W Richard McCombie - Publications

Stony Brook University, Stony Brook, NY, United States 
Genetics, Oncology, Cell Biology

117 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Noyes MD, Harvey WT, Porubsky D, Sulovari A, Li R, Rose NR, Audano PA, Munson KM, Lewis AP, Hoekzema K, Mantere T, Graves-Lindsay TA, Sanders AD, Goodwin S, Kramer M, ... ... McCombie WR, et al. Familial long-read sequencing increases yield of de novo mutations. American Journal of Human Genetics. PMID 35290762 DOI: 10.1016/j.ajhg.2022.02.014  0.346
2020 Aganezov S, Goodwin S, Sherman RM, Sedlazeck FJ, Arun G, Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, Kostroff K, Spector DL, Timp W, McCombie WR, Schatz MC. Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. Genome Research. PMID 32887686 DOI: 10.1101/Gr.260497.119  0.425
2020 Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, ... ... McCombie WR, et al. Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato. Cell. PMID 32553272 DOI: 10.1016/J.Cell.2020.05.021  0.49
2020 Aguirre-Chen C, Stec N, Mendivil Ramos O, Kim N, Kramer M, McCarthy S, Gillis J, McCombie WR, Hammell CM. A Model for Integrating the Functions of Neuropsychiatric Risk Genes Identifies Components Required for Normal Dendritic Morphology. G3 (Bethesda, Md.). PMID 32132169 DOI: 10.1534/G3.119.400925  0.389
2020 Iyer SV, Goodwin S, Kramer M, McCombie WR. Abstract 1360: Understanding genetic variation in cancer using targeted nanopore long read sequencing Cancer Research. 80: 1360-1360. DOI: 10.1158/1538-7445.Am2020-1360  0.453
2019 Li Y, Brooks M, Yeoh-Wang J, McCoy RM, Rock TM, Pasquino A, Moon CI, Patrick RM, Tanurdzic M, Ruffel S, Widhalm JR, McCombie WR, Coruzzi GM. SDG8-mediated histone methylation and RNA processing function in the response to nitrate signaling. Plant Physiology. PMID 31641075 DOI: 10.1104/Pp.19.00682  0.652
2019 McCombie WR, McPherson JD. Future Promises and Concerns of Ubiquitous Next-Generation Sequencing. Cold Spring Harbor Perspectives in Medicine. 9. PMID 30478095 DOI: 10.1101/Cshperspect.A025783  0.434
2019 Iyer S, Goodwin S, McCombie WR. Abstract 5136: Adapting long read sequencing technologies for targeted and single cell applications Cancer Research. 79: 5136-5136. DOI: 10.1158/1538-7445.Am2019-5136  0.449
2019 Ryan N, Lihm J, Kramer M, McCarthy S, Evans K, Ghiban E, Millar JK, Scotland G, McIntosh A, Blackwood D, Lawrie S, Porteous D, McCombie WR, Thomson P. Beyond The Translocation: Whole Genome Sequencing Analysis Of The Scottish T(1;11) Family European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.08.196  0.373
2018 McCombie WR, McPherson JD, Mardis ER. Next-Generation Sequencing Technologies. Cold Spring Harbor Perspectives in Medicine. PMID 30478097 DOI: 10.1101/Cshperspect.A036798  0.469
2018 Nattestad M, Goodwin S, Ng K, Baslan T, Sedlazeck F, Rescheneder P, Garvin T, Fang H, Gurtowski J, Hutton E, Tseng E, Chin J, Beck T, Sundaravadanam Y, Kramer M, ... ... McCombie WR, et al. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Research. PMID 29954844 DOI: 10.1101/Gr.231100.117  0.46
2018 Ryan NM, Lihm J, Kramer M, McCarthy S, Morris SW, Arnau-Soler A, Davies G, Duff B, Ghiban E, Hayward C, Deary IJ, Blackwood DHR, Lawrie SM, McIntosh AM, Evans KL, ... ... McCombie WR, et al. DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders. Molecular Psychiatry. PMID 29880880 DOI: 10.1038/S41380-018-0087-4  0.439
2018 Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM. Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. Proceedings of the National Academy of Sciences of the United States of America. PMID 29769331 DOI: 10.1073/Pnas.1721487115  0.613
2018 Wang B, Regulski M, Tseng E, Olson A, Goodwin S, McCombie WR, Ware D. A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Research. PMID 29712755 DOI: 10.1101/Gr.227462.117  0.484
