Publications

2021

Mahmoud, Medhat; Doddapaneni, Harshavardhan; Timp, Winston; Sedlazeck, Fritz J

PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation Journal Article

In: Genome Biology, 22 (1), pp. 268, 2021.

Abstract | BibTeX

Fan, Yunfan; Gale, Andrew N; Bailey, Anna; Barnes, Kali; Colotti, Kiersten; Mass, Michal; Morina, Luke B; Robertson, Bailey; Schwab, Remy; Tselepidakis, Niki; Timp, Winston

Genome and transcriptome of a pathogenic yeast, Candida nivariensis Journal Article

In: G3 Genes|Genomes|Genetics, 2021.

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Thielen, Peter M; Wohl, Shirlee; Mehoke, Thomas; Ramakrishnan, Srividya; Kirsche, Melanie; Falade-Nwulia, Oluwaseun; Trovão, Nídia S; Ernlund, Amanda; Howser, Craig; Sadowski, Norah; Morris, Paul C; Hopkins, Mark; Schwartz, Matthew; Fan, Yunfan; Gniazdowski, Victoria; Lessler, Justin; Sauer, Lauren; Schatz, Michael C; Evans, Jared D; Ray, Stuart C; Timp, Winston; Mostafa, Heba H

Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area Journal Article

In: JCI Insight, 6 (6), 2021.

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Weinguny, Marcus; Klanert, Gerald; Eisenhut, Peter; Lee, Isac; Timp, Winston; Borth, Nicole

Subcloning induces changes in the DNA-methylation pattern of outgrowing Chinese hamster ovary cell colonies Journal Article

In: Biotechnology Journal, pp. 2000350, 2021.

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Vornhagen, Jay; Bassis, Christine M.; Ramakrishnan, Srividya; Hein, Robert; Mason, Sophia; Bergman, Yehudit; Sunshine, Nicole; Fan, Yunfan; Holmes, Caitlyn L.; Timp, Winston; Schatz, Michael C.; Young, Vincent B.; Simner, Patricia J.; Bachman, Michael A.

A plasmid locus associated with textitKlebsiella clinical infections encodes a microbiome-dependent gut fitness factor Journal Article

In: PLOS Pathogens, 17 (4, author+an=8=student; 10=pi), pp. 1-34, 2021.

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Nurk, Sergey; Koren, Sergey; Rhie, Arang; Rautiainen, Mikko; Bzikadze, Andrey V.; Mikheenko, Alla; Vollger, Mitchell R.; Altemose, Nicolas; Uralsky, Lev; Gershman, Ariel; Aganezov, Sergey; Hoyt, Savannah J.; Diekhans, Mark; Logsdon, Glennis A.; Alonge, Michael; Antonarakis, Stylianos E.; Borchers, Matthew; Bouffard, Gerard G.; Brooks, Shelise Y.; Caldas, Gina V.; Cheng, Haoyu; Chin, Chen-Shan; Chow, William; Lima, Leonardo G.; Dishuck, Philip C.; Durbin, Richard; Dvorkina, Tatiana; Fiddes, Ian T.; Formenti, Giulio; Fulton, Robert S.; Fungtammasan, Arkarachai; Garrison, Erik; Grady, Patrick G. S.; Graves-Lindsay, Tina A.; Hall, Ira M.; Hansen, Nancy F.; Hartley, Gabrielle A.; Haukness, Marina; Howe, Kerstin; Hunkapiller, Michael W.; Jain, Chirag; Jain, Miten; Jarvis, Erich D.; Kerpedjiev, Peter; Kirsche, Melanie; Kolmogorov, Mikhail; Korlach, Jonas; Kremitzki, Milinn; Li, Heng; Maduro, Valerie V.; Marschall, Tobias; McCartney, Ann M.; McDaniel, Jennifer; Miller, Danny E.; Mullikin, James C.; Myers, Eugene W.; Olson, Nathan D.; Paten, Benedict; Peluso, Paul; Pevzner, Pavel A.; Porubsky, David; Potapova, Tamara; Rogaev, Evgeny I.; Rosenfeld, Jeffrey A.; Salzberg, Steven L.; Schneider, Valerie A.; Sedlazeck, Fritz J.; Shafin, Kishwar; Shew, Colin J.; Shumate, Alaina; Sims, Yumi; Smit, Arian F. A.; Soto, Daniela C.; Sovi'c, Ivan; Storer, Jessica M.; Streets, Aaron; Sullivan, Beth A.; coise Thibaud-Nissen, Franc; Torrance, James; Wagner, Justin; Walenz, Brian P.; Wenger, Aaron; Wood, Jonathan M. D.; Xiao, Chunlin; Yan, Stephanie M.; Young, Alice C.; Zarate, Samantha; Surti, Urvashi; McCoy, Rajiv C.; Dennis, Megan Y.; Alexandrov, Ivan A.; Gerton, Jennifer L.; OtextquoterightNeill, Rachel J.; Timp, Winston; Zook, Justin M.; Schatz, Michael C.; Eichler, Evan E.; Miga, Karen H.; Phillippy, Adam M.

