267(top 1%)
PR articles
180.8K(top 0.1%)
PR citations
115(top 0.1%)
PR h-index
134(top 0.1%)
h-index
330
documents
222.6K
doc citations
7.8K
citing journals
100
times ranked

Publications

276 PR articles • 195,125 PR citations • Sorted by year • Download PDF (PDF by citations)
Sort: Year | Citations
#ArticleIFCitationsLinks
1PSAURON: a tool for assessing protein annotation across a broad range of species
NAR Genomics and Bioinformatics, 2025, 7,
2.218Citations (PDF)
2Conservation assessment of human splice site annotation based on a 470-genome alignment
Nucleic Acids Research, 2025, 53,
15.50Citations (PDF)
3Reply to Austin and Korem, “Compositional transformations can reasonably introduce phenotype-associated values into sparse features”
MSystems, 2025, 10,
4.40Citations (PDF)
4Discovering Intron Gain Events in Humans Through Large-Scale Evolutionary Comparisons
Genome Biology and Evolution, 2025, 17,
2.40Citations (PDF)
5Phenotype to genotype: A new and rapid approach using whole-genome sequencing
PLoS Genetics, 2025, 21, e1011702
3.21Citations (PDF)
6Implementing governmental oversight of enhanced potential pandemic pathogen research
Journal of Virology, 2024, 98,
3.63Citations (PDF)
7A genome sequence for the threatened whitebark pine
G3: Genes, Genomes, Genetics, 2024, 14,
1.910Citations (PDF)
8Genomic variability in Zika virus in GBS cases in Colombia
PLoS ONE, 2024, 19, e0313545
2.30Citations (PDF)
9Upstream open reading frames may contain hundreds of novel human exons
PLoS Computational Biology, 2024, 20, e1012543
3.13Citations (PDF)
10JASPER: A fast genome polishing tool that improves accuracy of genome assemblies
PLoS Computational Biology, 2023, 19, e1011032
3.111Citations (PDF)
11Investigating open reading frames in known and novel transcripts using ORFanage
Nature Computational Science, 2023, 3, 700-708
11.623Citations (PDF)
12The complete sequence of a human Y chromosome
Nature, 2023, 621, 344-354
37.9362Citations (PDF)
13Major data analysis errors invalidate cancer microbiome findings
MBio, 2023, 14,
4.4151Citations (PDF)
14PhyloCSF++: a fast and user-friendly implementation of PhyloCSF with annotation tools
Bioinformatics, 2022, 38, 1440-1442
4.716Citations (PDF)
15Genome‐wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia
Plant Journal, 2022, 109, 7-22
6.236Citations (PDF)
16The SAMBA tool uses long reads to improve the contiguity of genome assemblies
PLoS Computational Biology, 2022, 18, e1009860
3.145Citations (PDF)
17Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin
G3: Genes, Genomes, Genetics, 2022, 12,
1.948Citations (PDF)
18A reference-quality, fully annotated genome from a Puerto Rican individual
Genetics, 2022, 220,
4.217Citations (PDF)
19Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data
Nature Genetics, 2022, 54, 263-273
25.2308Citations (PDF)
20The complete sequence of a human genome
Science, 2022, 376, 44-53
36.22,665Citations (PDF)
21Next-generation sequencing: insights to advance clinical investigations of the microbiome
Journal of Clinical Investigation, 2022, 132,
10.6344Citations (PDF)
22High-quality genome and methylomes illustrate features underlying evolutionary success of oaks
Nature Communications, 2022, 13,
13.761Citations (PDF)
23The Human “Contaminome” and Understanding Infectious Disease
New England Journal of Medicine, 2022, 387, 943-946
34.616Citations (PDF)
24Metagenome analysis using the Kraken software suite
Nature Protocols, 2022, 17, 2815-2839
14.4583Citations (PDF)
25Semi-automated assembly of high-quality diploid human reference genomes
Nature, 2022, 611, 519-531
37.9176Citations (PDF)
263D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources
GigaScience, 2022, 11,
3.227Citations (PDF)
27Effects of transcriptional noise on estimates of gene and transcript expression in RNA sequencing experiments
Genome Research, 2021, 31, 301-308
4.631Citations (PDF)
28Liftoff: accurate mapping of gene annotations
Bioinformatics, 2021, 37, 1639-1643
4.7812Citations (PDF)
29Dissecting the Polygenic Basis of Cold Adaptation Using Genome-Wide Association of Traits and Environmental Data in Douglas-fir
Genes, 2021, 12, 110
2.529Citations (PDF)
30Balrog: A universal protein model for prokaryotic gene prediction
PLoS Computational Biology, 2021, 17, e1008727
3.130Citations (PDF)