2017 Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, et al. Hybrid assembly with long and short reads improves discovery of gene family expansions. Bmc Genomics. 18: 541. PMID 28724409 DOI: 10.1186/S12864-017-3927-8  0.475
2017 Goodwin S, Wappel R, McCombie WR. 1D Genome Sequencing on the Oxford Nanopore MinION. Current Protocols in Human Genetics. 94: 18.11.1-18.11.14. PMID 28696556 DOI: 10.1002/Cphg.39  0.467
2017 Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, ... ... McCombie WR, et al. Improved maize reference genome with single-molecule technologies. Nature. PMID 28605751 DOI: 10.1038/Nature22971  0.526
2016 Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CK, Severn-Ellis A, McCombie WR, Parkin IA, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, et al. The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications. 7: 13390. PMID 27834372 DOI: 10.1038/Ncomms13390  0.495
2016 Mardis E, McCombie WR. Preparing Polymerase Chain Reaction (PCR) Products for Capillary Sequencing. Cold Spring Harbor Protocols. PMID 27803282 DOI: 10.1101/Pdb.Prot094599  0.315
2016 Mardis E, McCombie WR. Agarose Gel Size Selection for DNA Sequencing Libraries. Cold Spring Harbor Protocols. PMID 27803281 DOI: 10.1101/Pdb.Prot094698  0.302
2016 Mardis E, McCombie WR. Whole-Genome Sequencing: Manual Library Preparation. Cold Spring Harbor Protocols. PMID 27803280 DOI: 10.1101/Pdb.Prot094615  0.448
2016 Mardis E, McCombie WR. Whole-Genome Sequencing: Automated, Nonindexed Library Preparation. Cold Spring Harbor Protocols. PMID 27803279 DOI: 10.1101/Pdb.Prot094623  0.367
2016 Mardis E, McCombie WR. Automated Library Preparation for DNA Sequencing. Cold Spring Harbor Protocols. PMID 27803276 DOI: 10.1101/Pdb.Prot094631  0.307
2016 Mardis E, McCombie WR. RNA-Seq: RNA Conversion to cDNA and Amplification. Cold Spring Harbor Protocols. PMID 27803275 DOI: 10.1101/Pdb.Prot094672  0.366
2016 Mardis E, McCombie WR. Solution-Phase Exome Capture. Cold Spring Harbor Protocols. PMID 27803274 DOI: 10.1101/Pdb.Prot094680  0.424
2016 Mardis E, McCombie WR. Preparation of a 3-kb Mate-Pair Library for Illumina Sequencing. Cold Spring Harbor Protocols. PMID 27803272 DOI: 10.1101/Pdb.Prot094656  0.375
2016 Mardis E, McCombie WR. Cycle-Sequencing Reactions. Cold Spring Harbor Protocols. PMID 27803269 DOI: 10.1101/Pdb.Prot094607  0.414
2016 Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews. Genetics. 17: 333-51. PMID 27184599 DOI: 10.1038/Nrg.2016.49  0.47
2015 Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC, McCombie WR. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Research. 25: 1750-6. PMID 26447147 DOI: 10.1101/Gr.191395.115  0.431
2015 Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proceedings of the National Academy of Sciences of the United States of America. 112: 12462-7. PMID 26392545 DOI: 10.1073/Pnas.1516718112  0.476
2015 Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, ... ... McCombie WR, et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nature Methods. PMID 26121404 DOI: 10.1038/Nmeth.3454  0.432
2015 Li Y, Mukherjee I, Thum KE, Tanurdzic M, Katari MS, Obertello M, Edwards MB, McCombie WR, Martienssen RA, Coruzzi GM. The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants. Genome Biology. 16: 79. PMID 25928034 DOI: 10.1186/S13059-015-0640-2  0.744
2015 Wang X, Yu X, Zhu W, McCombie WR, Antoniou E, Powers RS, Davidson NO, Li E, Williams J. A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing. Bioinformatics (Oxford, England). 31: 2040-2. PMID 25681254 DOI: 10.1093/Bioinformatics/Btv089  0.39
2014 Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biology. 15: 506. PMID 25468217 DOI: 10.1186/S13059-014-0506-Z  0.481
2014 Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, ... ... McCombie WR, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 515: 216-21. PMID 25363768 DOI: 10.1038/Nature13908  0.338
