SG
Sante Gnerre
Evolution, MolecularGenomeGenomicsSoftwareGenome, HumanGenome, BacterialGenome, FungalHigh-Throughput Nucleotide SequencingPhylogenyAlgorithms
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
36 papers in the corpus · 2002–2025Detection of oncogenic fusions in colorectal cancer using a partner-agnostic next-generation sequencing approach.40696295 · Pellatt, Andrew J, Barnett, Reagan M, Gnerre, Sante et al.2025 · 1 citationBMC cancer. 2025;25(1):1201
High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.31768066 · Razavi, Pedram, Li, Bob T, Brown, David N et al.2020 · 774 citationsNature medicine. 2019;25(12):1928-1937
Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium.30891595 · Li, B T, Janku, F, Jung, B et al.2020 · 156 citationsAnnals of oncology : official journal of the European Society for Medical Oncology. 2019;30(4):597-603
Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.28536309 · Janku, Filip, Zhang, Shile, Waters, Jill et al.2018 · 53 citationsClinical cancer research : an official journal of the American Association for Cancer Research. 2017;23(18):5648-5656
Gibbon genome and the fast karyotype evolution of small apes.25209798 · Carbone, Lucia, Harris, R Alan, Gnerre, Sante et al.2014 · 359 citationsNature. 2014;513(7517):195-201
The genomic substrate for adaptive radiation in African cichlid fish.25186727 · Brawand, David, Wagner, Catherine E, Li, Yang I et al.2014 · 987 citationsNature. 2014;513(7518):375-381
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
The African coelacanth genome provides insights into tetrapod evolution.23598338 · Amemiya, Chris T, Alföldi, Jessica, Lee, Alison P et al.2013 · 670 citationsNature. 2013;496(7445):311-6
De novo assembly of highly diverse viral populations.22974120 · Yang, Xiao, Charlebois, Patrick, Gnerre, Sante et al.2013 · 211 citationsBMC genomics. 2012;13:475
A direct characterization of human mutation based on microsatellites.22922873 · Sun, James X, Helgason, Agnar, Masson, Gisli et al.2012 · 341 citationsNature genetics. 2012;44(10):1161-5
Finished bacterial genomes from shotgun sequence data.22829535 · Ribeiro, Filipe J, Przybylski, Dariusz, Yin, Shuangye et al.2013 · 211 citationsGenome research. 2012;22(11):2270-7
Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.22412369 · Henn, Matthew R, Boutwell, Christian L, Charlebois, Patrick et al.2012 · 317 citationsPLoS pathogens. 2012;8(3):e1002529
A high-resolution map of human evolutionary constraint using 29 mammals.21993624 · Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or et al.2012 · 1,107 citationsNature. 2011;478(7370):476-82
Assemblathon 1: a competitive assessment of de novo short read assembly methods.21926179 · Earl, Dent, Bradnam, Keith, St John, John et al.2012 · 507 citationsGenome research. 2011;21(12):2224-41
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts.21304167 · D'Souza, C A, Kronstad, J W, Taylor, G et al.2011 · 202 citationsmBio. 2011;2(1):e00342-10
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.21187386 · Gnerre, Sante, Maccallum, Iain, Przybylski, Dariusz et al.2011 · 1,533 citationsProceedings of the National Academy of Sciences of the United States of America. 2011;108(4):1513-8
Genome sequence, comparative analysis, and population genetics of the domestic horse.19892987 · Wade, C M, Giulotto, E, Sigurdsson, S et al.2009 · 822 citationsScience (New York, N.Y.). 2009;326(5954):865-7
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.19741609 · Haas, Brian J, Kamoun, Sophien, Zody, Michael C et al.2009 · 1,472 citationsNature. 2009;461(7262):393-8
The difficulty of avoiding false positives in genome scans for natural selection.19411606 · Mallick, Swapan, Gnerre, Sante, Muller, Paul et al.2009 · 105 citationsGenome research. 2009;19(5):922-33
Closing gaps in the human genome using sequencing by synthesis.19490611 · Garber, Manuel, Zody, Michael C, Arachchi, Harindra M et al.2009 · 25 citationsGenome biology. 2009;10(6):R60
Assisted assembly: how to improve a de novo genome assembly by using related species.19712469 · Gnerre, Sante, Lander, Eric S, Lindblad-Toh, Kerstin et al.2009 · 64 citationsGenome biology. 2009;10(8):R88
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.19796385 · Maccallum, Iain, Przybylski, Dariusz, Gnerre, Sante et al.2010 · 179 citationsGenome biology. 2009;10(10):R103
Analysis of chimpanzee history based on genome sequence alignments.18421364 · Caswell, Jennifer L, Mallick, Swapan, Richter, Daniel J et al.2008 · 125 citationsPLoS genetics. 2008;4(4):e1000057
Evolution of genes and genomes on the Drosophila phylogeny.17994087 · Drosophila 12 Genomes Consortium, Clark, Andrew G, Eisen, Michael B et al.2008 · 2,008 citationsNature. 2007;450(7167):203-18
Initial sequence and comparative analysis of the cat genome.17975172 · Pontius, Joan U, Mullikin, James C, Smith, Douglas R et al.2008 · 367 citationsGenome research. 2007;17(11):1675-89
The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization.17823352 · Cuomo, Christina A, Güldener, Ulrich, Xu, Jin-Rong et al.2007 · 898 citationsScience (New York, N.Y.). 2007;317(5843):1400-2
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.17571346 · ENCODE Project Consortium, Birney, Ewan, Stamatoyannopoulos, John A et al.2007 · 5,226 citationsNature. 2007;447(7146):799-816
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.17567995 · Margulies, Elliott H, Cooper, Gregory M, Asimenos, George et al.2007 · 211 citationsGenome research. 2007;17(6):760-74
A genome-wide map of diversity in Plasmodium falciparum.17159979 · Volkman, Sarah K, Sabeti, Pardis C, DeCaprio, David et al.2007 · 364 citationsNature genetics. 2007;39(1):113-9
Genetic evidence for complex speciation of humans and chimpanzees.16710306 · Patterson, Nick, Richter, Daniel J, Gnerre, Sante et al.2006 · 582 citationsNature. 2006;441(7097):1103-8
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.16625196 · Zody, Michael C, Garber, Manuel, Adams, David J et al.2006 · 162 citationsNature. 2006;440(7087):1045-9
Genome sequence, comparative analysis and haplotype structure of the domestic dog.16341006 · Lindblad-Toh, Kerstin, Wade, Claire M, Mikkelsen, Tarjei S et al.2005 · 2,566 citationsNature. 2005;438(7069):803-19
The genome sequence of the filamentous fungus Neurospora crassa.12712197 · Galagan, James E, Calvo, Sarah E, Borkovich, Katherine A et al.2003 · 1,672 citationsNature. 2003;422(6934):859-68
Whole-genome sequence assembly for mammalian genomes: Arachne 2.12529310 · Jaffe, David B, Butler, Jonathan, Gnerre, Sante et al.2003 · 308 citationsGenome research. 2003;13(1):91-6
Initial sequencing and comparative analysis of the mouse genome.12466850 · Mouse Genome Sequencing Consortium, Waterston, Robert H, Lindblad-Toh, Kerstin et al.2002 · 7,179 citationsNature. 2002;420(6915):520-62
ARACHNE: a whole-genome shotgun assembler.11779843 · Batzoglou, Serafim, Jaffe, David B, Stanley, Ken et al.2002 · 0 citationsGenome research. 2002;12(1):177-89
Career total: 93 works. 36 are in this corpus.
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