Works by McCombie, W. Richard

Results: 42

Sorghum Genome Sequencing by Methylation Filtration.

Published in:

PLoS Biology, 2005, v. 3, n. 1, p. 1, doi. 10.1371/journal.pbio.0030013

By:

Bedell, Joseph A;
Budiman, Muhammad A;
Nunberg, Andrew;
Citek, Robert W;
Robbins, Dan;
Jones, Joshua;
Flick, Elizabeth;
Rohlfing, Theresa;
Fries, Jason;
Bradford, Kourtney;
McMenamy, Jennifer;
Smith, Michael;
Holeman, Heather;
Roe, Bruce A;
Wiley, Graham;
Korf, Ian F;
Rabinowicz, Pablo D;
Lakey, Nathan;
McCombie, W. Richard;
Jeddeloh, Jeffrey A

Publication type:

Article

Sorghum Genome Sequencing by Methylation Filtration.

Published in:

PLoS Biology, 2005, v. 3, n. 1, p. 103, doi. 10.1371/journal.pbio.0030013

By:

Bedell, Joseph A.;
Budiman, Muhammad A.;
Nunberg, Andrew;
Citek, Robert W.;
Robbins, Dan;
Jones, Joshua;
Flick, Elizabeth;
Rohlfing, Theresa;
Fries, Jason;
Bradford, Kourtney;
McMenamy, Jennifer;
Smith, Michael;
Holeman, Heather;
Roe, Bruce A.;
Wiley, Graham;
Korf, Ian F.;
Rabinowicz, Pablo D.;
Lakey, Nathan;
McCombie, W. Richard;
Jeddeloh, Jeffrey A.

Publication type:

Article

Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum.

Published in:

Plant Journal, 2014, v. 79, n. 1, p. 162, doi. 10.1111/tpj.12539

By:

Grativol, Clícia;
Regulski, Michael;
Bertalan, Marcelo;
McCombie, W. Richard;
Silva, Felipe Rodrigues;
Zerlotini Neto, Adhemar;
Vicentini, Renato;
Farinelli, Laurent;
Hemerly, Adriana Silva;
Martienssen, Robert A.;
Ferreira, Paulo Cavalcanti Gomes

Publication type:

Article

MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-55195-w

By:

Cahn, Jonathan;
Regulski, Michael;
Lynn, Jason;
Ernst, Evan;
de Santis Alves, Cristiane;
Ramakrishnan, Srividya;
Chougule, Kapeel;
Wei, Sharon;
Lu, Zhenyuan;
Xu, Xiaosa;
Ramu, Umamaheswari;
Drenkow, Jorg;
Kramer, Melissa;
Seetharam, Arun;
Hufford, Matthew B.;
McCombie, W. Richard;
Ware, Doreen;
Jackson, David;
Schatz, Michael C.;
Gingeras, Thomas R.

Publication type:

Article

PHYLOGENOMIC ANALYSIS OF TRANSCRIPTOME DATA ELUCIDATES CO-OCCURRENCE OF A PALEOPOLYPLOID EVENT AND THE ORIGIN OF BIMODAL KARYOTYPES IN AGAVOIDEAE (ASPARAGACEA).

Published in:

American Journal of Botany, 2012, v. 99, n. 2, p. 397, doi. 10.3732/ajb.1100537

By:

McKain, Michael R.;
Wickett, Norman;
Yeting Zhang;
Ayyampalayam, Saravanaraj;
McCombie, W. Richard;
Chase, Mark W.;
Pires, J. Chris;
DePamphilis, Claude W.;
Leebens-Mack, Jim

Publication type:

Article

Translating next generation sequencing to practice: Opportunities and necessary steps.

Published in:

Molecular Oncology, 2013, v. 7, n. 4, p. 743, doi. 10.1016/j.molonc.2013.04.008

By:

Kamalakaran, Sitharthan;
Varadan, Vinay;
Janevski, Angel;
Banerjee, Nilanjana;
Tuck, David;
McCombie, W. Richard;
Dimitrova, Nevenka;
Harris, Lyndsay N.

Publication type:

Article

Role of transposable elements in heterochromatin and epigenetic control.

Published in:

Nature, 2004, v. 430, n. 6998, p. 471, doi. 10.1038/nature02651

By:

Lippman, Zachary;
Anne-Valérie Gendrel;
Black, Michael;
Vaughn, Matthew W.;
Dedhia, Neilay;
Mccombie, W. Richard;
Lavine, Kimberly;
Mittal, Vivek;
May, Bruce;
Kasschau, Kristin D.;
Carrington, James C.;
Doerge, Rebecca W.;
Colot, Vincent;
Martienssen, Rob

Publication type:

Article

A resource for large-scale RNA-interference-based screens in mammals.