2014 Pirooznia M, Kramer M, Parla J, Goes FS, Potash JB, McCombie WR, Zandi PP. Validation and assessment of variant calling pipelines for next-generation sequencing. Human Genomics. 8: 14. PMID 25078893 DOI: 10.1186/1479-7364-8-14  0.359
2014 Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ. Two waves of de novo methylation during mouse germ cell development. Genes & Development. 28: 1544-9. PMID 25030694 DOI: 10.1101/Gad.244350.114  0.36
2014 Para A, Li Y, Marshall-Colón A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America. 111: 10371-6. PMID 24958886 DOI: 10.1073/Pnas.1404657111  0.59
2014 Grativol C, Regulski M, Bertalan M, McCombie WR, da Silva FR, Zerlotini Neto A, Vicentini R, Farinelli L, Hemerly AS, Martienssen RA, Ferreira PC. Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum. The Plant Journal : For Cell and Molecular Biology. 79: 162-72. PMID 24773339 DOI: 10.1111/Tpj.12539  0.55
2014 Yao J, Zhang KX, Kramer M, Pellegrini M, McCombie WR. FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. Bioinformatics (Oxford, England). PMID 24395755 DOI: 10.1093/Bioinformatics/Btt749  0.382
2014 Streppel MM, Lata S, Delabastide M, Montgomery EA, Wang JS, Canto MI, MacGregor-Das AM, Pai S, Morsink FHM, Offerhaus GJ, Antoniou E, Maitra A, McCombie WR. Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett's esophagus Oncogene. 33: 347-357. PMID 23318448 DOI: 10.1038/Onc.2012.586  0.344
2013 Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice (New York, N.Y.). 6: 4. PMID 24280374 DOI: 10.1186/1939-8433-6-4  0.476
2013 Vidal EA, Moyano TC, Krouk G, Katari MS, Tanurdzic M, McCombie WR, Coruzzi GM, Gutiérrez RA. Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. Bmc Genomics. 14: 701. PMID 24119003 DOI: 10.1186/1471-2164-14-701  0.777
2013 Xu X, Zhang Y, Williams J, Antoniou E, McCombie WR, Wu S, Zhu W, Davidson NO, Denoya P, Li E. 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. Bmc Bioinformatics. 14: S1. PMID 23902433 DOI: 10.1186/1471-2105-14-S9-S1  0.368
2013 May P, Liao W, Wu Y, Shuai B, McCombie WR, Zhang MQ, Liu QA. The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development. Nature Communications. 4: 2145. PMID 23900278 DOI: 10.1038/Ncomms3145  0.303
2013 Kamalakaran S, Varadan V, Janevski A, Banerjee N, Tuck D, McCombie WR, Dimitrova N, Harris LN. Translating next generation sequencing to practice: opportunities and necessary steps. Molecular Oncology. 7: 743-55. PMID 23769412 DOI: 10.1016/J.Molonc.2013.04.008  0.325
2013 Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, ... ... McCombie WR, et al. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences of the United States of America. 110: 7940-5. PMID 23610408 DOI: 10.1073/Pnas.1219082110  0.496
2013 Chen YC, Carter H, Parla J, Kramer M, Goes FS, Pirooznia M, Zandi PP, McCombie WR, Potash JB, Karchin R. A hybrid likelihood model for sequence-based disease association studies. Plos Genetics. 9: e1003224. PMID 23358228 DOI: 10.1371/Journal.Pgen.1003224  0.43
2013 Paul S, Kuo A, Schalch T, Vogel H, Joshua-Tor L, McCombie WR, Gozani O, Hammell M, Mills AA. Chd5 requires PHD-mediated histone 3 binding for tumor suppression. Cell Reports. 3: 92-102. PMID 23318260 DOI: 10.1016/J.Celrep.2012.12.009  0.343
2012 Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, ... ... McCombie WR, et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 491: 705-10. PMID 23192148 DOI: 10.1038/Nature11650  0.551
2012 Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Adam M Phillippy. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nature Biotechnology. 30: 693-700. PMID 22750884 DOI: 10.1038/Nbt.2280  0.421
2012 Schatz MC, Witkowski J, McCombie WR. Current challenges in de novo plant genome sequencing and assembly. Genome Biology. 13: 243. PMID 22546054 DOI: 10.1186/Gb-2012-13-4-243  0.463