31Guillain-Barré Syndrome Outbreak in Peru 2019 Associated With Campylobacter jejuni Infection
Neurology: Neuroimmunology and NeuroInflammation, 2021, 8,
6.730Citations (PDF)
32Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
Nature, 2021, 590, 290-299
37.91,952Citations (PDF)
33Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie
Genetics, 2021, 218,
4.269Citations (PDF)
34Genome sequencing unveils a regulatory landscape of platelet reactivity
Nature Communications, 2021, 12,
13.746Citations (PDF)
35Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach
F1000Research, 2021, 10, 820
0.56Citations (PDF)
36Rapidly fatal infection with Bacillus cereus/thuringiensis: genome assembly of the responsible pathogen and consideration of possibly contributing toxins
Diagnostic Microbiology and Infectious Disease, 2021, 101, 115534
1.68Citations (PDF)
37Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification
Bioinformatics, 2020, 36, 1303-1304
4.7453Citations (PDF)
38Inherited causes of clonal haematopoiesis in 97,691 whole genomes
Nature, 2020, 586, 763-768
37.9655Citations (PDF)
39Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance
Plant Journal, 2020, 104, 365-376
6.248Citations (PDF)
40The tuatara genome reveals ancient features of amniote evolution
Nature, 2020, 584, 403-409
37.9124Citations (PDF)
41A Reference Genome Sequence for Giant Sequoia
G3: Genes, Genomes, Genetics, 2020, 10, 3907-3919
1.985Citations (PDF)
42Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2
Microbiome, 2020, 8,
11.5233Citations (PDF)
43Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies
Genetics, 2020, 216, 599-608
4.249Citations (PDF)
44Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
Genome Biology, 2020, 21,
8.1217Citations (PDF)
45High-quality chromosome-scale assembly of the walnut ( Juglans regia L.) reference genome
GigaScience, 2020, 9,
3.2120Citations (PDF)
46Assembly and annotation of an Ashkenazi human reference genome
Genome Biology, 2020, 21,
8.154Citations (PDF)
47The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies
PLoS Computational Biology, 2020, 16, e1007981
3.1368Citations (PDF)
48Pan-genomics in the human genome era
Nature Reviews Genetics, 2020, 21, 243-254
47.0310Citations (PDF)
49De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population
Proceedings of the National Academy of Sciences of the United States of America, 2020, 117, 2560-2569
7.5105Citations (PDF)
50Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing
PLoS Genetics, 2020, 16, e1008571
3.2138Citations (PDF)
51SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes
PLoS Computational Biology, 2020, 16, e1008439
3.160Citations (PDF)
52The genome of the American groundhog, Marmota monax
F1000Research, 2020, 9, 1137
0.54Citations (PDF)
53The Terabase Search Engine: a large-scale relational database of short-read sequences
Bioinformatics, 2019, 35, 665-670
4.78Citations (PDF)
54Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Nature Biotechnology, 2019, 37, 907-915
29.812,746Citations (PDF)
55Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma
Chest, 2019, 156, 1068-1079
1.06Citations (PDF)
56Human contamination in bacterial genomes has created thousands of spurious proteins
Genome Research, 2019, 29, 954-960
4.6150Citations (PDF)
57Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations
Nature Communications, 2019, 10,
13.789Citations (PDF)
58Transcriptome assembly from long-read RNA-seq alignments with StringTie2
Genome Biology, 2019, 20,
8.11,757Citations (PDF)
59Genomic architecture of complex traits in loblolly pine
New Phytologist, 2019, 221, 1789-1801
8.171Citations (PDF)
60A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics, 2019, 20, 1125-1136
6.6486Citations (PDF)
61CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise
Genome Biology, 2018, 19,
8.1312Citations (PDF)
62Genomic Variation Among and Within SixJuglansSpecies
G3: Genes, Genomes, Genetics, 2018, 8, 2153-2165
1.989Citations (PDF)
63Removing contaminants from databases of draft genomes
PLoS Computational Biology, 2018, 14, e1006277
3.1119Citations (PDF)
64Development and Optimization of Metagenomic Next-Generation Sequencing Methods for Cerebrospinal Fluid Diagnostics
Journal of Clinical Microbiology, 2018, 56,
4.095Citations (PDF)
65Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing
2018, 59, 280
63Citations (PDF)