Published in:

Nature, 2004, v. 428, n. 6981, p. 427, doi. 10.1038/nature02370

By:

Paddison, Patrick J.;
Silva, Jose M.;
Conklin, Douglas S.;
Schlabach, Mike;
Li, Mamie;
Aruleba, Shola;
Balija, Vivekanand;
O'Shaughnessy, Andy;
Gnoj, Lidia;
Scobie, Kim;
Chang, Kenneth;
Westbrook, Thomas;
Cleary, Michele;
Sachidanandam, Ravi;
McCombie, W. Richard;
Elledge, Stephen J.;
Hannon, Gregory J.

Publication type:

Article

Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis.

Published in:

Plant Journal, 2008, v. 55, n. 3, p. 514, doi. 10.1111/j.1365-313X.2008.03517.x

By:

Rosin, Faye M.;
Watanabe, Naohide;
Cacas, Jean-Luc;
Kato, Naohiro;
Arroyo, Juana M.;
Yuda Fang;
May, Bruce;
Vaughn, Matthew;
Simorowski, Joseph;
Ramu, Umamaheswari;
McCombie, Richard W.;
Spector, David L.;
Martienssen, Robert A.;
Lam, Eric

Publication type:

Article

Genome-wide in situ exon capture for selective resequencing.

Published in:

Nature Genetics, 2007, v. 39, n. 12, p. 1522, doi. 10.1038/ng.2007.42

By:

Hodges, Emily;
Zhenyu Xuan;
Balija, Vivekanand;
Kramer, Melissa;
Molla, Michael N.;
Smith, Steven W.;
Middle, Christina M.;
Rodesch, Matthew J.;
Albert, Thomas J.;
Hannon, Gregory J.;
McCombie, W. Richard

Publication type:

Article

Second-generation shRNA libraries covering the mouse and human genomes.

Published in:

Nature Genetics, 2005, v. 37, n. 11, p. 1281, doi. 10.1038/ng1650

By:

Silva, Jose M.;
Li, Mamie Z.;
Chang, Ken;
Wei Ge;
Golding, Michael C.;
Rickles, Richard J.;
Siolas, Despina;
Hu, Guang;
Paddison, Patrick J;
Schlabach, Michael R;
Sheth, Nihar;
Bradshaw, Jeff;
Burchard, Julia;
Kulkarni, Amit;
Cavet, Guy;
Sachidanandam, Ravi;
McCombie, W. Richard;
Cleary, Michele A.;
Elledge, Stephen J.;
Hannon, Gregory J.

Publication type:

Article

Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome.

Published in:

Nature Genetics, 1999, v. 23, n. 3, p. 305, doi. 10.1038/15479

By:

Rabinowicz, Pablo D.;
Schutz, Kristin;
Dedhia, Neilay;
Yordan, Cristina;
Parnell, Laurence D.;
Stein, Lincoln;
McCombie, W. Richard;
Martienssen, Robert A.

Publication type:

Article

A map for sequence analysis of the Arabidopsis thaliana genome.

Published in:

Nature Genetics, 1999, v. 22, n. 3, p. 265, doi. 10.1038/10327

By:

Marra, Marco;
Kucaba, Tamara;
Sekhon, Mandeep;
Hillier, LaDeana;
Martienssen, Robert;
Chinwalla, Asif;
Crockett, Jye'mon;
Fedele, Jacqueline;
Grover, Heather;
Gund, Christopher;
McCombie, W. Richard;
McDonald, Ken;
McPherson, John;
Mudd, Nancy;
Parnell, Larry;
Schein, Jacqueline;
Seim, Ryan;
Shelby, Proteon;
Waterston, Robert

Publication type:

Article

A Hybrid Likelihood Model for Sequence-Based Disease Association Studies.

Published in:

PLoS Genetics, 2013, v. 9, n. 1, p. 1, doi. 10.1371/journal.pgen.1003224

By:

Yun-Ching Chen;
Carter, Hannah;
Parla, Jennifer;
Kramer, Melissa;
Goes, Fernando S.;
Pirooznia, Mehdi;
Zandi, Peter P.;
McCombie, W. Richard;
Potash, James B.;
Karchin, Rachel

Publication type:

Article

A Functional Phylogenomic View of the Seed Plants.

