DJ
David B Jaffe
Evolution, Molecularalg-geomGenomeGenome, Humanmath.AGAlgorithmsgenomicsGenomicsSoftwareGenome, Bacterial
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
63 papers in the corpus · 1994–2025Better antibodies engineered with a GLIMPSE of human data10.1101/2025.06.08.658113v2 · Hepler, N. L., Hill, A. J., Jaffe, D. B. et al.2025 · 2 citationsbioRxiv
Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes.37034676 · Hurtado, Jonathan, Rogers, Thomas F, Jaffe, David B et al.2024 · 17 citationsbioRxiv : the preprint server for biology. 2023
Functional antibodies exhibit light chain coherence.36289331 · Jaffe, David B, Shahi, Payam, Adams, Bruce A et al.2022 · 110 citationsNature. 2022;611(7935):352-357
enclone: precision clonotyping and analysis of immune receptors10.1101/2022.04.21.489084v2 · Jaffe, D. B., Shahi, P., Adams, B. A. et al.2022 · 13 citationsbioRxiv
Genomic architecture and introgression shape a butterfly radiation.31672890 · Edelman, Nathaniel B, Frandsen, Paul B, Miyagi, Miriam et al.2020 · 611 citationsScience (New York, N.Y.). 2019;366(6465):594-599
Corrigendum: Direct determination of diploid genome sequences.29610250 · Weisenfeld, Neil I, Kumar, Vijay, Shah, Preyas et al.2019 · 22 citationsGenome research. 2018;28(4):606.1
Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly.29474918 · Aneichyk, Tatsiana, Hendriks, William T, Yadav, Rachita et al.2019 · 228 citationsCell. 2018;172(5):897-909.e21
Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library.29423234 · Hulse-Kemp, Amanda M, Maheshwari, Shamoni, Stoffel, Kevin et al.2020 · 153 citationsHorticulture research. 2018;5:4
Improved de novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low Cost10.1101/128348v2 · Mohr, D. W., Naguib, A., Weisenfeld, N. et al.2017 · 20 citationsbioRxiv
Direct determination of diploid genome sequences.28381613 · Weisenfeld, Neil I, Kumar, Vijay, Shah, Preyas et al.2018 · 803 citationsGenome research. 2017;27(5):757-767
Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly.26944054 · Love, R Rebecca, Weisenfeld, Neil I, Jaffe, David B et al.2016 · 49 citationsBMC genomics. 2016;17:187
Comprehensive variation discovery in single human genomes.25326702 · Weisenfeld, Neil I, Yin, Shuangye, Sharpe, Ted et al.2015 · 199 citationsNature genetics. 2014;46(12):1350-5
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
Characterizing and measuring bias in sequence data.23718773 · Ross, Michael G, Russ, Carsten, Costello, Maura et al.2015 · 904 citationsGenome biology. 2013;14(5):R51
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
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples.23396013 · Cibulskis, Kristian, Lawrence, Michael S, Carter, Scott L et al.2013 · 4,994 citationsNature biotechnology. 2013;31(3):213-9
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.23396133 · Kirby, Andrew, Gnirke, Andreas, Jaffe, David B et al.2013 · 306 citationsNature genetics. 2013;45(3):299-303
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
Paired-end sequencing of Fosmid libraries by Illumina.22800726 · Williams, Louise J S, Tabbaa, Diana G, Li, Na et al.2013 · 53 citationsGenome research. 2012;22(11):2241-9
Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing.22277967 · Calvo, Sarah E, Compton, Alison G, Hershman, Steven G et al.2012 · 478 citationsScience translational medicine. 2012;4(118):118ra10
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
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.21338519 · Aird, Daniel, Ross, Michael G, Chen, Wei-Sheng et al.2012 · 1,172 citationsGenome biology. 2011;12(2):R18
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
Integrative analysis of the melanoma transcriptome.20179022 · Berger, Michael F, Levin, Joshua Z, Vijayendran, Krishna et al.2010 · 305 citationsGenome research. 2010;20(4):413-27
A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454.20137071 · Lennon, Niall J, Lintner, Robert E, Anderson, Scott et al.2010 · 106 citationsGenome biology. 2010;11(2):R15
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.19182786 · Gnirke, Andreas, Melnikov, Alexandre, Maguire, Jared et al.2009 · 1,432 citationsNature biotechnology. 2009;27(2):182-9
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
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.19079253 · Nusbaum, Chad, Ohsumi, Toshiro K, Gomez, James et al.2009 · 62 citationsNature methods. 2009;6(1):67-9
High-resolution mapping of copy-number alterations with massively parallel sequencing.19043412 · Chiang, Derek Y, Getz, Gad, Jaffe, David B et al.2009 · 511 citationsNature methods. 2009;6(1):99-103
Genome-scale DNA methylation maps of pluripotent and differentiated cells.18600261 · Meissner, Alexander, Mikkelsen, Tarjei S, Gu, Hongcang et al.2008 · 2,534 citationsNature. 2008;454(7205):766-70
ALLPATHS: de novo assembly of whole-genome shotgun microreads.18340039 · Butler, Jonathan, MacCallum, Iain, Kleber, Michael et al.2008 · 808 citationsGenome research. 2008;18(5):810-20
Quality scores and SNP detection in sequencing-by-synthesis systems.18212088 · Brockman, William, Alvarez, Pablo, Young, Sarah et al.2008 · 265 citationsGenome research. 2008;18(5):763-70
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
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.17603471 · Mikkelsen, Tarjei S, Ku, Manching, Jaffe, David B et al.2007 · 4,127 citationsNature. 2007;448(7153):553-60
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
Genome sequence of Aedes aegypti, a major arbovirus vector.17510324 · Nene, Vishvanath, Wortman, Jennifer R, Lawson, Daniel et al.2007 · 1,078 citationsScience (New York, N.Y.). 2007;316(5832):1718-23
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
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.17080091 · Kämper, Jörg, Kahmann, Regine, Bölker, Michael et al.2006 · 1,208 citationsNature. 2006;444(7115):97-101
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
Analysis of the DNA sequence and duplication history of human chromosome 15.16572171 · Zody, Michael C, Garber, Manuel, Sharpe, Ted et al.2006 · 78 citationsNature. 2006;440(7084):671-5
Human chromosome 11 DNA sequence and analysis including novel gene identification.16554811 · Taylor, Todd D, Noguchi, Hideki, Totoki, Yasushi et al.2006 · 82 citationsNature. 2006;440(7083):497-500
DNA sequence and analysis of human chromosome 8.16421571 · Nusbaum, Chad, Mikkelsen, Tarjei S, Zody, Michael C et al.2006 · 120 citationsNature. 2006;439(7074):331-5
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
DNA sequence and analysis of human chromosome 18.16177791 · Nusbaum, Chad, Zody, Michael C, Borowsky, Mark L et al.2005 · 90 citationsNature. 2005;437(7058):551-5
Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping.16012527 · Hitte, Christophe, Madeoy, Jennifer, Kirkness, Ewen F et al.2005 · 74 citationsNature reviews. Genetics. 2005;6(8):643-8
Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.16077012 · Vinson, Jade P, Jaffe, David B, O'Neill, Keith et al.2005 · 184 citationsGenome research. 2005;15(8):1127-35
Career total: 153 works. 63 are in this corpus.Showing the 50 most recent.
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