2012 McKain MR, Wickett N, Zhang Y, Ayyampalayam S, McCombie WR, Chase MW, Pires JC, dePamphilis CW, Leebens-Mack J. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae). American Journal of Botany. 99: 397-406. PMID 22301890 DOI: 10.3732/Ajb.1100537  0.321
2012 Varshney RK, Chen W, Li Y, Bharti AK, Saxena RK, Schlueter JA, Donoghue MT, Azam S, Fan G, Whaley AM, Farmer AD, Sheridan J, Iwata A, Tuteja R, Penmetsa RV, ... ... McCombie WR, et al. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nature Biotechnology. 30: 83-9. PMID 22057054 DOI: 10.1038/Nbt.2022  0.531
2011 Lee EK, Cibrian-Jaramillo A, Kolokotronis SO, Katari MS, Stamatakis A, Ott M, Chiu JC, Little DP, Stevenson DW, McCombie WR, Martienssen RA, Coruzzi G, Desalle R. A functional phylogenomic view of the seed plants. Plos Genetics. 7: e1002411. PMID 22194700 DOI: 10.1371/Journal.Pgen.1002411  0.773
2011 Tyekucheva S, Yolken RH, McCombie WR, Parla J, Kramer M, Wheelan SJ, Sabunciyan S. Establishing the baseline level of repetitive element expression in the human cortex. Bmc Genomics. 12: 495. PMID 21985647 DOI: 10.1186/1471-2164-12-495  0.379
2011 Parla JS, Iossifov I, Grabill I, Spector MS, Kramer M, McCombie WR. A comparative analysis of exome capture Genome Biology. 12: R97. PMID 21958622 DOI: 10.1186/Gb-2011-12-9-R97  0.448
2011 Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell. 146: 1029-41. PMID 21925323 DOI: 10.1016/J.Cell.2011.08.016  0.327
2011 Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Molecular Cell. 44: 17-28. PMID 21924933 DOI: 10.1016/J.Molcel.2011.08.026  0.387
2011 Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (Oxford, England). 27: 3010-6. PMID 21896509 DOI: 10.1093/Bioinformatics/Btr508  0.357
2011 Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M. Tumour evolution inferred by single-cell sequencing. Nature. 472: 90-4. PMID 21399628 DOI: 10.1038/Nature09807  0.385
2011 Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, ... ... McCombie WR, et al. The genome of Theobroma cacao Nature Genetics. 43: 101-108. PMID 21186351 DOI: 10.1038/Ng.736  0.497
2011 Wall CE, Cozza S, Riquelme CA, McCombie WR, Heimiller JK, Marr TG, Leinwand LA. Whole transcriptome analysis of the fasting and fed Burmese python heart: Insights into extreme physiological cardiac adaptation Physiological Genomics. 43: 69-76. PMID 21045117 DOI: 10.1152/Physiolgenomics.00162.2010  0.394
2010 Argout X, Salse J, Aury JM, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Guiltinan M, Maximova S, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, ... ... McCombie WR, et al. Deciphering the genome structure and paleohistory of Theobroma cacao Nature Precedings. 5: 1-1. DOI: 10.1038/Npre.2010.4908.1  0.489
2009 Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, ... ... McCombie WR, et al. The B73 maize genome: complexity, diversity, and dynamics. Science (New York, N.Y.). 326: 1112-5. PMID 19965430 DOI: 10.1126/Science.1178534  0.543
2009 Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, Pasternak S, Narechania A, Zhang L, Yeh CT, Ying K, ... ... McCombie WR, et al. Detailed analysis of a contiguous 22-Mb region of the maize genome. Plos Genetics. 5: e1000728. PMID 19936048 DOI: 10.1371/Journal.Pgen.1000728  0.551
2009 Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research. 19: 1593-605. PMID 19581485 DOI: 10.1101/Gr.095190.109  0.395
2009 Irvine DV, Goto DB, Vaughn MW, Nakaseko Y, McCombie WR, Yanagida M, Martienssen R. Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome Research. 19: 1077-83. PMID 19423874 DOI: 10.1101/Gr.089318.108  0.461
2008 Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, Ma B, Zender P, Kubicka S, Luk JM, Schirmacher P, McCombie WR, Wigler M, Hicks J, Hannon GJ, Powers S, et al. An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer. Cell. 135: 852-64. PMID 19012953 DOI: 10.1016/J.Cell.2008.09.061  0.377