Published in:

PLoS Genetics, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pgen.1002411

By:

Lee, Ernest K.;
Cibrian-Jaramillo, Angelica;
Kolokotronis, Sergios-Orestis;
Katari, Manpreet S.;
Stamatakis, Alexandros;
Ott, Michael;
Chiu, Joanna C.;
Little, Damon P.;
Stevenson, Dennis Wm.;
McCombie, W. Richard;
Martienssen, Robert A.;
Coruzzi, Gloria;
DeSalle, Rob

Publication type:

Article

A Caenorhabditis elegans Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology.

Published in:

G3: Genes | Genomes | Genetics, 2020, v. 10, n. 5, p. 1617, doi. 10.1534/g3.119.400925

By:

Aguirre-Chen, Cristina;
Stec, Natalia;
Ramos, Olivia Mendivil;
Nuri Kim;
Kramer, Melissa;
McCarthy, Shane;
Gillis, Jesse;
McCombie, W. Richard;
Hammell, Christopher M.

Publication type:

Article

Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats.

Published in:

Genome Biology & Evolution, 2023, v. 15, n. 9, p. 1, doi. 10.1093/gbe/evad148

By:

Scheben, Armin;
Ramos, Olivia Mendivil;
Kramer, Melissa;
Goodwin, Sara;
Oppenheim, Sara;
Becker, Daniel J;
Schatz, Michael C;
Simmons, Nancy B;
Siepel, Adam;
McCombie, W Richard

Publication type:

Article

Unlocking the Treasure Trove: From Genes to Schizophrenia Biology.

Published in:

Schizophrenia Bulletin, 2014, v. 40, n. 3, p. 492, doi. 10.1093/schbul/sbu042

By:

McCarthy, Shane E.;
McCombie, W. Richard;
Corvin, Aiden

Publication type:

Article

The human origin recognition complex is essential for pre-RC assembly, mitosis, and maintenance of nuclear structure.

Published in:

eLife, 2021, p. 1, doi. 10.7554/eLife.61797

By:

Hsiang-Chen Chou;
Bhalla, Kuhulika;
Demerdesh, Osama E. L.;
Klingbeil, Olaf;
Hanington, Kaarina;
Aganezov, Sergey;
Andrews, Peter;
Alsudani, Habeeb;
Chang, Kenneth;
Vakoc, Christopher R.;
Schatz, Michael C.;
McCombie, W. Richard;
Stillman, Bruce

Publication type:

Article

Creutzfeldt-Jakob disease cosegregates with the codon 178<sup>Asn</sup> PRNP mutation in families of European origin.

Published in:

Annals of Neurology, 1992, v. 31, n. 3, p. 274, doi. 10.1002/ana.410310308

By:

Goldfarb, Lev G.;
Brown, Paul;
Haltia, Matti;
Cathala, Françoise;
McCombie, W. Richard;
Kovanen, Jussi;
Červen̆áková, Larisa;
Goldin, Lynn;
Nieto, Ana;
Godec, Mark S.;
Asher, David M.;
Gajdusek, D. Carleton

Publication type:

Article

A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing.

Published in:

Bioinformatics, 2015, v. 31, n. 12, p. 2040, doi. 10.1093/bioinformatics/btv089

By:

Xuefeng Wang;
Xiaoqing Yu;
Wei Zhu;
McCombie, W. Richard;
Antoniou, Eric;
Powers, R. Scott;
Davidson, Nicholas O.;
Li, Ellen;
Williams, Jennie

Publication type:

Article

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.

Published in:

Bioinformatics, 2014, v. 30, n. 8, p. 1175, doi. 10.1093/bioinformatics/btt749

By:

Yao, Jianchao;
Zhang, Kelvin Xi;
Kramer, Melissa;
Pellegrini, Matteo;
McCombie, W. Richard

Publication type:

Article

SpliceTrap: a method to quantify alternative splicing under single cellular conditions.

Published in:

Bioinformatics, 2011, v. 27, n. 21, p. 3010, doi. 10.1093/bioinformatics/btr508

By:

Wu, Jie;
Akerman, Martin;
Sun, Shuying;
McCombie, W. Richard;
Krainer, Adrian R.;
Zhang, Michael Q.

Publication type:

Article

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-701

By:

Vidal, Elena A.;
Moyano, Tomás C.;
Krouk, Gabriel;
Katari, Manpreet S.;
Tanurdzic, Milos;
McCombie, W. Richard;
Coruzzi, Gloria M.;
Gutiérrez, Rodrigo A.

Publication type:

Article

The pangenome of an agronomically important crop plant Brassica oleracea.