The complete sequence of a human genome Journal Article

In: bioRxiv, 2021.

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Vollger, Mitchell R.; Guitart, Xavi; Dishuck, Philip C.; Mercuri, Ludovica; Harvey, William T.; Gershman, Ariel; Diekhans, Mark; Sulovari, Arvis; Munson, Katherine M.; Lewis, Alexandra M.; Hoekzema, Kendra; Porubsky, David; Li, Ruiyang; Nurk, Sergey; Koren, Sergey; Miga, Karen H.; Phillippy, Adam M.; Timp, Winston; Ventura, Mario; Eichler, Evan E.

Segmental duplications and their variation in a complete human genome Journal Article

In: bioRxiv, 2021.

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Gershman, Ariel; Sauria, Michael E. G.; Hook, Paul W.; Hoyt, Savannah J.; Razaghi, Roham; Koren, Sergey; Altemose, Nicolas; Caldas, Gina V.; Vollger, Mitchell R.; Logsdon, Glennis A.; Rhie, Arang; Eichler, Evan E.; Schatz, Michael C.; OtextquoterightNeill, Rachel J.; Phillippy, Adam M.; Miga, Karen H.; Timp, Winston

Epigenetic Patterns in a Complete Human Genome Journal Article

In: bioRxiv, 2021.

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Lietard, Jory; Leger, Adrien; Erlich, Yaniv; Sadowski, Norah; Timp, Winston; Somoza, Mark M

Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries Journal Article

In: Nucleic Acids Research, 2021, ISSN: 0305-1048, (gkab505).

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Polinski, Jennifer M.; Zimin, Aleksey V.; Clark, K. Fraser; Kohn, Andrea B.; Sadowski, Norah; Timp, Winston; Ptitsyn, Andrey; Khanna, Prarthana; Romanova, Daria Y.; Williams, Peter; Greenwood, Spencer J.; Moroz, Leonid L.; Walt, David R.; Bodnar, Andrea G.

The American lobster genome reveals insights on longevity, neural, and immune adaptations Journal Article

In: Science Advances, author+an=5=student;6=pi, 7 (26), 2021.

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Hoyt, Savannah J.; Storer, Jessica M.; Hartley, Gabrielle A.; Grady, Patrick G. S.; Gershman, Ariel; Lima, Leonardo G.; Limouse, Charles; Halabian, Reza; Wojenski, Luke; Rodriguez, Matias; Altemose, Nicolas; Core, Leighton J.; Gerton, Jennifer L.; Makalowski, Wojciech; Olson, Daniel; Rosen, Jeb; Smit, Arian F. A.; Straight, Aaron F.; Vollger, Mitchell R.; Wheeler, Travis J.; Schatz, Michael C.; Eichler, Evan E.; Phillippy, Adam M.; Timp, Winston; Miga, Karen H.; OtextquoterightNeill, Rachel J.

From telomere to telomere: the transcriptional and epigenetic state of human repeat elements Journal Article

In: bioRxiv, 2021.

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Sholes, Samantha L.; Karimian, Kayarash; Gershman, Ariel; Kelly, Thomas J.; Timp, Winston; Greider, Carol W.

Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing Journal Article

In: bioRxiv, 2021.

