (2017) (0)
Keratoconus transcriptome analysis by RNA-Seq of individual corneas identifies dysregulated cell survival and mesenchymal regulatory programs. (2015) (0)
Liftoff: A pipeline for mapping genes onto high-quality genome assemblies (2019) (0)
Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale (2020) (0)
The tuatara genome reveals ancient features of amniote evolution (2020) (0)
Use and mis-use of supplementary material in science publications (2015) (0)
Foreword by Steven Salzberg (2007) (0)
SMRT sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL effector gene relationships (2015) (0)
Sequestration: inadvertently killing biomedical research to score political points (2013) (0)
Open access: the sooner the better. (2009) (0)
Abstracts of Beyond the Genome: The true gene count, human evolution and disease genomics. Boston, Massachusetts, USA. October 11-13, 2010. (2010) (0)
BIOINFORMATICS ORIGINAL PAPER (2009) (0)
Artificial Intelligence Approaches to Problems in the Human Genome Project (2001) (0)
The status of the human gene catalogue (2023) (0)
Computational challenges in next-generation genomics (2013) (0)
Experimental results with NGE (1990) (0)
Whole-genome sequence analysis for pathogen detection and diagnostics (2010) (0)
Faculty Opinions recommendation of A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule. (2016) (0)
Pan-genomics in the human genome era (2020) (0)
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 (2020) (0)
Assembly of a pan-genome from deep sequencing of 910 humans of African descent (2018) (0)
Faculty Opinions recommendation of Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. (2009) (0)
Faculty Opinions recommendation of Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. (2010) (0)
Open questions: How many genes do we have? (2018) (0)
Horizontal gene transfer is not a hallmark of the human genome (2017) (0)
Cornea Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing (2018) (0)
The Tetrahymena thermophila genome sequence: 1. Genome‐wide uniformity of macronuclear chromosome copy number in spite of amitotic (random) copy distribution (2005) (0)
The NGE learning algorithm (1990) (0)
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank (2020) (0)
Deep-coverage whole genome sequences and blood lipids among 16,324 individuals (2018) (0)
Terminating contamination – Large-scale search identifies >2,000,000 contaminated entries in GenBank (2019) (0)
CHAPTER 21: Targeting of the rice transcriptome by TAL effectors of Xanthomonas oryzae (2017) (0)
A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo. (2012) (0)
CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise (2018) (0)
Keynote talk Genome paleontology: discoveries from complete genomes (2003) (0)
Additional files 1 (2011) (0)
Next-generation sequencing in neuropathological diagnosis of infections of the nervous system (2016) (0)
Clonal haematopoiesis and risk of chronic liver disease (2023) (0)
Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium (2021) (0)
Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries (2018) (0)
Quality-aware error correction of sequencing reads (2010) (0)
Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach (2021) (0)
Title 16 GT : A fast and sensitive variant caller using a 16-genotypeprobabilistic model (2017) (0)
The genomes of two key bumblebee species with primitive eusocial organization (2015) (0)
Role of the Dihydrofolate Reductase DfrA (Rv2763c) in Trimethoprim- Sulfamethoxazole (Co-Trimoxazole) Resistance in Mycobacterium tuberculosis (2010) (0)
Open source, open access, and open data: why science moves faster in an open world (2016) (0)
JASPER: A fast genome polishing tool that improves accuracy of genome assemblies (2023) (0)
Investigating Open Reading Frames in Known and Novel Transcripts using ORFanage (2023) (0)
Generating Hypotheses to Explain (1983) (0)
Keynotes BIBM 2008 Assembling Genomes from Very Short Reads (2008) (0)
Faculty Opinions recommendation of Exome sequencing identifies the cause of a mendelian disorder. (2010) (0)
RAD tag (SgrAI) derived SNPs from Bombus impatiens (2015) (0)
The Complete Genome Sequence of Bacillus anthracis, Ames Ancestor. Genome Announcements (2009) (0)
Genome Paleontology: Discoveries from Complete Genomes (2003) (0)
Faculty Opinions recommendation of Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. (2018) (0)
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX (2012) (0)
Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations (2019) (0)
Author Correction: Assembly of a pan-genome from deep sequencing of 910 humans of African descent (2019) (0)

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