Published in:

Nature Communications, 2016, v. 7, n. 11, p. 13390, doi. 10.1038/ncomms13390

By:

Golicz, Agnieszka A.;
Bayer, Philipp E.;
Barker, Guy C.;
Edger, Patrick P.;
Kim, HyeRan;
Martinez, Paula A.;
Chan, Chon Kit Kenneth;
Severn-Ellis, Anita;
McCombie, W. Richard;
Parkin, Isobel A. P.;
Paterson, Andrew H.;
Pires, J. Chris;
Sharpe, Andrew G.;
Tang, Haibao;
Teakle, Graham R.;
Town, Christopher D.;
Batley, Jacqueline;
Edwards, David

Publication type:

Article

The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development.

Published in:

Nature Communications, 2013, v. 4, n. 7, p. 2145, doi. 10.1038/ncomms3145

By:

May, Patrick;
Liao, Will;
Wu, Yijin;
Shuai, Bin;
Richard McCombie, W.;
Zhang, Michael Q.;
Liu, Qiong A.

Publication type:

Article

SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling.

Published in:

Plant Physiology, 2020, v. 182, n. 1, p. 215, doi. 10.1104/pp.19.00682

By:

Ying Li;
Brooks, Matthew;
Yeoh-Wang, Jenny;
McCoy, Rachel M.;
Rock, Tara M.;
Pasquino, Angelo;
Chang In Moon;
Patrick, Ryan M.;
Tanurdzic, Milos;
Ruffel, Sandrine;
Widhalm, Joshua R.;
McCombie, W. Richard;
Coruzzi, Gloria M.

Publication type:

Article

Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets.

Published in:

BMC Bioinformatics, 2013, v. 14, n. Suppl 9, p. 1, doi. 10.1186/1471-2105-14-S9-S1

By:

Xiao Xu;
Yuanhao Zhang;
Williams, Jennie;
Antoniou, Eric;
Richard McCombie, W.;
Song Wu;
Wei Zhu;
Davidson, Nicholas O.;
Denoya, Paula;
Ellen Li

Publication type:

Article

The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants

Published in:

Genome Biology, 2015, v. 16, n. 1, p. 79, doi. 10.1186/s13059-015-0640-2

By:

Ying Li;
Mukherjee, Indrani;
Thum, Karen E;
Tanurdzic, Milos;
Katari, Manpreet S;
Obertello, Mariana;
Edwards, Molly B;
McCombie, W Richard;
Martienssen, Robert A;
Coruzzi, Gloria M

Publication type:

Article

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.

Published in:

Genome Biology, 2014, v. 15, n. 11, p. 1, doi. 10.1186/s13059-014-0506-z

By:

Schatz, Michael C.;
Maron, Lyza G.;
Stein, Joshua C.;
Wences, Alejandro Hernandez;
Gurtowski, James;
Biggers, Eric;
Lee, Hayan;
Kramer, Melissa;
Antoniou, Eric;
Ghiban, Elena;
Wright, Mark H.;
Jer-ming Chia;
Ware, Doreen;
McCouch, Susan R.;
McCombie, W. Richard

Publication type:

Article

Current challenges in de novo plant genome sequencing and assembly.

Published in:

Genome Biology, 2012, v. 13, n. 4, p. 243, doi. 10.1186/gb-2012-13-4-243

By:

Schatz, Michael C.;
Witkowski, Jan;
McCombie, W. Richard

Publication type:

Article

A comparative analysis of exome capture.

Published in:

Genome Biology, 2011, v. 12, n. 9, p. 1, doi. 10.1186/gb-2011-12-9-r97

By:

Parla, Jennifer S.;
Iossifov, Ivan;
Grabill, Ian;
Spector, Mona S.;
Kramer, Melissa;
Richard McCombie, W.

Publication type:

Article

Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A. thaliana.

Published in:

Theoretical & Applied Genetics, 2005, v. 111, n. 5, p. 949, doi. 10.1007/s00122-005-0029-9

By:

Muqiang Gao;
Genyi Li;
McCombie, W. Richard;
Quiros, Carlos F.

Publication type:

Article

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing.

Published in:

Nature Methods, 2008, v. 5, n. 8, p. 679, doi. 10.1038/nmeth.1230

By:

Erlich, Yaniv;
Mitra, Partha P;
delaBastide, Melissa;
McCombie, W Richard;
Hannon, Gregory J.

Publication type:

Article

Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.