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Altemose, Nicolas; Logsdon, Glennis A.; Bzikadze, Andrey V.; Sidhwani, Pragya; Langley, Sasha A.; Caldas, Gina V.; Hoyt, Savannah J.; Uralsky, Lev; Ryabov, Fedor D.; Shew, Colin J.; Sauria, Michael E. G.; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A.; Dvorkina, Tatiana; Kunyavskaya, Olga; Vollger, Mitchell R.; Rhie, Arang; McCartney, Ann M.; Asri, Mobin; Lorig-Roach, Ryan; Shafin, Kishwar; Aganezov, Sergey; Olson, Daniel; Lima, Leonardo Gomes; Potapova, Tamara; Hartley, Gabrielle A.; Haukness, Marina; Kerpedjiev, Peter; Gusev, Fedor; Tigyi, Kristof; Brooks, Shelise; Young, Alice; Nurk, Sergey; Koren, Sergey; Salama, Sofie R.; Paten, Benedict; Rogaev, Evgeny I.; Streets, Aaron; Karpen, Gary H.; Dernburg, Abby F.; Sullivan, Beth A.; Straight, Aaron F.; Wheeler, Travis J.; Gerton, Jennifer L.; Eichler, Evan E.; Phillippy, Adam M.; Timp, Winston; Dennis, Megan Y.; OtextquoterightNeill, Rachel J.; Zook, Justin M.; Schatz, Michael C.; Pevzner, Pavel A.; Diekhans, Mark; Langley, Charles H.; Alexandrov, Ivan A.; Miga, Karen H.

Complete genomic and epigenetic maps of human centromeres Journal Article

In: bioRxiv, 2021.

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Gershman, Ariel; Romer, Tatiana G; Fan, Yunfan; Razaghi, Roham; Smith, Wendy A; Timp, Winston

De novo genome assembly of the tobacco hornworm moth (Manduca sexta) Journal Article

In: G3 Genes|Genomes|Genetics, 11 (1), 2021, ISSN: 2160-1836, (jkaa047).

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Clark, Helen R; McKenney, Connor; Livingston, Nathan M; Gershman, Ariel; Sajjan, Seema; Chan, Isaac S; Ewald, Andrew J; Timp, Winston; Wu, Bin; Singh, Abhyudai; Regot, Sergi

Epigenetically regulated digital signaling defines epithelial innate immunity at the tissue level Journal Article

In: Nature Communications, 12 (1), pp. 1–13, 2021.

BibTeX

2020

Lee, Isac; Razaghi, Roham; Gilpatrick, Timothy; Molnar, Michael; Gershman, Ariel; Sadowski, Norah; Sedlazeck, Fritz J; Hansen, Kasper D; Simpson, Jared T; Timp, Winston

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing Journal Article

In: Nature Methods, 17 (12), pp. 1191–1199, 2020, ISSN: 1548-7105.

Abstract | Links | BibTeX | Altmetric

Kovaka, Sam; Fan, Yunfan; Ni, Bohan; Timp, Winston; Schatz, Michael C

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED Journal Article

In: Nature Biotechnology, pp. 1–11, 2020, ISSN: 1546-1696.

Abstract | Links | BibTeX | Altmetric

Kovaka, Sam; Fan, Yunfan; Ni, Bohan; Timp, Winston; Schatz, Michael C

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED Journal Article

In: Nature Biotechnology, pp. 1–11, 2020, ISSN: 1546-1696, (Publisher: Nature Publishing Group).

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Pokrass, Michael J; Ryan, Kathleen A; Xin, Tianchi; Pielstick, Brittany; Timp, Winston; Greco, Valentina; Regot, Sergi

Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo Journal Article

In: Developmental Cell, 55 (3), pp. 328–340.e5, 2020, ISSN: 1878-1551.

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Vergara, Candelaria; Duggal, Priya; Thio, Chloe L; Valencia, Ana; Brien, Thomas R O’; Latanich, Rachel; Timp, Winston; Johnson, Eric O; Kral, Alex H; Mangia, Alessandra; Goedert, James J; Piazzola, Valeria; Mehta, Shruti H; Kirk, Gregory D; Peters, Marion G; Donfield, Sharyne M; Edlin, Brian R; Busch, Michael P; Alexander, Graeme; Murphy, Edward L; Kim, Arthur Y; Lauer, Georg M; Chung, Raymond T; Cramp, Matthew E; Cox, Andrea L; Khakoo, Salim I; Rosen, Hugo R; Alric, Laurent; Wheelan, Sarah J; Wojcik, Genevieve L; Thomas, David L; Taub, Margaret A

Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection Journal Article

In: Genes & Immunity, pp. 1–12, 2020, ISSN: 1476-5470.