66Assembly of a pan-genome from deep sequencing of 910 humans of African descent
Nature Genetics, 2018, 51, 30-35
25.2358Citations (PDF)
67MUMmer4: A fast and versatile genome alignment system
PLoS Computational Biology, 2018, 14, e1005944
3.12,317Citations (PDF)
68Short Read Mapping: An Algorithmic Tour
Proceedings of the IEEE, 2017, 105, 436-458
9.570Citations (PDF)
69The novel fusion transcript NR5A2‐KLHL29FT is generated by an insertion at the KLHL29 locus
Cancer, 2017, 123, 1507-1515
4.06Citations (PDF)
70Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii , a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
Genome Research, 2017, 27, 787-792
4.6474Citations (PDF)
7116GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
GigaScience, 2017, 6,
3.212Citations (PDF)
72First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (Formerly Scedosporium prolificans )
G3: Genes, Genomes, Genetics, 2017, 7, 3831-3836
1.921Citations (PDF)
73The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae
G3: Genes, Genomes, Genetics, 2017, 7, 3157-3167
1.9120Citations (PDF)
74Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
Nature, 2017, 551, 498-502
37.9657Citations (PDF)
75Presence of Human Hepegivirus-1 in a Cohort of People Who Inject Drugs
Annals of Internal Medicine, 2017, 167, 1-7
9.733Citations (PDF)
76The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum
GigaScience, 2017, 6,
3.2251Citations (PDF)
77An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing
GigaScience, 2017, 6,
3.297Citations (PDF)
78First Draft Assembly and Annotation of the Genome of a California Endemic OakQuercus lobataNée (Fagaceae)
G3: Genes, Genomes, Genetics, 2016, 6, 3485-3495
1.9113Citations (PDF)
79Reminder to deposit DNA sequences
Nature, 2016, 533, 179-179
37.910Citations (PDF)
80Centrifuge: rapid and sensitive classification of metagenomic sequences
Genome Research, 2016, 26, 1721-1729
4.61,397Citations (PDF)
81Sequence of the Sugar Pine Megagenome
Genetics, 2016, 204, 1613-1626
4.2196Citations (PDF)
82The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non‐structural polyphenols
Plant Journal, 2016, 87, 507-532
6.2271Citations (PDF)
83Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system
Neurology: Neuroimmunology and NeuroInflammation, 2016, 3,
6.7173Citations (PDF)
84Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships
Microbial Genomics, 2015, 1,
2.095Citations (PDF)
85Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations
Nature, 2015, 517, 381-385
37.9500Citations (PDF)
86StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Nature Biotechnology, 2015, 33, 290-295
29.812,805Citations (PDF)
87HISAT: a fast spliced aligner with low memory requirements
Nature Methods, 2015, 12, 357-360
24.622,430Citations (PDF)
88Ballgown bridges the gap between transcriptome assembly and expression analysis
Nature Biotechnology, 2015, 33, 243-246
29.8841Citations (PDF)
89The genomes of two key bumblebee species with primitive eusocial organization
Genome Biology, 2015, 16,
12.2376Citations (PDF)
90Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
Genome Research, 2015, 25, 1401-1409
4.6107Citations (PDF)
91Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection
F1000Research, 2015, 4, 180
0.59Citations (PDF)
92Re-analysis of metagenomic sequences from acute flaccid myelitis patients reveals alternatives to enterovirus D68 infection
F1000Research, 2015, 4, 180
0.56Citations (PDF)
93A new rhesus macaque assembly and annotation for next-generation sequencing analyses
Biology Direct, 2014, 9,
4.3176Citations (PDF)
94Sequencing and Assembly of the 22-Gb Loblolly Pine Genome
Genetics, 2014, 196, 875-890
4.2307Citations (PDF)
95Kraken: ultrafast metagenomic sequence classification using exact alignments
Genome Biology, 2014, 15,
8.14,386Citations (PDF)
96Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies
Genome Biology, 2014, 15,
8.1463Citations (PDF)
97DIAMUND : Direct Comparison of Genomes to Detect Mutations
Human Mutation, 2014, 35, 283-288
4.59Citations (PDF)
98Genomic Features of a Bumble Bee Symbiont Reflect Its Host Environment
Applied and Environmental Microbiology, 2014, 80, 3793-3803
3.667Citations (PDF)
99Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation
Genetics, 2014, 196, 891-909
4.2220Citations (PDF)
100TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Genome Biology, 2013, 14,