Published in:

Nature Methods, 2004, v. 1, n. 3, p. 241, doi. 10.1038/nmeth724

By:

Cleary, Michele A.;
Kilian, Kristopher;
Yanqun Wang;
Bradshaw, Jeff;
Cavet, Guy;
Wei Ge;
Kulkarni, Amit;
Paddison, Patrick J.;
Chang, Kenneth;
Sheth, Nihar;
Leproust, Eric;
Coffey, Ernest M.;
Burchard, Julja;
McCombie, W. Richard;
Linsley, Peter;
Hannon, Gregory J.

Publication type:

Article

Tumour evolution inferred by single-cell sequencing.

Published in:

Nature, 2011, v. 472, n. 7341, p. 90, doi. 10.1038/nature09807

By:

Navin, Nicholas;
Kendall, Jude;
Troge, Jennifer;
Andrews, Peter;
Rodgers, Linda;
McIndoo, Jeanne;
Cook, Kerry;
Stepansky, Asya;
Levy, Dan;
Esposito, Diane;
Muthuswamy, Lakshmi;
Krasnitz, Alex;
McCombie, W. Richard;
Hicks, James;
Wigler, Michael

Publication type:

Article

A Workshop Report on Wheat Genome Sequencing: International Genome Research on Wheat Consortium.

Published in:

Genetics, 2004, v. 168, n. 2, p. 1087, doi. 10.1534/genetics.104.034769

By:

Gill, Bikram S.;
Appels, Rudi;
Botha-Oberholster, Anna-Maria;
Buell, C. Robin;
Bennetzen, Jeffrey L.;
Chalhoub, Boulos;
Chumley, Forrest;
Dvořák, Jan;
Iwanaga, Masaru;
Keller, Beat;
Wanlong Li;
McCombie, W. Richard;
Ogthara, Yasunari;
Quetier, Francis;
Sasaki, Takuji

Publication type:

Article

Hybrid assembly with long and short reads improves discovery of gene family expansions.

Published in:

BMC Genomics, 2017, v. 18, p. 1, doi. 10.1186/s12864-017-3927-8

By:

Miller, Jason R.;
Peng Zhou;
Mudge, Joann;
Gurtowski, James;
Hayan Lee;
Ramaraj, Thiruvarangan;
Walenz, Brian P.;
Junqi Liu;
Stupar, Robert M.;
Denny, Roxanne;
Li Song;
Singh, Namrata;
Maron, Lyza G.;
McCouch, Susan R.;
McCombie, W. Richard;
Schatz, Michael C.;
Tiffin, Peter;
Young, Nevin D.;
Silverstein, Kevin A. T.

Publication type:

Article

Validation and assessment of variant calling pipelines for next-generation sequencing.

Published in:

Human Genomics, 2014, v. 8, n. 1, p. 14, doi. 10.1186/1479-7364-8-14

By:

Pirooznia, Mehdi Pirooznia;
Kramer, Melissa;
Parla, Jennifer;
Goes, Fernando S;
Potash, James B;
McCombie, W Richard;
Zandi, Peter P

Publication type:

Article

The contribution of de novo coding mutations to autism spectrum disorder.

Published in:

Nature, 2014, v. 515, n. 7526, p. 216, doi. 10.1038/nature13908

By:

Iossifov, Ivan;
Ronemus, Michael;
Levy, Dan;
Yamrom, Boris;
Lee, Yoon-ha;
Wang, Zihua;
Marks, Steven;
Andrews, Peter;
Leotta, Anthony;
Kendall, Jude;
Hakker, Inessa;
Rosenbaum, Julie;
Ma, Beicong;
Rodgers, Linda;
Troge, Jennifer;
Yoon, Seungtai;
Schatz, Michael C.;
McCombie, W. Richard;
Wigler, Michael;
Grabowska, Ewa

Publication type:

Article

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Published in:

Nature Biotechnology, 2012, v. 30, n. 7, p. 693, doi. 10.1038/nbt.2280

By:

Koren, Sergey;
Schatz, Michael C;
Walenz, Brian P;
Martin, Jeffrey;
Howard, Jason T;
Ganapathy, Ganeshkumar;
Wang, Zhong;
Rasko, David A;
McCombie, W Richard;
Jarvis, Erich D;
Phillippy, Adam M

Publication type:

Article

Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence.

Published in:

Genome, 2004, v. 47, n. 4, p. 666, doi. 10.1139/G04-021

By:

Gao, Muqiang;
Genyi Li;
Bo Yang;
McCombie, W. Richard;
Quiros, Carlos F.

Publication type:

Article