2008 Erlich Y, Mitra PP, delaBastide M, McCombie WR, Hannon GJ. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nature Methods. 5: 679-82. PMID 18604217 DOI: 10.1038/Nmeth.1230  0.372
2007 de la Bastide M, McCombie WR. Assembling genomic DNA sequences with PHRAP. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit11.4. PMID 18428783 DOI: 10.1002/0471250953.Bi1104S17  0.4
2007 Hodges E, Xuan Z, Balija V, Kramer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR. Genome-wide in situ exon capture for selective resequencing. Nature Genetics. 39: 1522-7. PMID 17982454 DOI: 10.1038/Ng.2007.42  0.463
2007 Vaughn MW, Tanurdzić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, Colot V, Doerge RW, Martienssen RA. Epigenetic natural variation in Arabidopsis thaliana. Plos Biology. 5: e174. PMID 17579518 DOI: 10.1371/Journal.Pbio.0050174  0.412
2007 Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, ... ... McCombie WR, et al. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research. 17: 175-83. PMID 17210932 DOI: 10.1101/Gr.5509507  0.528
2006 Gao M, Li G, Potter D, McCombie WR, Quiros CF. Comparative analysis of methylthioalkylmalate synthase (MAM) gene family and flanking DNA sequences in Brassica oleracea and Arabidopsis thaliana. Plant Cell Reports. 25: 592-8. PMID 16432629 DOI: 10.1007/S00299-005-0078-1  0.465
2005 Brenner ED, Katari MS, Stevenson DW, Rudd SA, Douglas AW, Moss WN, Twigg RW, Runko SJ, Stellari GM, McCombie WR, Coruzzi GM. EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes. Bmc Genomics. 6: 143. PMID 16225698 DOI: 10.1186/1471-2164-6-143  0.777
2005 Rabinowicz PD, Citek R, Budiman MA, Nunberg A, Bedell JA, Lakey N, O'Shaughnessy AL, Nascimento LU, McCombie WR, Martienssen RA. Differential methylation of genes and repeats in land plants. Genome Research. 15: 1431-40. PMID 16204196 DOI: 10.1101/Gr.4100405  0.527
2005 Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach MR, Sheth N, Bradshaw J, Burchard J, Kulkarni A, Cavet G, ... ... McCombie WR, et al. Second-generation shRNA libraries covering the mouse and human genomes. Nature Genetics. 37: 1281-8. PMID 16200065 DOI: 10.1038/Ng1650  0.407
2005 Buell CR, Yuan Q, Ouyang S, Liu J, Zhu W, Wang A, Maiti R, Haas B, Wortman J, Pertea M, Jones KM, Kim M, Overton L, Tsitrin T, Fadrosh D, ... ... McCombie WR, et al. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome Research. 15: 1284-91. PMID 16109971 DOI: 10.1101/Gr.3869505  0.454
2005 Gao M, Li G, McCombie WR, Quiros CF. Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A. thaliana. Tag. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik. 111: 949-55. PMID 16044267 DOI: 10.1007/S00122-005-0029-9  0.502
2005 Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR. Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Research. 15: 496-504. PMID 15805491 DOI: 10.1101/Gr.3239105  0.781
2004 Cleary MA, Kilian K, Wang Y, Bradshaw J, Cavet G, Ge W, Kulkarni A, Paddison PJ, Chang K, Sheth N, Leproust E, Coffey EM, Burchard J, McCombie WR, Linsley P, et al. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nature Methods. 1: 241-8. PMID 15782200 DOI: 10.1038/Nmeth724  0.413
2004 Dike S, Balija VS, Nascimento LU, Xuan Z, Ou J, Zutavern T, Palmer LE, Hannon G, Zhang MQ, McCombie WR. The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome Research. 14: 2424-9. PMID 15574821 DOI: 10.1101/Gr.3158304  0.519
2004 Gill BS, Appels R, Botha-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B, Chumley F, Dvorák J, Iwanaga M, Keller B, Li W, McCombie WR, Ogihara Y, Quetier F, Sasaki T. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics. 168: 1087-96. PMID 15514080 DOI: 10.1534/Genetics.104.034769  0.354
2004 Gao M, Li G, Yang B, McCombie WR, Quiros CF. Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence. Genome / National Research Council Canada = GéNome / Conseil National De Recherches Canada. 47: 666-79. PMID 15284871 DOI: 10.1139/G04-021  0.485