8.112,644Citations (PDF)
101The MaSuRCA genome assembler
Bioinformatics, 2013, 29, 2669-2677
4.71,418Citations (PDF)
102GAGE-B: an evaluation of genome assemblers for bacterial organisms
Bioinformatics, 2013, 29, 1718-1725
4.7139Citations (PDF)
103Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies
Briefings in Bioinformatics, 2013, 14, 213-224
6.656Citations (PDF)
104NIH funding: It does support innovators
Nature, 2013, 493, 26-26
37.91Citations (PDF)
105Sequestration: inadvertently killing biomedical research to score political points
Genome Biology, 2013, 14, 109
12.22Citations (PDF)
106Genome-Guided Transcriptome Assembly in the Age of Next-Generation Sequencing
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013, 10, 1234-1240
2.918Citations (PDF)
107The COMBREX Project: Design, Methodology, and Initial Results
PLoS Biology, 2013, 11, e1001638
5.055Citations (PDF)
108EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes
Evolutionary Bioinformatics, 2013, 9,
1.3157Citations (PDF)
109Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences
PLoS ONE, 2013, 8, e72439
2.348Citations (PDF)
110Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
F1000Research, 2013, 2, 188
0.5462Citations (PDF)
111Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues
F1000Research, 2013, 2, 188
0.5320Citations (PDF)
112Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
Nucleic Acids Research, 2012, 40, e9-e9
15.5182Citations (PDF)
113Thousands of missed genes found in bacterial genomes and their analysis with COMBREX
Biology Direct, 2012, 7, 37
4.328Citations (PDF)
114Fast gapped-read alignment with Bowtie 2
Nature Methods, 2012, 9, 357-359
24.654,882Citations (PDF)
115GAGE: A critical evaluation of genome assemblies and assembly algorithms
Genome Research, 2012, 22, 557-567
4.6634Citations (PDF)
116Mis-Assembled “Segmental Duplications” in Two Versions of the Bos taurus Genome
PLoS ONE, 2012, 7, e42680
2.323Citations (PDF)
117Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp
Journal of Bacteriology, 2011, 193, 5450-5464
2.9199Citations (PDF)
118TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Genome Biology, 2011, 12,
8.1739Citations (PDF)
119Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths
Genome Biology, 2011, 12,
8.162Citations (PDF)
120Genome Assembly Has a Major Impact on Gene Content: A Comparison of Annotation in Two Bos Taurus Assemblies
PLoS ONE, 2011, 6, e21400
2.372Citations (PDF)
121PhymmBL expanded: confidence scores, custom databases, parallelization and more
Nature Methods, 2011, 8, 367-367
24.6107Citations (PDF)
122Improving pan-genome annotation using whole genome multiple alignment
BMC Bioinformatics, 2011, 12,
3.039Citations (PDF)
123Detection of lineage-specific evolutionary changes among primate species
BMC Bioinformatics, 2011, 12,
3.020Citations (PDF)
124COMBREX: a project to accelerate the functional annotation of prokaryotic genomes
Nucleic Acids Research, 2011, 39, D11-D14
15.546Citations (PDF)
125FLASH: fast length adjustment of short reads to improve genome assemblies
Bioinformatics, 2011, 27, 2957-2963
4.714,629Citations (PDF)
126Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108, 5027-5032
7.5163Citations (PDF)
127Mugsy: fast multiple alignment of closely related whole genomes
Bioinformatics, 2011, 27, 334-342
4.7477Citations (PDF)
128Repetitive DNA and next-generation sequencing: computational challenges and solutions
Nature Reviews Genetics, 2011, 13, 36-46
47.01,590Citations (PDF)
129Assembly of large genomes using second-generation sequencing
Genome Research, 2010, 20, 1165-1173
4.6425Citations (PDF)
130Clustering metagenomic sequences with interpolated Markov models
BMC Bioinformatics, 2010, 11,
3.098Citations (PDF)
131Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification
BMC Genomics, 2010, 11,
3.382Citations (PDF)
132Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis
PLoS Biology, 2010, 8, e1000475
5.0371Citations (PDF)
133Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Nature Biotechnology, 2010, 28, 511-515
29.815,291Citations (PDF)
134Do-it-yourself genetic testing
Genome Biology, 2010, 11,
8.118Citations (PDF)
135Detection and correction of false segmental duplications caused by genome mis-assembly
Genome Biology, 2010, 11,
8.1103Citations (PDF)