Abstract | Links | BibTeX | Altmetric

Vergara, Candelaria; Duggal, Priya; Thio, Chloe L; Valencia, Ana; Brien, Thomas R O’; Latanich, Rachel; Timp, Winston; Johnson, Eric O; Kral, Alex H; Mangia, Alessandra; Goedert, James J; Piazzola, Valeria; Mehta, Shruti H; Kirk, Gregory D; Peters, Marion G; Donfield, Sharyne M; Edlin, Brian R; Busch, Michael P; Alexander, Graeme; Murphy, Edward L; Kim, Arthur Y; Lauer, Georg M; Chung, Raymond T; Cramp, Matthew E; Cox, Andrea L; Khakoo, Salim I; Rosen, Hugo R; Alric, Laurent; Wheelan, Sarah J; Wojcik, Genevieve L; Thomas, David L; Taub, Margaret A

Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection Journal Article

In: Genes & Immunity, pp. 1–12, 2020, ISSN: 1476-5470.

Abstract | Links | BibTeX | Altmetric

Pokrass, Michael J; Ryan, Kathleen A; Xin, Tianchi; Pielstick, Brittany; Timp, Winston; Greco, Valentina; Regot, Sergi

Cell-Cycle-Dependent ERK Signaling Dynamics Direct Fate Specification in the Mammalian Preimplantation Embryo Journal Article

In: Developmental Cell, 0 (0), 2020, ISSN: 1534-5807, (Publisher: Elsevier).

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Scott, Alison D; Zimin, Aleksey V; Puiu, Daniela; Workman, Rachael; Britton, Monica; Zaman, Sumaira; Caballero, Madison; Read, Andrew C; Bogdanove, Adam J; Burns, Emily; Wegrzyn, Jill; Timp, Winston; Salzberg, Steven L; Neale, David B

A Reference Genome Sequence for Giant Sequoia Journal Article

In: G3: Genes, Genomes, Genetics, 10 (11), pp. 3907–3919, 2020, ISSN: 2160-1836.

Abstract | Links | BibTeX | Altmetric

Gale, Andrew N; Sakhawala, Rima M; Levitan, Anton; Sharan, Roded; Berman, Judith; Timp, Winston; Cunningham, Kyle W

Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions Journal Article

In: G3: Genes, Genomes, Genetics, 10 (10), pp. 3859–3870, 2020, ISSN: 2160-1836.

Abstract | Links | BibTeX | Altmetric

Yee, Rebecca; Breitwieser, Florian P; Hao, Stephanie; Opene, Belita N A; Workman, Rachael E; Tamma, Pranita D; Dien-Bard, Jennifer; Timp, Winston; Simner, Patricia J

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms Journal Article

In: European Journal of Clinical Microbiology & Infectious Diseases, 2020, ISSN: 1435-4373.

Abstract | Links | BibTeX | Altmetric

Yee, Rebecca; Breitwieser, Florian P; Hao, Stephanie; Opene, Belita N A; Workman, Rachael E; Tamma, Pranita D; Dien-Bard, Jennifer; Timp, Winston; Simner, Patricia J

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms Journal Article

In: European Journal of Clinical Microbiology & Infectious Diseases, 2020, ISSN: 1435-4373.

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Miga, Karen H; Koren, Sergey; Rhie, Arang; Vollger, Mitchell R; Gershman, Ariel; Bzikadze, Andrey; Brooks, Shelise; Howe, Edmund; Porubsky, David; Logsdon, Glennis A; Schneider, Valerie A; Potapova, Tamara; Wood, Jonathan; Chow, William; Armstrong, Joel; Fredrickson, Jeanne; Pak, Evgenia; Tigyi, Kristof; Kremitzki, Milinn; Markovic, Christopher; Maduro, Valerie; Dutra, Amalia; Bouffard, Gerard G; Chang, Alexander M; Hansen, Nancy F; Wilfert, Amy B; Thibaud-Nissen, Françoise; Schmitt, Anthony D; Belton, Jon-Matthew; Selvaraj, Siddarth; Dennis, Megan Y; Soto, Daniela C; Sahasrabudhe, Ruta; Kaya, Gulhan; Quick, Josh; Loman, Nicholas J; Holmes, Nadine; Loose, Matthew; Surti, Urvashi; ana Risques, Rosa; Lindsay, Tina Graves A; Fulton, Robert; Hall, Ira; Paten, Benedict; Howe, Kerstin; Timp, Winston; Young, Alice; Mullikin, James C; Pevzner, Pavel A; Gerton, Jennifer L; Sullivan, Beth A; Eichler, Evan E; Phillippy, Adam M

