Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

Tekijä Chaisson, Mark J, Tesler, Glenn
Julkaistu 2012

Short read fragment assembly of bacterial genomes

Tekijä Chaisson, Mark J., Pevzner, Pavel A.
Julkaistu 2008

lra: A long read aligner for sequences and contigs

Tekijä Ren, Jingwen, Chaisson, Mark J. P.
Julkaisussa PLoS Comput Biol (2021)

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Tekijä Lu, Tsung-Yu, Chaisson, Mark J. P.
Julkaisussa Nat Commun (2021)

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Tekijä Chaisson, Mark J., Brinza, Dumitru, Pevzner, Pavel A.
Julkaistu 2009

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

Tekijä Fan, Xian, Chaisson, Mark, Nakhleh, Luay, Chen, Ken
Julkaisussa Genome Res (2017)

Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers

Tekijä Medvedev, Paul, Pham, Son, Chaisson, Mark, Tesler, Glenn, Pevzner, Pavel
Julkaistu 2011

Genetic variation and the de novo assembly of human genomes

Tekijä Chaisson, Mark J. P., Wilson, Richard K., Eichler, Evan E.
Julkaisussa Nat Rev Genet (2015)

Resolving multicopy duplications de novo using polyploid phasing

Tekijä Chaisson, Mark J., Mukherjee, Sudipto, Kannan, Sreeram, Eichler, Evan E.
Julkaisussa Res Comput Mol Biol (2017)

Assembly of long error-prone reads using de Bruijn graphs

Tekijä Lin, Yu, Yuan, Jeffrey, Kolmogorov, Mikhail, Shen, Max W., Chaisson, Mark, Pevzner, Pavel A.
Julkaisussa Proc Natl Acad Sci U S A (2016)

STAR: ultrafast universal RNA-seq aligner

Tekijä Dobin, Alexander, Davis, Carrie A., Schlesinger, Felix, Drenkow, Jorg, Zaleski, Chris, Jha, Sonali, Batut, Philippe, Chaisson, Mark, Gingeras, Thomas R.
Julkaistu 2013

Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ

Tekijä Samstag, Colby L., Hoekstra, Jake G., Huang, Chiu-Hui, Chaisson, Mark J., Youle, Richard J., Kennedy, Scott R., Pallanck, Leo J.
Julkaisussa PLoS Genet (2018)

Human-specific tandem repeat expansion and differential gene expression during primate evolution

Tekijä Sulovari, Arvis, Li, Ruiyang, Audano, Peter A., Porubsky, David, Vollger, Mitchell R., Logsdon, Glennis A., Warren, Wesley C., Pollen, Alex A., Chaisson, Mark J. P., Eichler, Evan E.
Julkaisussa Proc Natl Acad Sci U S A (2019)

Long-read sequence and assembly of segmental duplications

Tekijä Vollger, Mitchell R., Dishuck, Philip C., Sorensen, Melanie, Welch, AnneMarie E., Dang, Vy, Dougherty, Max L., Graves-Lindsay, Tina A., Wilson, Richard K., Chaisson, Mark J. P., Eichler, Evan E.
Julkaisussa Nat Methods (2018)

Reconstructing complex regions of genomes using long-read sequencing technology

Tekijä Huddleston, John, Ranade, Swati, Malig, Maika, Antonacci, Francesca, Chaisson, Mark, Hon, Lawrence, Sudmant, Peter H., Graves, Tina A., Alkan, Can, Dennis, Megan Y., Wilson, Richard K., Turner, Stephen W., Korlach, Jonas, Eichler, Evan E.
Julkaistu 2014

Resolving the complexity of the human genome using single-molecule sequencing

Tekijä Chaisson, Mark J.P., Huddleston, John, Dennis, Megan Y., Sudmant, Peter H., Malig, Maika, Hormozdiari, Fereydoun, Antonacci, Francesca, Surti, Urvashi, Sandstrom, Richard, Boitano, Matthew, Landolin, Jane M., Stamatoyannopoulos, John A., Hunkapiller, Michael W., Korlach, Jonas, Eichler, Evan E.
Julkaisussa Nature (2014)

Discovery and genotyping of structural variation from long-read haploid genome sequence data

Tekijä Huddleston, John, Chaisson, Mark J.P., Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A., Munson, Katherine M., Kronenberg, Zev N., Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K., Eichler, Evan E.
Julkaisussa Genome Res (2017)

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

Tekijä Huddleston, John, Chaisson, Mark J.P., Steinberg, Karyn Meltz, Warren, Wes, Hoekzema, Kendra, Gordon, David, Graves-Lindsay, Tina A., Munson, Katherine M., Kronenberg, Zev N., Vives, Laura, Peluso, Paul, Boitano, Matthew, Chin, Chen-Shin, Korlach, Jonas, Wilson, Richard K., Eichler, Evan E.
Julkaisussa Genome Res (2018)

Long-read sequence assembly of the gorilla genome

Tekijä Gordon, David, Huddleston, John, Chaisson, Mark J. P., Hill, Christopher M., Kronenberg, Zev N., Munson, Katherine M., Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W., Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K., Haussler, David, Chin, Chen-Shan, Eichler, Evan E.
Julkaisussa Science (2016)

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Tekijä Porubsky, David, Ebert, Peter, Audano, Peter A., Vollger, Mitchell R., Harvey, William T., Marijon, Pierre, Ebler, Jana, Munson, Katherine M., Sorensen, Melanie, Sulovari, Arvis, Haukness, Marina, Ghareghani, Maryam, Lansdorp, Peter M., Paten, Benedict, Devine, Scott E., Sanders, Ashley D., Lee, Charles, Chaisson, Mark J. P., Korbel, Jan O., Eichler, Evan E., Marschall, Tobias
Julkaisussa Nat Biotechnol (2020)