DS
David C. Schwartz
Genome, BacterialRestriction MappingAlgorithmsGenomeGenomicsGenome, FungalOptics and PhotonicsSequence Analysis, DNADNAGenome, Plant
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
123 papers in the corpus · 1983–2024'Gel-Stacks' gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study.38655877 · Calle-Casteñeda, Susana, Winden, Eamon, Vasquez-Echeverri, Alejandro et al.2024 · 0 citationsBioTechniques. 2024;76(6):285-289
A database of restriction maps to expand the utility of bacterial artificial chromosomes.37753479 · Winden, Eamon, Vasquez-Echeverri, Alejandro, Calle-Castañeda, Susana et al.2024 · 1 citationGigaByte (Hong Kong, China). 2023;2023:gigabyte93
Trench field-effect transistors integrated in a microfluidic channel and design considerations for charge detection.35578730 · Park, Dong-Wook, Tsvid, Gene, Hernandez-Ortiz, Juan P et al.2023 · 1 citationApplied physics letters. 2022;120(19):192102
The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes.32005944 · Zhang, Yong, Yang, He, Turra, David et al.2021 · 107 citationsCommunications biology. 2020;3(1):50
Biophysics and the Genomic Sciences.31409480 · Schwartz, David C2020 · 2 citationsBiophysical journal. 2019;117(11):2047-2053
A simple dialysis device for large DNA molecules.30744406 · Krerowicz, Samuel Jw, Hernandez-Ortiz, Juan P, Schwartz, David C2020 · 3 citationsBioTechniques. 2019;66(2):93-95
Microscale Objects via Restructuring of Large, Double-Stranded DNA Molecules.30403478 · Krerowicz, Samuel J W, Hernandez-Ortiz, Juan P, Schwartz, David C2019 · 1 citationACS applied materials & interfaces. 2018;10(48):41215-41223
Discrete and Continuum Models for the Salt in Crowded Environments of Suspended Charged Particles.30044624 · Molina, Jarol E, Vasquez-Echeverri, Alejandro, Schwartz, David C et al.2018 · 1 citationJournal of chemical theory and computation. 2018;14(9):4901-4913
Electrostatic confinement and manipulation of DNA molecules for genome analysis.29203667 · Kounovsky-Shafer, Kristy L, Hernandez-Ortiz, Juan P, Potamousis, Konstantinos et al.2018 · 35 citationsProceedings of the National Academy of Sciences of the United States of America. 2017;114(51):13400-13405
In silico evidence for sequence-dependent nucleosome sliding.29078285 · Lequieu, Joshua, Schwartz, David C, de Pablo, Juan J2018 · 92 citationsProceedings of the National Academy of Sciences of the United States of America. 2017;114(44):E9197-E9205
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters.28851275 · Dallery, Jean-Félix, Lapalu, Nicolas, Zampounis, Antonios et al.2018 · 113 citationsBMC genomics. 2017;18(1):667
Tension-Dependent Free Energies of Nucleosome Unwrapping.27725965 · Lequieu, Joshua, Córdoba, Andrés, Schwartz, David C et al.2020 · 85 citationsACS central science. 2016;2(9):660-666
Genome Sequence and Annotation of Colletotrichum higginsianum, a Causal Agent of Crucifer Anthracnose Disease.27540062 · Zampounis, Antonios, Pigné, Sandrine, Dallery, Jean-Félix et al.2016 · 40 citationsGenome announcements. 2016;4(4)
Allele-Specific Quantification of Structural Variations in Cancer Genomes.27453446 · Li, Yang, Zhou, Shiguo, Schwartz, David C et al.2019 · 46 citationsCell systems. 2016;3(1):21-34
A gapless genome sequence of the fungus Botrytis cinerea.26913498 · Van Kan, Jan A L, Stassen, Joost H M, Mosbach, Andreas et al.2017 · 322 citationsMolecular plant pathology. 2017;18(1):75-89
Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.26641089 · Yuan, Bo, Liu, Pengfei, Gupta, Aditya et al.2016 · 25 citationsPLoS genetics. 2015;11(12):e1005686
Maligner: a fast ordered restriction map aligner.26637292 · Mendelowitz, Lee M, Schwartz, David C, Pop, Mihai2017 · 26 citationsBioinformatics (Oxford, England). 2016;32(7):1016-22
A clone-free, single molecule map of the domestic cow (Bos taurus) genome.26314885 · Zhou, Shiguo, Goldstein, Steve, Place, Michael et al.2016 · 15 citationsBMC genomics. 2015;16:644
DNA binding fluorescent proteins for the direct visualization of large DNA molecules.26264666 · Lee, Seonghyun, Oh, Yeeun, Lee, Jungyoon et al.2016 · 32 citationsNucleic acids research. 2016;44(1):e6
Single-molecule analysis reveals widespread structural variation in multiple myeloma.26056298 · Gupta, Aditya, Place, Michael, Goldstein, Steven et al.2015 · 56 citationsProceedings of the National Academy of Sciences of the United States of America. 2015;112(25):7689-94
Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense.26046933 · Zhu, Yingjie, Xu, Jiang, Sun, Chao et al.2016 · 78 citationsScientific reports. 2015;5:11087
High-coverage sequencing and annotated assemblies of the budgerigar genome.25061512 · Ganapathy, Ganeshkumar, Howard, Jason T, Ward, James M et al.2014 · 81 citationsGigaScience. 2014;3:11
An improved genome release (version Mt4.0) for the model legume Medicago truncatula.24767513 · Tang, Haibao, Krishnakumar, Vivek, Bidwell, Shelby et al.2015 · 468 citationsBMC genomics. 2014;15:312