2004 Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, Carrington JC, Doerge RW, Colot V, Martienssen R. Role of transposable elements in heterochromatin and epigenetic control. Nature. 430: 471-6. PMID 15269773 DOI: 10.1038/Nature02651  0.46
2004 Singh NK, Raghuvanshi S, Srivastava SK, Gaur A, Pal AK, Dalal V, Singh A, Ghazi IA, Bhargav A, Yadav M, Dixit A, Batra K, Gaikwad K, Sharma TR, Mohanty A, ... ... McCombie WR, et al. Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Functional & Integrative Genomics. 4: 102-17. PMID 15085449 DOI: 10.1007/S10142-004-0109-Y  0.52
2004 Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O'Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, et al. A resource for large-scale RNA-interference-based screens in mammals. Nature. 428: 427-31. PMID 15042091 DOI: 10.1038/Nature02370  0.39
2004 Martienssen RA, Rabinowicz PD, O'Shaughnessy A, McCombie WR. Sequencing the maize genome. Current Opinion in Plant Biology. 7: 102-7. PMID 15003207 DOI: 10.1016/J.Pbi.2004.01.010  0.512
2003 Palmer LE, Rabinowicz PD, O'Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR. Maize genome sequencing by methylation filtration. Science (New York, N.Y.). 302: 2115-7. PMID 14684820 DOI: 10.1126/Science.1091265  0.541
2003 Rabinowicz PD, Palmer LE, May BP, Hemann MT, Lowe SW, McCombie WR, Martienssen RA. Genes and transposons are differentially methylated in plants, but not in mammals. Genome Research. 13: 2658-64. PMID 14656970 DOI: 10.1101/Gr.1784803  0.437
2003 Cannon SB, McCombie WR, Sato S, Tabata S, Denny R, Palmer L, Katari M, Young ND, Stacey G. Evolution and microsynteny of the apyrase gene family in three legume genomes Molecular Genetics and Genomics. 270: 347-361. PMID 14598165 DOI: 10.1007/S00438-003-0928-X  0.773
2003 Groover AT, Fontana JR, Arroyo JM, Yordan C, McCombie WR, Martienssen RA. Secretion trap tagging of secreted and membrane-spanning proteins using Arabidopsis gene traps. Plant Physiology. 132: 698-708. PMID 12805598 DOI: 10.1104/Pp.103.020099  0.396
2003 Palmer LE, O'Shaughnessy AL, Preston RR, Santos L, Balija VS, Nascimento LU, Zutavern TL, Henthorn PS, Hannon GJ, McCombie WR. A survey of canine expressed sequence tags and a display of their annotations through a flexible web-based interface. The Journal of Heredity. 94: 15-22. PMID 12692157 DOI: 10.1093/Jhered/Esg003  0.327
2003 Rabinowicz PD, McCombie WR, Martienssen RA. Gene enrichment in plant genomic shotgun libraries. Current Opinion in Plant Biology. 6: 150-6. PMID 12667872 DOI: 10.1016/S1369-5266(03)00008-6  0.535
2003 Zhu H, Kim DJ, Baek JM, Choi HK, Ellis LC, Küester H, McCombie WR, Peng HM, Cook DR. Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization. Plant Physiology. 131: 1018-26. PMID 12644654 DOI: 10.1104/Pp.102.016436  0.522
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... McCombie WR, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.515
2002 Palmer LE, McCombie WR. On the importance of being finished. Genome Biology. 3: COMMENT2010. PMID 12372139 DOI: 10.1186/Gb-2002-3-10-Comment2010  0.427
2002 Xuan Z, McCombie WR, Zhang MQ. GFScan: a gene family search tool at genomic DNA level. Genome Research. 12: 1142-9. PMID 12097353 DOI: 10.1101/Gr.220102  0.414
2002 Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, ... ... McCombie WR, et al. The genome sequence of Schizosaccharomyces pombe. Nature. 415: 871-80. PMID 11859360 DOI: 10.1038/Nature724  0.425
2001 Wines ME, Lee L, Katari MS, Zhang L, DeRossi C, Shi Y, Perkins S, Feldman M, McCombie WR, Holdener BC. Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis. Genomics. 72: 88-98. PMID 11247670 DOI: 10.1006/Geno.2000.6466  0.733
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... McCombie WR, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.453