Telomere-to-telomere assembly of a complete human X chromosome Journal Article

In: Nature, pp. 1–9, 2020, ISSN: 1476-4687, (Publisher: Nature Publishing Group).

Abstract | Links | BibTeX | Altmetric

Miga, Karen H; Koren, Sergey; Rhie, Arang; Vollger, Mitchell R; Gershman, Ariel; Bzikadze, Andrey; Brooks, Shelise; Howe, Edmund; Porubsky, David; Logsdon, Glennis A; Schneider, Valerie A; Potapova, Tamara; Wood, Jonathan; Chow, William; Armstrong, Joel; Fredrickson, Jeanne; Pak, Evgenia; Tigyi, Kristof; Kremitzki, Milinn; Markovic, Christopher; Maduro, Valerie; Dutra, Amalia; Bouffard, Gerard G; Chang, Alexander M; Hansen, Nancy F; Wilfert, Amy B; Thibaud-Nissen, Françoise; Schmitt, Anthony D; Belton, Jon-Matthew; Selvaraj, Siddarth; Dennis, Megan Y; Soto, Daniela C; Sahasrabudhe, Ruta; Kaya, Gulhan; Quick, Josh; Loman, Nicholas J; Holmes, Nadine; Loose, Matthew; Surti, Urvashi; ana Risques, Rosa; Lindsay, Tina Graves A; Fulton, Robert; Hall, Ira; Paten, Benedict; Howe, Kerstin; Timp, Winston; Young, Alice; Mullikin, James C; Pevzner, Pavel A; Gerton, Jennifer L; Sullivan, Beth A; Eichler, Evan E; Phillippy, Adam M

Telomere-to-telomere assembly of a complete human X chromosome Journal Article

In: Nature, pp. 1–9, 2020, ISSN: 1476-4687, (Publisher: Nature Publishing Group).

Abstract | Links | BibTeX | Altmetric

Marrano, Annarita; Britton, Monica; Zaini, Paulo A; Zimin, Aleksey V; Workman, Rachael E; Puiu, Daniela; Bianco, Luca; Pierro, Erica Adele Di; Allen, Brian J; Chakraborty, Sandeep; Troggio, Michela; Leslie, Charles A; Timp, Winston; Dandekar, Abhaya; Salzberg, Steven L; Neale, David B

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome Journal Article

In: GigaScience, 9 (5), 2020, ISSN: 2047-217X.

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Stephenson, William; Razaghi, Roham; Busan, Steven; Weeks, Kevin M; Timp, Winston; Smibert, Peter

Direct detection of RNA modifications and structure using single molecule nanopore sequencing Journal Article

In: bioRxiv, 2020.

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McKelvey, Brittany A; Gilpatrick, Timothy; Wang, Yongchun; Timp, Winston; Umbricht, Christopher B; Zeiger, Martha A

Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines Journal Article

In: Thyroid, 2020, ISSN: 1050-7256, (Publisher: Mary Ann Liebert, Inc., publishers).

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Olson, Nathan D; Kumar, Senthil M; Li, Shan; Braccia, Domenick J; Hao, Stephanie; Timp, Winston; Salit, Marc L; Stine, Colin O; Bravo, Hector Corrada

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures. Journal Article

In: Microbiome, 8 (1), pp. 35, 2020, ISSN: 2049-2618.

Abstract | Links | BibTeX | Altmetric

McKelvey, Brittany A; Gilpatrick, Timothy; Wang, Yongchun; Timp, Winston; Umbricht, Christopher B; Zeiger, Martha A

Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines Journal Article

In: Thyroid, 2020, ISSN: 1050-7256, (Publisher: Mary Ann Liebert, Inc., publishers).