136Between a chicken and a grape: estimating the number of human genes
Genome Biology, 2010, 11, 206
12.2196Citations (PDF)
137The genome of woodland strawberry (Fragaria vesca)
Nature Genetics, 2010, 43, 109-116
25.21,165Citations (PDF)
138Recent advances in RNA sequence analysis
F1000 Biology Reports, 2010, 2,
2.213Citations (PDF)
139EFFORTS TO DEREGULATE RAINBOW PAPAYA IN JAPAN: MOLECULAR CHARACTERIZATION OF TRANSGENE AND VECTOR INSERTS
Acta Horticulturae, 2010, , 235-240
0.30Citations (PDF)
140Between a chicken and a grape: estimating the number of human genes
Genome Biology, 2010, 11, I1
12.20Citations (PDF)
1412009 Swine-Origin Influenza A (H1N1) Resembles Previous Influenza Isolates
PLoS ONE, 2009, 4, e6402
2.333Citations (PDF)
142OperonDB: a comprehensive database of predicted operons in microbial genomes
Nucleic Acids Research, 2009, 37, D479-D482
15.586Citations (PDF)
143Insignia: a DNA signature search web server for diagnostic assay development
Nucleic Acids Research, 2009, 37, W229-W234
15.541Citations (PDF)
144Efficient oligonucleotide probe selection for pan-genomic tiling arrays
BMC Bioinformatics, 2009, 10,
3.025Citations (PDF)
145The genome of the blood fluke Schistosoma mansoni
Nature, 2009, 460, 352-358
37.9981Citations (PDF)
146How to map billions of short reads onto genomes
Nature Biotechnology, 2009, 27, 455-457
29.8262Citations (PDF)
147Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models
Nature Methods, 2009, 6, 673-676
24.6551Citations (PDF)
148TopHat: discovering splice junctions with RNA-Seq
Bioinformatics, 2009, 25, 1105-1111
4.711,795Citations (PDF)
149A whole-genome assembly of the domestic cow, Bos taurus
Genome Biology, 2009, 10, R42
12.21,057Citations (PDF)
150Genome-Wide Analysis of Repetitive Elements in Papaya
Tropical Plant Biology, 2008, 1, 191-201
1.324Citations (PDF)
151Characterization of Insertion Sites in Rainbow Papaya, the First Commercialized Transgenic Fruit Crop
Tropical Plant Biology, 2008, 1, 293-309
1.329Citations (PDF)
152The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)
Nature, 2008, 452, 991-996
37.91,017Citations (PDF)
153Comparative genomics of the neglected human malaria parasite Plasmodium vivax
Nature, 2008, 455, 757-763
37.9792Citations (PDF)
154Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
BMC Genomics, 2008, 9, 204
3.3343Citations (PDF)
155Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
BMC Genomics, 2008, 9, 534
3.339Citations (PDF)
156Bioinformatics challenges of new sequencing technology
Trends in Genetics, 2008, 24, 142-149
9.8454Citations (PDF)
157Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Genome Biology, 2008, 9, R7
12.23,675Citations (PDF)
158What are decision trees?
Nature Biotechnology, 2008, 26, 1011-1013
29.8616Citations (PDF)
159Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
PLoS Computational Biology, 2008, 4, e1000186
3.146Citations (PDF)
160Re-Assembly of the Genome of Francisella tularensis Subsp. holarctica OSU18
PLoS ONE, 2008, 3, e3427
2.39Citations (PDF)
161Acquisition and Evolution of Plant Pathogenesis–Associated Gene Clusters and Candidate Determinants of Tissue-Specificity in Xanthomonas
PLoS ONE, 2008, 3, e3828
2.3100Citations (PDF)
162Comprehensive DNA Signature Discovery and Validation
PLoS Computational Biology, 2007, 3, e98
3.165Citations (PDF)
163A Unified Model Explaining the Offsets of Overlapping and Near-Overlapping Prokaryotic Genes
Molecular Biology and Evolution, 2007, 24, 2091-2098
4.712Citations (PDF)
164Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
Genome Biology, 2007, 8, R22
12.2471Citations (PDF)
165Draft Genome of the Filarial Nematode Parasite Brugia malayi
Science, 2007, 317, 1756-1760
36.2591Citations (PDF)
166Identifying bacterial genes and endosymbiont DNA with Glimmer
Bioinformatics, 2007, 23, 673-679
4.72,994Citations (PDF)
167Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses
Emerging Infectious Diseases, 2007, 13, 713-718
3.8199Citations (PDF)
168Evolution of genes and genomes on the Drosophila phylogeny
Nature, 2007, 450, 203-218
37.91,992Citations (PDF)
169A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana
BMC Bioinformatics, 2007, 8,
3.085Citations (PDF)
170A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons
Algorithms for Molecular Biology, 2006, 1,
1.211Citations (PDF)
171Title is missing!
