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1.

Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages.

Lotto, Jeremy; Drissler, Sibyl; Cullum, Rebecca; Wei, Wei; Setty, Manu; Bell, Erin M; Boutet, Stéphane C; Nowotschin, Sonja; Kuo, Ying-Yi; Garg, Vidur; Pe'er, Dana; Church, Deanna M; Hadjantonakis, Anna-Katerina; Hoodless, Pamela A.

Cell ; 183(3): 702-716.e14, 2020 10 29.

Artigo em Inglês | MEDLINE | ID: mdl-33125890

2.

Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly.

Aneichyk, Tatsiana; Hendriks, William T; Yadav, Rachita; Shin, David; Gao, Dadi; Vaine, Christine A; Collins, Ryan L; Domingo, Aloysius; Currall, Benjamin; Stortchevoi, Alexei; Multhaupt-Buell, Trisha; Penney, Ellen B; Cruz, Lilian; Dhakal, Jyotsna; Brand, Harrison; Hanscom, Carrie; Antolik, Caroline; Dy, Marisela; Ragavendran, Ashok; Underwood, Jason; Cantsilieris, Stuart; Munson, Katherine M; Eichler, Evan E; Acuña, Patrick; Go, Criscely; Jamora, R Dominic G; Rosales, Raymond L; Church, Deanna M; Williams, Stephen R; Garcia, Sarah; Klein, Christine; Müller, Ulrich; Wilhelmsen, Kirk C; Timmers, H T Marc; Sapir, Yechiam; Wainger, Brian J; Henderson, Daniel; Ito, Naoto; Weisenfeld, Neil; Jaffe, David; Sharma, Nutan; Breakefield, Xandra O; Ozelius, Laurie J; Bragg, D Cristopher; Talkowski, Michael E.

Cell ; 172(5): 897-909.e21, 2018 02 22.

Artigo em Inglês | MEDLINE | ID: mdl-29474918

3.

The emergent landscape of the mouse gut endoderm at single-cell resolution.

Nowotschin, Sonja; Setty, Manu; Kuo, Ying-Yi; Liu, Vincent; Garg, Vidur; Sharma, Roshan; Simon, Claire S; Saiz, Nestor; Gardner, Rui; Boutet, Stéphane C; Church, Deanna M; Hoodless, Pamela A; Hadjantonakis, Anna-Katerina; Pe'er, Dana.

Nature ; 569(7756): 361-367, 2019 05.

Artigo em Inglês | MEDLINE | ID: mdl-30959515

4.

Resolving the full spectrum of human genome variation using Linked-Reads.

Marks, Patrick; Garcia, Sarah; Barrio, Alvaro Martinez; Belhocine, Kamila; Bernate, Jorge; Bharadwaj, Rajiv; Bjornson, Keith; Catalanotti, Claudia; Delaney, Josh; Fehr, Adrian; Fiddes, Ian T; Galvin, Brendan; Heaton, Haynes; Herschleb, Jill; Hindson, Christopher; Holt, Esty; Jabara, Cassandra B; Jett, Susanna; Keivanfar, Nikka; Kyriazopoulou-Panagiotopoulou, Sofia; Lek, Monkol; Lin, Bill; Lowe, Adam; Mahamdallie, Shazia; Maheshwari, Shamoni; Makarewicz, Tony; Marshall, Jamie; Meschi, Francesca; O'Keefe, Christopher J; Ordonez, Heather; Patel, Pranav; Price, Andrew; Royall, Ariel; Ruark, Elise; Seal, Sheila; Schnall-Levin, Michael; Shah, Preyas; Stafford, David; Williams, Stephen; Wu, Indira; Xu, Andrew Wei; Rahman, Nazneen; MacArthur, Daniel; Church, Deanna M.

Genome Res ; 29(4): 635-645, 2019 04.

Artigo em Inglês | MEDLINE | ID: mdl-30894395

5.

Thousands of human sequences provide deep insight into single genomes.

Church, Deanna M.

Nature ; 581(7809): 385-386, 2020 05.

Artigo em Inglês | MEDLINE | ID: mdl-32461645

6.

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly.