Abstract | Links | BibTeX | Altmetric

Olson, Nathan D; Kumar, Senthil M; Li, Shan; Braccia, Domenick J; Hao, Stephanie; Timp, Winston; Salit, Marc L; Stine, Colin O; Bravo, Hector Corrada

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures. Journal Article

In: Microbiome, 8 (1), pp. 35, 2020, ISSN: 2049-2618.

Abstract | Links | BibTeX | Altmetric

Gilpatrick, Timothy; Lee, Isac; Graham, James E; Raimondeau, Etienne; Bowen, Rebecca; Heron, Andrew; Downs, Bradley; Sukumar, Saraswati; Sedlazeck, Fritz J; Timp, Winston

Targeted nanopore sequencing with Cas9-guided adapter ligation Journal Article

In: Nature Biotechnology, 2020, ISSN: 1546-1696.

Abstract | Links | BibTeX | Altmetric

Gilpatrick, Timothy; Lee, Isac; Graham, James E; Raimondeau, Etienne; Bowen, Rebecca; Heron, Andrew; Downs, Bradley; Sukumar, Saraswati; Sedlazeck, Fritz J; Timp, Winston

Targeted nanopore sequencing with Cas9-guided adapter ligation Journal Article

In: Nature Biotechnology, 2020, ISSN: 1546-1696.

Abstract | Links | BibTeX | Altmetric

Marrano, Annarita; Britton, Monica; Zaini, Paulo A; Zimin, Aleksey V; Workman, Rachael E; Puiu, Daniela; Bianco, Luca; Pierro, Erica Adele Di; Allen, Brian J; Chakraborty, Sandeep; Troggio, Michela; Leslie, Charles A; Timp, Winston; Dandekar, Abhaya; Salzberg, Steven L; Neale, David B

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome Journal Article

In: GigaScience, 9 (5), 2020, ISSN: 2047-217X, (giaa050).

Links | BibTeX | Altmetric

Aganezov, Sergey; Goodwin, Sara; Sherman, Rachel M; Sedlazeck, Fritz J; Arun, Gayatri; Bhatia, Sonam; Lee, Isac; Kirsche, Melanie; Wappel, Robert; Kramer, Melissa; Kostroff, Karen; Spector, David L; Timp, Winston; McCombie, Richard W; Schatz, Michael C

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing Journal Article

In: Genome Research, 2020.

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Gale, Andrew N; Sakhawala, Rima M; Levitan, Anton; Sharan, Roded; Berman, Judith; Timp, Winston; Cunningham, Kyle W

Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions Journal Article

In: G3: Genes, Genomes, Genetics, 2020.

Abstract | Links | BibTeX | Altmetric

Roach, Nathan P; Sadowski, Norah; Alessi, Amelia F; Timp, Winston; Taylor, James; Kim, John K

The full-length transcriptome of C. elegans using direct RNA sequencing Journal Article

In: Genome Research, 2020.

Abstract | Links | BibTeX | Altmetric

Scott, Alison D; Zimin, Aleksey V; Puiu, Daniela; Workman, Rachael; Britton, Monica; Zaman, Sumaira; Caballero, Madison; Read, Andrew C; Bogdanove, Adam J; Burns, Emily; Wegrzyn, Jill; Timp, Winston; Salzberg, Steven L; Neale, David B

A Reference Genome Sequence for Giant Sequoia Journal Article

In: G3: Genes, Genomes, Genetics, 10 (11), pp. 3907–3919, 2020.

Abstract | Links | BibTeX | Altmetric

Timp, Winston; Timp, Gregory

Beyond mass spectrometry, the next step in proteomics Journal Article

In: Science Advances, 6 (2), 2020.

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2019

Workman, Rachael E; Tang, Alison D; Tang, Paul S; Jain, Miten; Tyson, John R; Razaghi, Roham; Zuzarte, Philip C; Gilpatrick, Timothy; Payne, Alexander; Quick, Joshua; Sadowski, Norah; Holmes, Nadine; de Jesus, Jaqueline Goes; Jones, Karen L; Soulette, Cameron M; Snutch, Terrance P; Loman, Nicholas; Paten, Benedict; Loose, Matthew; Simpson, Jared T; Olsen, Hugh E; Brooks, Angela N; Akeson, Mark; Timp, Winston

Nanopore native RNA sequencing of a human poly(A) transcriptome Journal Article

In: Nature Methods, pp. 1–9, 2019, ISSN: 1548-7105.