Genome Biology, 2006, 7, S9
12.262Citations (PDF)
172Shared data are key to beating threat from flu
Nature, 2006, 440, 605-605
37.95Citations (PDF)
173Physiogenomic resources for rat models of heart, lung and blood disorders
Nature Genetics, 2006, 38, 234-239
25.249Citations (PDF)
174It is time to end the patenting of software
Bioinformatics, 2006, 22, 1416-1417
4.72Citations (PDF)
175Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote
PLoS Biology, 2006, 4, e286
5.0702Citations (PDF)
176Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution
Nature, 2005, 437, 1162-1166
37.9438Citations (PDF)
177Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
Nature, 2005, 438, 1151-1156
37.91,325Citations (PDF)
178Beware of mis-assembled genomes
Bioinformatics, 2005, 21, 4320-4321
4.7172Citations (PDF)
179Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species
Genome Research, 2005, 15, 1284-1291
4.674Citations (PDF)
180JIGSAW: integration of multiple sources of evidence for gene prediction
Bioinformatics, 2005, 21, 3596-3603
4.7151Citations (PDF)
181Efficient implementation of a generalized pair hidden Markov model for comparative gene finding
Bioinformatics, 2005, 21, 1782-1788
4.739Citations (PDF)
182Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses
PLoS Biology, 2005, 3, e300
5.0353Citations (PDF)
183Title is missing!
Genome Biology, 2005, 6, R23
12.2131Citations (PDF)
184Automated correction of genome sequence errors
Nucleic Acids Research, 2004, 32, 562-569
15.542Citations (PDF)
185TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders
Bioinformatics, 2004, 20, 2878-2879
4.71,813Citations (PDF)
186Comparative genome assembly
Briefings in Bioinformatics, 2004, 5, 237-248
6.6199Citations (PDF)
187Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
PLoS Biology, 2004, 2, e303
5.0294Citations (PDF)
188DAGchainer: a tool for mining segmental genome duplications and synteny
Bioinformatics, 2004, 20, 3643-3646
4.7372Citations (PDF)
189Gene synteny and evolution of genome architecture in trypanosomatids
Molecular and Biochemical Parasitology, 2004, 134, 183-191
1.394Citations (PDF)
190Title is missing!
BMC Bioinformatics, 2004, 5, 206
3.025Citations (PDF)
191Title is missing!
Genome Biology, 2004, 5, R61
12.2186Citations (PDF)
192Insight into the genome of Aspergillus fumigatus: analysis of a 922kb region encompassing the nitrate assimilation gene cluster
Fungal Genetics and Biology, 2004, 41, 443-453
2.163Citations (PDF)
193The Genome Assembly Archive: A New Public Resource
PLoS Biology, 2004, 2, e285
5.030Citations (PDF)
194Title is missing!
Plant Molecular Biology, 2003, 51, 859-866
3.2117Citations (PDF)
195Unrestricted free access works and must continue
Nature, 2003, 422, 801-801
37.97Citations (PDF)
196Using MUMmer to Identify Similar Regions in Large Sequence Sets
Current Protocols in Bioinformatics, 2003, 00,
3.3552Citations (PDF)
197The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria
Nature, 2003, 423, 81-86
37.9779Citations (PDF)
198The sequence and analysis of Trypanosoma brucei chromosome II
Nucleic Acids Research, 2003, 31, 4856-4863
15.559Citations (PDF)
199Computational Discovery of Internal Micro-Exons
Genome Research, 2003, 13, 1216-1221
4.669Citations (PDF)
200GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
Nucleic Acids Research, 2003, 31, 3601-3604
15.563Citations (PDF)
201Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae
Nucleic Acids Research, 2003, 31, 2134-2147
15.5267Citations (PDF)
202Using GlimmerM to Find Genes in Eukaryotic Genomes
Current Protocols in Bioinformatics, 2003, 00,
3.35Citations (PDF)
203Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
Nucleic Acids Research, 2003, 31, 5654-5666
15.52,200Citations (PDF)
204Hierarchical Scaffolding With Bambus
Genome Research, 2003, 14, 149-159
4.6175Citations (PDF)
205Computational Gene Prediction Using Multiple Sources of Evidence
Genome Research, 2003, 14, 142-148
4.6115Citations (PDF)
206A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome
Science, 2002, 296, 1661-1671
36.2349Citations (PDF)
207Comparative Genome and Proteome Analysis of Anopheles gambiae and Drosophila melanogaster
Science, 2002, 298, 149-159
36.2542Citations (PDF)
208The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts
Proceedings of the National Academy of Sciences of the United States of America, 2002, 99, 13148-13153
7.5433Citations (PDF)
209Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains
Journal of Bacteriology, 2002, 184, 5479-5490
2.9662Citations (PDF)
210Fast algorithms for large-scale genome alignment and comparison
Nucleic Acids Research, 2002, 30, 2478-2483
15.5989Citations (PDF)
211The Genome Sequence of the Malaria Mosquito Anopheles gambiae
Science, 2002, 298, 129-149
36.21,916Citations (PDF)
212Title is missing!