Bayega, Anthony; Djambazian, Haig; Tsoumani, Konstantina T; Gregoriou, Maria-Eleni; Sagri, Efthimia; Drosopoulou, Eleni; Mavragani-Tsipidou, Penelope; Giorda, Kristina; Tsiamis, George; Bourtzis, Kostas; Oikonomopoulos, Spyridon; Dewar, Ken; Church, Deanna M; Papanicolaou, Alexie; Mathiopoulos, Kostas D; Ragoussis, Jiannis.

BMC Genomics ; 21(1): 259, 2020 Mar 30.

Artigo em Inglês | MEDLINE | ID: mdl-32228451

7.

Direct determination of diploid genome sequences.

Weisenfeld, Neil I; Kumar, Vijay; Shah, Preyas; Church, Deanna M; Jaffe, David B.

Genome Res ; 27(5): 757-767, 2017 05.

Artigo em Inglês | MEDLINE | ID: mdl-28381613

8.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

Schneider, Valerie A; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A; Murphy, Terence D; Pruitt, Kim D; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T; Threadgold, Glen; Torrance, James; Wood, Jonathan M; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M; Durbin, Richard; Wilson, Richard K; Flicek, Paul; Eichler, Evan E; Church, Deanna M.

Genome Res ; 27(5): 849-864, 2017 05.

Artigo em Inglês | MEDLINE | ID: mdl-28396521

9.

Assembly: a resource for assembled genomes at NCBI.

Kitts, Paul A; Church, Deanna M; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D; Pruitt, Kim D; Kimchi, Avi.

Nucleic Acids Res ; 44(D1): D73-80, 2016 Jan 04.

Artigo em Inglês | MEDLINE | ID: mdl-26578580

10.

Single haplotype assembly of the human genome from a hydatidiform mole.

Steinberg, Karyn Meltz; Schneider, Valerie A; Graves-Lindsay, Tina A; Fulton, Robert S; Agarwala, Richa; Huddleston, John; Shiryev, Sergey A; Morgulis, Aleksandr; Surti, Urvashi; Warren, Wesley C; Church, Deanna M; Eichler, Evan E; Wilson, Richard K.

Genome Res ; 24(12): 2066-76, 2014 12.

Artigo em Inglês | MEDLINE | ID: mdl-25373144

11.

Corrigendum: Direct determination of diploid genome sequences.

Weisenfeld, Neil I; Kumar, Vijay; Shah, Preyas; Church, Deanna M; Jaffe, David B.

Genome Res ; 28(4): 606.1, 2018 04.

Artigo em Inglês | MEDLINE | ID: mdl-29610250

12.

ClinVar: public archive of relationships among sequence variation and human phenotype.

Landrum, Melissa J; Lee, Jennifer M; Riley, George R; Jang, Wonhee; Rubinstein, Wendy S; Church, Deanna M; Maglott, Donna R.

Nucleic Acids Res ; 42(Database issue): D980-5, 2014 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-24234437

13.

Clone DB: an integrated NCBI resource for clone-associated data.

Schneider, Valerie A; Chen, Hsiu-Chuan; Clausen, Cliff; Meric, Peter A; Zhou, Zhigang; Bouk, Nathan; Husain, Nora; Maglott, Donna R; Church, Deanna M.

Nucleic Acids Res ; 41(Database issue): D1070-8, 2013 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-23193260

14.

DbVar and DGVa: public archives for genomic structural variation.

Lappalainen, Ilkka; Lopez, John; Skipper, Lisa; Hefferon, Timothy; Spalding, J Dylan; Garner, John; Chen, Chao; Maguire, Michael; Corbett, Matt; Zhou, George; Paschall, Justin; Ananiev, Victor; Flicek, Paul; Church, Deanna M.

Nucleic Acids Res ; 41(Database issue): D936-41, 2013 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-23193291

15.

Database resources of the National Center for Biotechnology Information.

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Krasnov, Sergey; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Karsch-Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian.

Nucleic Acids Res ; 40(Database issue): D13-25, 2012 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-22140104

16.

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Miller, David T; Adam, Margaret P; Aradhya, Swaroop; Biesecker, Leslie G; Brothman, Arthur R; Carter, Nigel P; Church, Deanna M; Crolla, John A; Eichler, Evan E; Epstein, Charles J; Faucett, W Andrew; Feuk, Lars; Friedman, Jan M; Hamosh, Ada; Jackson, Laird; Kaminsky, Erin B; Kok, Klaas; Krantz, Ian D; Kuhn, Robert M; Lee, Charles; Ostell, James M; Rosenberg, Carla; Scherer, Stephen W; Spinner, Nancy B; Stavropoulos, Dimitri J; Tepperberg, James H; Thorland, Erik C; Vermeesch, Joris R; Waggoner, Darrel J; Watson, Michael S; Martin, Christa Lese; Ledbetter, David H.