Presentation of large DNA molecules for analysis as nanoconfined dumbbells.24683272 · Kounovsky-Shafer, Kristy L, Hernández-Ortiz, Juan P, Jo, Kyubong et al.2025 · 39 citationsMacromolecules. 2013;46(20):8356-8368
Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis.23885787 · Ray, Mohana, Goldstein, Steve, Zhou, Shiguo et al.2013 · 32 citationsBMC genomics. 2013;14:505
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
Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.23590730 · van Heesch, Sebastiaan, Kloosterman, Wigard P, Lansu, Nico et al.2013 · 39 citationsBMC genomics. 2013;14:257
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.24280374 · Kawahara, Yoshihiro, de la Bastide, Melissa, Hamilton, John P et al.2013 · 2,251 citationsRice (New York, N.Y.). 2013;6(1):4
Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.23316438 · Manning, Viola A, Pandelova, Iovanna, Dhillon, Braham et al.2013 · 168 citationsG3 (Bethesda, Md.). 2013;3(1):41-63
Comparative genomics of cryptosporidium.23738321 · Mazurie, Aurélien J, Alves, João M, Ozaki, Luiz S et al.2013 · 37 citationsInternational journal of genomics. 2013;2013:832756
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.22885923 · O'Connell, Richard J, Thon, Michael R, Hacquard, Stéphane et al.2012 · 1,045 citationsNature genetics. 2012;44(9):1060-5
AGORA: Assembly Guided by Optical Restriction Alignment.22856673 · Lin, Henry C, Goldstein, Steve, Mendelowitz, Lee et al.2013 · 47 citationsBMC bioinformatics. 2012;13:189
Genome sequence of the model medicinal mushroom Ganoderma lucidum.22735441 · Chen, Shilin, Xu, Jiang, Liu, Chang et al.2012 · 579 citationsNature communications. 2012;3:913
Statistical significance of optical map alignments.22506568 · Sarkar, Deepayan, Goldstein, Steve, Schwartz, David C et al.2012 · 16 citationsJournal of computational biology : a journal of computational molecular cell biology. 2012;19(5):478-92
Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association.22409516 · Bannantine, John P, Wu, Chia-wei, Hsu, Chungyi et al.2012 · 55 citationsBMC genomics. 2012;13:89
The Medicago genome provides insight into the evolution of rhizobial symbioses.22089132 · Young, Nevin D, Debellé, Frédéric, Oldroyd, Giles E D et al.2012 · 1,276 citationsNature. 2011;480(7378):520-4
Complete genome sequence of Rhodospirillum rubrum type strain (S1).21886856 · Munk, A Christine, Copeland, Alex, Lucas, Susan et al.2011 · 55 citationsStandards in genomic sciences. 2011;4(3):293-302
Nanochannel confinement: DNA stretch approaching full contour length.21431167 · Kim, Yoori, Kim, Ki Seok, Kounovsky, Kristy L et al.2011 · 143 citationsLab on a chip. 2011;11(10):1721-9
A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk.20729854 · Antonacci, Francesca, Kidd, Jeffrey M, Marques-Bonet, Tomas et al.2010 · 99 citationsNature genetics. 2010;42(9):745-50
High-resolution human genome structure by single-molecule analysis.20534489 · Teague, Brian, Waterman, Michael S, Goldstein, Steven et al.2010 · 175 citationsProceedings of the National Academy of Sciences of the United States of America. 2010;107(24):10848-53
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.20237561 · Ma, Li-Jun, van der Does, H Charlotte, Borkovich, Katherine A et al.2010 · 1,774 citationsNature. 2010;464(7287):367-73
New Generations: Sequencing Machines and Their Computational Challenges.22121326 · Schwartz, David C, Waterman, Michael S2025 · 15 citationsJournal of computer science and technology. 2010;25(1):3-9
The B73 maize genome: complexity, diversity, and dynamics.19965430 · Schnable, Patrick S, Ware, Doreen, Fulton, Robert S et al.2009 · 4,050 citationsScience (New York, N.Y.). 2009;326(5956):1112-5
The challenges of sequencing by synthesis.19898456 · Fuller, Carl W, Middendorf, Lyle R, Benner, Steven A et al.2010 · 281 citationsNature biotechnology. 2009;27(11):1013-23
Detailed analysis of a contiguous 22-Mb region of the maize genome.19936048 · Wei, Fusheng, Stein, Joshua C, Liang, Chengzhi et al.2010 · 46 citationsPLoS genetics. 2009;5(11):e1000728
The physical and genetic framework of the maize B73 genome.19936061 · Wei, Fusheng, Zhang, Jianwei, Zhou, Shiguo et al.2010 · 104 citationsPLoS genetics. 2009;5(11):e1000715
A single molecule scaffold for the maize genome.19936062 · Zhou, Shiguo, Wei, Fusheng, Nguyen, John et al.2010 · 135 citationsPLoS genetics. 2009;5(11):e1000711
Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis.19815517 · Sambriski, E J, Schwartz, D C, de Pablo, J J2009 · 55 citationsProceedings of the National Academy of Sciences of the United States of America. 2009;106(43):18125-30
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
Engineering BspQI nicking enzymes and application of N.BspQI in DNA labeling and production of single-strand DNA.19747545 · Zhang, Penghua, Too, Priscilla Hiu-Mei, Samuelson, James C et al.2010 · 33 citationsProtein expression and purification. 2010;69(2):226-34
Career total: 182 works. 123 are in this corpus.Showing the 50 most recent.
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