Genome Biology, 2002, 3, research0029.1
12.2156Citations (PDF)
213Contamination in the Draft of the Human Genome Masquerades As Lateral Gene Transfer
DNA Sequence, 2002, 13, 75-76
0.518Citations (PDF)
214A preliminary comparison of the mouse and human genomes
International Congress Series, 2002, 1246, 169-181
0.22Citations (PDF)
215Genome sequence assembly: algorithms and issues
Computer, 2002, 35, 47-54
0.762Citations (PDF)
216Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14
Nature, 2002, 419, 531-534
37.9170Citations (PDF)
217Genome sequence of the human malaria parasite Plasmodium falciparum
Nature, 2002, 419, 498-511
37.94,102Citations (PDF)
218Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii
Nature, 2002, 419, 512-519
37.9676Citations (PDF)
219Title is missing!
Plant Molecular Biology, 2002, 48, 39-48
3.242Citations (PDF)
220Title is missing!
Genome Biology, 2001, 2, research0027.1
12.2123Citations (PDF)
221GeneSplicer: a new computational method for splice site prediction
Nucleic Acids Research, 2001, 29, 1185-1190
15.5560Citations (PDF)
222The Sequence of the Human Genome
Science, 2001, 291, 1304-1351
36.213,090Citations (PDF)
223Complete genome sequence of Caulobacter crescentus
Proceedings of the National Academy of Sciences of the United States of America, 2001, 98, 4136-4141
7.5507Citations (PDF)
224Sequence and analysis of the Arabidopsis genome
Current Opinion in Plant Biology, 2001, 4, 105-110
7.268Citations (PDF)
225Understanding the Adaptation of Halobacterium Species NRC-1 to Its Extreme Environment through Computational Analysis of Its Genome Sequence
Genome Research, 2001, 11, 1641-1650
4.6309Citations (PDF)
226Prediction of operons in microbial genomes
Nucleic Acids Research, 2001, 29, 1216-1221
15.5261Citations (PDF)
227A probabilistic method for identifying start codons in bacterial genomes
Bioinformatics, 2001, 17, 1123-1130
4.7184Citations (PDF)
228Rice Bioinformatics. Analysis of Rice Sequence Data and Leveraging the Data to Other Plant Species
Plant Physiology, 2001, 125, 1166-1174
5.547Citations (PDF)
229Gene Index analysis of the human genome estimates approximately 120,000 genes
Nature Genetics, 2000, 25, 239-240
25.2265Citations (PDF)
230Finding genes in Plasmodium falciparum
Nature, 2000, 404, 34-34
37.919Citations (PDF)
231DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae
Nature, 2000, 406, 477-483
37.91,802Citations (PDF)
232Microbial genome sequencing
Nature, 2000, 406, 799-803
37.9170Citations (PDF)
233Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana
Nature, 2000, 408, 816-820
37.9251Citations (PDF)
234Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana
Nature, 2000, 408, 820-823
37.9200Citations (PDF)
235Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39
Nucleic Acids Research, 2000, 28, 1397-1406
15.5708Citations (PDF)
236An optimized protocol for analysis of EST sequences
Nucleic Acids Research, 2000, 28, 3657-3665
15.5121Citations (PDF)
237Prediction of transcription terminators in bacterial genomes 1 1Edited by F. E. Cohen
Journal of Molecular Biology, 2000, 301, 27-33
4.1238Citations (PDF)
238Title is missing!