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... McCombie WR, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.457
2000 Tabata S, Kaneko T, Nakamura Y, Kotani H, Kato T, Asamizu E, Miyajima N, Sasamoto S, Kimura T, Hosouchi T, Kawashima K, Kohara M, Matsumoto M, Matsuno A, Muraki A, ... ... McCombie WR, et al. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 408: 823-6. PMID 11130714 DOI: 10.1038/35048507  0.404
1999 Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD, McCombie WR, Martienssen RA, Marra M, Preuss D. Genetic definition and sequence analysis of Arabidopsis centromeres. Science (New York, N.Y.). 286: 2468-74. PMID 10617454 DOI: 10.1126/Science.286.5449.2468  0.314
1999 Mayer K, Schüller C, Wambutt R, Murphy G, Volckaert G, Pohl T, Düsterhöft A, Stiekema W, Entian KD, Terryn N, Harris B, Ansorge W, Brandt P, Grivell L, Rieger M, ... ... McCombie WR, et al. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 402: 769-77. PMID 10617198 DOI: 10.1038/47134  0.462
1999 Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA. Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nature Genetics. 23: 305-8. PMID 10545948 DOI: 10.1038/15479  0.494
1999 Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gund C, McCombie WR, McDonald K, McPherson J, Mudd N, Parnell L, et al. zA map for sequence analysis of the Arabidopsis thaliana genome. Nature Genetics. 22: 265-70. PMID 10391214 DOI: 10.1038/10327  0.415
1995 Springer PS, McCombie WR, Sundaresan V, Martienssen RA. Gene trap tagging of PROLIFERA, an essential MCM2-3-5-like gene in Arabidopsis. Science (New York, N.Y.). 268: 877-80. PMID 7754372 DOI: 10.1126/Science.7754372  0.358
1992 Venter JC, Adams MD, Martin-Gallardo A, McCombie WR, Fields C. Genome sequence analysis: scientific objectives and practical strategies. Trends in Biotechnology. 10: 8-11. PMID 1367941 DOI: 10.1016/0167-7799(92)90158-R  0.343
1992 McCombie WR, Martin-Gallardo A, Gocayne JD, FitzGerald M, Dubnick M, Kelley JM, Castilla L, Liu LI, Wallace S, Trapp S, Tagle D, Whaley WL, Cheng S, Gusella J, Frischauf AM, et al. Expressed genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3 Nature Genetics. 1: 348-353. PMID 1338771 DOI: 10.1038/Ng0892-348  0.382
1992 Martin-Gallardo A, Marchuk DA, Gocayne J, Kerlavage AR, McCombie WR, Venter JC, Collins FS, Wallace MR. Sequencing and analysis of genomic fragments from the NF1 locus. Dna Sequence : the Journal of Dna Sequencing and Mapping. 3: 237-43. PMID 1338369 DOI: 10.3109/10425179209034023  0.351
1992 McCombie WR, Adams MD, Kelley JM, FitzGerald MG, Utterback TR, Khan M, Dubnick M, Kerlavage AR, Venter JC, Fields C. Caenorhabditis elegans expressed sequence tags identify gene families and potential disease gene homologues. Nature Genetics. 1: 124-31. PMID 1302005 DOI: 10.1038/ng0592-124  0.396
1992 Martin-Gallardo A, McCombie WR, Gocayne JD, FitzGerald MG, Wallace S, Lee BMB, Lamerdin J, Trapp S, Kelley JM, Liu LI, Dubnick M, Johnston-Dow LA, Kerlavage AR, De Jong P, Carrano A, et al. Automated DNA sequencing and analysis of 106 kilobases from human chromosome 19q13.3 Nature Genetics. 1: 34-39. PMID 1301997  0.326
1991 Goldfarb LG, Haltia M, Brown P, Nieto A, Kovanen J, McCombie WR, Trapp S, Gajdusek DC. New mutation in scrapie amyloid precursor gene (at codon 178) in Finnish Creutzfeldt-Jakob kindred. Lancet. 337: 425. PMID 1671440 DOI: 10.1016/0140-6736(91)91198-4  0.302
1990 Venter JC, McCombie WR, McConnell JB. Genome Sequencing Conference I: Summary Genomics. 8: 186-188. DOI: 10.1016/0888-7543(90)90245-P  0.472
1989 Onai T, FitzGerald MG, Arakawa S, Gocayne JD, Urquhart DA, Hall LM, Fraser CM, McCombie WR, Venter JC. Cloning, sequence analysis and chromosome localization of a Drosophila muscarinic acetylcholine receptor Febs Letters. 255: 219-225. PMID 2507354 DOI: 10.1016/0014-5793(89)81095-6  0.35
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