Am J Hum Genet ; 86(5): 749-64, 2010 May 14.

Artigo em Inglês | MEDLINE | ID: mdl-20466091

17.

Database resources of the National Center for Biotechnology Information.

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; DiCuccio, Michael; Federhen, Scott; Feolo, Michael; Fingerman, Ian M; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Phan, Lon; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; Wilbur, W John; Yaschenko, Eugene; Ye, Jian.

Nucleic Acids Res ; 39(Database issue): D38-51, 2011 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-21097890

18.

Lineage-specific biology revealed by a finished genome assembly of the mouse.

Church, Deanna M; Goodstadt, Leo; Hillier, Ladeana W; Zody, Michael C; Goldstein, Steve; She, Xinwe; Bult, Carol J; Agarwala, Richa; Cherry, Joshua L; DiCuccio, Michael; Hlavina, Wratko; Kapustin, Yuri; Meric, Peter; Maglott, Donna; Birtle, Zoë; Marques, Ana C; Graves, Tina; Zhou, Shiguo; Teague, Brian; Potamousis, Konstantinos; Churas, Christopher; Place, Michael; Herschleb, Jill; Runnheim, Ron; Forrest, Daniel; Amos-Landgraf, James; Schwartz, David C; Cheng, Ze; Lindblad-Toh, Kerstin; Eichler, Evan E; Ponting, Chris P.

PLoS Biol ; 7(5): e1000112, 2009 May 05.

Artigo em Inglês | MEDLINE | ID: mdl-19468303

19.

Database resources of the National Center for Biotechnology Information.

Sayers, Eric W; Barrett, Tanya; Benson, Dennis A; Bolton, Evan; Bryant, Stephen H; Canese, Kathi; Chetvernin, Vyacheslav; Church, Deanna M; Dicuccio, Michael; Federhen, Scott; Feolo, Michael; Geer, Lewis Y; Helmberg, Wolfgang; Kapustin, Yuri; Landsman, David; Lipman, David J; Lu, Zhiyong; Madden, Thomas L; Madej, Tom; Maglott, Donna R; Marchler-Bauer, Aron; Miller, Vadim; Mizrachi, Ilene; Ostell, James; Panchenko, Anna; Pruitt, Kim D; Schuler, Gregory D; Sequeira, Edwin; Sherry, Stephen T; Shumway, Martin; Sirotkin, Karl; Slotta, Douglas; Souvorov, Alexandre; Starchenko, Grigory; Tatusova, Tatiana A; Wagner, Lukas; Wang, Yanli; John Wilbur, W; Yaschenko, Eugene; Ye, Jian.

Nucleic Acids Res ; 38(Database issue): D5-16, 2010 Jan.

Artigo em Inglês | MEDLINE | ID: mdl-19910364

20.

A next-generation human genome sequence.

Church, Deanna M.

Science ; 376(6588): 34-35, 2022 04.

Artigo em Inglês | MEDLINE | ID: mdl-35357937

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Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages.

Dissecting the Causal Mechanism of X-Linked Dystonia-Parkinsonism by Integrating Genome and Transcriptome Assembly.

The emergent landscape of the mouse gut endoderm at single-cell resolution.

Resolving the full spectrum of human genome variation using Linked-Reads.

Thousands of human sequences provide deep insight into single genomes.

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly.

Direct determination of diploid genome sequences.

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

Assembly: a resource for assembled genomes at NCBI.

Single haplotype assembly of the human genome from a hydatidiform mole.

Corrigendum: Direct determination of diploid genome sequences.

ClinVar: public archive of relationships among sequence variation and human phenotype.

Clone DB: an integrated NCBI resource for clone-associated data.

DbVar and DGVa: public archives for genomic structural variation.

Database resources of the National Center for Biotechnology Information.

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Database resources of the National Center for Biotechnology Information.

Lineage-specific biology revealed by a finished genome assembly of the mouse.

Database resources of the National Center for Biotechnology Information.

A next-generation human genome sequence.