Genome Biology, 2000, 1, research0011.1
12.2302Citations (PDF)
239Alignment of whole genomes
Nucleic Acids Research, 1999, 27, 2369-2376
15.5798Citations (PDF)
240Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
Nature, 1999, 399, 323-329
37.91,428Citations (PDF)
241Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana
Nature, 1999, 402, 761-768
37.9736Citations (PDF)
242DNA uptake signal sequences in naturally transformable bacteria
Research in Microbiology, 1999, 150, 603-616
3.0120Citations (PDF)
243Gene discovery in DNA sequences
IEEE Intelligent Systems, 1999, 14, 44-48
0.010Citations (PDF)
244Improved microbial gene identification with GLIMMER
Nucleic Acids Research, 1999, 27, 4636-4641
15.52,359Citations (PDF)
245Interpolated Markov Models for Eukaryotic Gene Finding
Genomics, 1999, 59, 24-31
2.8192Citations (PDF)
246Optimized Multiplex PCR: Efficiently Closing a Whole-Genome Shotgun Sequencing Project
Genomics, 1999, 62, 500-507
2.8132Citations (PDF)
247A probabilistic framework for memory-based reasoning
Artificial Intelligence, 1998, 104, 287-311
2.835Citations (PDF)
248Skewed oligomers and origins of replication
Gene, 1998, 217, 57-67
2.3172Citations (PDF)
249Complete Genome Sequence of Treponema pallidum , the Syphilis Spirochete
Science, 1998, 281, 375-388
36.21,025Citations (PDF)
250A Decision Tree System for Finding Genes in DNA
Journal of Computational Biology, 1998, 5, 667-680
1.5108Citations (PDF)
251Microbial gene identification using interpolated Markov models
Nucleic Acids Research, 1998, 26, 544-548
15.5921Citations (PDF)
252A method for identifying splice sites and translational start sites in eukaryotic mRNA
Bioinformatics, 1997, 13, 365-376
4.780Citations (PDF)
253Finding Genes in DNA with a Hidden Markov Model
Journal of Computational Biology, 1997, 4, 127-141
1.5205Citations (PDF)
254Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi
Nature, 1997, 390, 580-586
37.92,074Citations (PDF)
255Title is missing!
1997, 11, 343-370
20Citations (PDF)
256Title is missing!
Data Mining and Knowledge Discovery, 1997, 1, 317-328
2.7678Citations (PDF)
257Testing simple polygons
Computational Geometry: Theory and Applications, 1997, 8, 97-114
0.52Citations (PDF)
258Testing orthogonal shapes
Computational Geometry: Theory and Applications, 1995, 5, 33-49
0.53Citations (PDF)
259Decision trees for automated identification of cosmic-ray hits in Hubble Space Telescope images
Publications of the Astronomical Society of the Pacific, 1995, 107, 279
7.161Citations (PDF)
260Locating Protein Coding Regions in Human DNA Using a Decision Tree Algorithm
Journal of Computational Biology, 1995, 2, 473-485
1.568Citations (PDF)
261Best-case results for nearest-neighbor learning
IEEE Transactions on Pattern Analysis and Machine Intelligence, 1995, 17, 599-608
11.220Citations (PDF)
262A weighted nearest neighbor algorithm for learning with symbolic features
Machine Learning, 1993, 10, 57-78
1.7431Citations (PDF)
263Title is missing!
Machine Learning, 1993, 10, 57-78
1.7342Citations (PDF)
264Predicting protein secondary structure with a nearest-neighbor algorithm
Journal of Molecular Biology, 1992, 227, 371-374
4.184Citations (PDF)
265A nearest hyperrectangle learning method
Machine Learning, 1991, 6, 251-276
1.7224Citations (PDF)
266Title is missing!
Machine Learning, 1991, 6, 251-276
1.7181Citations (PDF)
267Managing information for concurrent engineering: Challenges and barriers
Research in Engineering Design - Theory, Applications, and Concurrent Engineering, 1990, 2, 35-52
1.434Citations (PDF)
268Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities
ELife, 0, 8,
1.652Citations (PDF)
269Bracken: estimating species abundance in metagenomics data
PeerJ Computer Science, 0, 3, e104
0.01,775Citations (PDF)
270Unexpected cross-species contamination in genome sequencing projects
PeerJ, 0, 2, e675
0.0166Citations (PDF)
271Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space
PeerJ, 0, 3, e808
0.038Citations (PDF)
272Structure-guided isoform identification for the human transcriptome
ELife, 0, 11,
1.636Citations (PDF)
273OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species
ELife, 0, 14,
1.61Citations (PDF)
274Translon: a single term for translated regions
Nature Methods, 0, 22, 2002-2006
24.64Citations (PDF)
275Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project
Science Translational Medicine, 0, 17,
12.516Citations (PDF)
276OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species
ELife, 0, 14,
1.60Citations (PDF)