Abstract | Links | BibTeX | Altmetric

Workman, Rachael E; Tang, Alison D; Tang, Paul S; Jain, Miten; Tyson, John R; Razaghi, Roham; Zuzarte, Philip C; Gilpatrick, Timothy; Payne, Alexander; Quick, Joshua; Sadowski, Norah; Holmes, Nadine; de Jesus, Jaqueline Goes; Jones, Karen L; Soulette, Cameron M; Snutch, Terrance P; Loman, Nicholas; Paten, Benedict; Loose, Matthew; Simpson, Jared T; Olsen, Hugh E; Brooks, Angela N; Akeson, Mark; Timp, Winston

Nanopore native RNA sequencing of a human poly(A) transcriptome Journal Article

In: Nature Methods, pp. 1–9, 2019, ISSN: 1548-7105.

Abstract | Links | BibTeX | Altmetric

Sakowski, Eric; Uritskiy, Gherman; Cooper, Rachel; Gomes, Maya; McLaren, Michael R; Meisel, Jacquelyn S; Mickol, Rebecca L; Mintz, David C; Mongodin, Emmanuel F; Pop, Mihai; Rahman, Mohammad Arifur; Sanchez, Alvaro; Timp, Winston; Vela, Jeseth Delgado; Wolz, Carly Muletz; Zackular, Joseph P; Chopyk, Jessica; Commichaux, Seth; Davis, Meghan; Dluzen, Douglas; Ganesan, Sukirth M; Haruna, Muyideen; Nasko, Dan; Regan, Mary J; Sarria, Saul; Shah, Nidhi; Stacy, Brook; Taylor, Dylan; DiRuggiero, Jocelyne; Preheim, Sarah P

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019 Journal Article

In: mSystems, 4 (5), 2019.

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Sakowski, Eric; Uritskiy, Gherman; Cooper, Rachel; Gomes, Maya; McLaren, Michael R; Meisel, Jacquelyn S; Mickol, Rebecca L; Mintz, David C; Mongodin, Emmanuel F; Pop, Mihai; Rahman, Mohammad Arifur; Sanchez, Alvaro; Timp, Winston; Vela, Jeseth Delgado; Wolz, Carly Muletz; Zackular, Joseph P; Chopyk, Jessica; Commichaux, Seth; Davis, Meghan; Dluzen, Douglas; Ganesan, Sukirth M; Haruna, Muyideen; Nasko, Dan; Regan, Mary J; Sarria, Saul; Shah, Nidhi; Stacy, Brook; Taylor, Dylan; DiRuggiero, Jocelyne; Preheim, Sarah P

Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019 Journal Article

In: mSystems, 4 (5), 2019.

Abstract | Links | BibTeX | Altmetric

Tiek, Deanna M; Razaghi, Roham; Jin, Lu; Sadowski, Norah; Alamillo-Ferrer, Carla; Hogg, Robert J; Haddad, Bassem R; Drewry, David H; Wells, Carrow I; Pickett, Julie E; Zuercher, William J; Timp, Winston; Riggins, Rebecca B

Targeting destabilized DNA G-quadruplexes and aberrant splicing in drug-resistant glioblastoma Journal Article

In: bioRxiv, 2019.

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Allen, Jawara; Hao, Stephanie; Sears, Cynthia L; Timp, Winston

Epigenetic changes induced by Bacteroides fragilis toxin (BFT) Journal Article

In: Infection and Immunity, 2019, ISSN: 0019-9567, 1098-5522.

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Allen, Jawara; Hao, Stephanie; Sears, Cynthia L; Timp, Winston

Epigenetic changes induced by Bacteroides fragilis toxin (BFT) Journal Article

In: Infection and Immunity, 2019, ISSN: 0019-9567, 1098-5522.

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Briem, Eirikur; Budkova, Zuzana; Sigurdardottir, Anna Karen; Hilmarsdottir, Bylgja; Kricker, Jennifer; Timp, Winston; Magnusson, Magnus Karl; Traustadottir, Gunnhildur Asta; Gudjonsson, Thorarinn

MiR-203a is differentially expressed during branching morphogenesis and EMT in breast progenitor cells and is a repressor of peroxidasin Journal Article

In: Mechanisms of Development, 155 , pp. 34–47, 2019, ISSN: 0925-4773.

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