| Year |
Citation |
Score |
| 2024 |
Kramer M, Goodwin S, Wappel R, Borio M, Offit K, Feldman DR, Stadler ZK, McCombie WR. Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees. Biorxiv : the Preprint Server For Biology. PMID 39005350 DOI: 10.1101/2024.06.27.601096 |
0.313 |
|
| 2024 |
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautianinen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, ... ... McCombie WR, et al. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Biorxiv : the Preprint Server For Biology. PMID 38529488 DOI: 10.1101/2024.03.15.585294 |
0.389 |
|
| 2024 |
Gustafson JA, Gibson SB, Damaraju N, Zalusky MP, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W, Olson ND, Guarracino A, Li Q, Miller AL, Goffena J, ... ... McCombie WR, et al. Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation. Medrxiv : the Preprint Server For Health Sciences. PMID 38496498 DOI: 10.1101/2024.03.05.24303792 |
0.377 |
|
| 2023 |
Scheben A, Mendivil Ramos O, Kramer M, Goodwin S, Oppenheim S, Becker DJ, Schatz MC, Simmons NB, Siepel A, McCombie WR. Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats. Genome Biology and Evolution. 15. PMID 37728212 DOI: 10.1093/gbe/evad148 |
0.328 |
|
| 2023 |
Stevenson DW, Ramakrishnan S, Alves CS, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, ... ... McCombie WR, et al. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. Biorxiv : the Preprint Server For Biology. PMID 37662366 DOI: 10.1101/2023.08.24.554647 |
0.791 |
|
| 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 |
0.359 |
|
| 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 |
0.436 |
|
| 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 |
0.494 |
|
| 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 |
0.383 |
|
| 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 |
0.461 |
|
| 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 |
0.653 |
|
| 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 |
0.448 |
|
| 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 |
0.461 |
|
| 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 |
0.379 |
|
| 2018 |
McCombie WR, McPherson JD, Mardis ER. Next-Generation Sequencing Technologies. Cold Spring Harbor Perspectives in Medicine. PMID 30478097 DOI: 10.1101/Cshperspect.A036798 |
0.485 |
|
| 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 |
0.472 |
|
| 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 |
0.448 |
|
| 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 |
0.609 |
|
| 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 |
0.488 |
|
| 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 |
0.488 |
|
| 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 |
0.482 |
|
| 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 |
0.54 |
|
| 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 |
0.498 |
|
| 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 |
0.318 |
|
| 2016 |
Mardis E, McCombie WR. Agarose Gel Size Selection for DNA Sequencing Libraries. Cold Spring Harbor Protocols. PMID 27803281 DOI: 10.1101/Pdb.Prot094698 |
0.309 |
|
| 2016 |
Mardis E, McCombie WR. Whole-Genome Sequencing: Manual Library Preparation. Cold Spring Harbor Protocols. PMID 27803280 DOI: 10.1101/Pdb.Prot094615 |
0.463 |
|
| 2016 |
Mardis E, McCombie WR. Whole-Genome Sequencing: Automated, Nonindexed Library Preparation. Cold Spring Harbor Protocols. PMID 27803279 DOI: 10.1101/Pdb.Prot094623 |
0.378 |
|
| 2016 |
Mardis E, McCombie WR. Preparing Plasmid Subclones for Capillary Sequencing. Cold Spring Harbor Protocols. PMID 27803278 DOI: 10.1101/Pdb.Prot094581 |
0.301 |
|
| 2016 |
Mardis E, McCombie WR. Automated Library Preparation for DNA Sequencing. Cold Spring Harbor Protocols. PMID 27803276 DOI: 10.1101/Pdb.Prot094631 |
0.31 |
|
| 2016 |
Mardis E, McCombie WR. RNA-Seq: RNA Conversion to cDNA and Amplification. Cold Spring Harbor Protocols. PMID 27803275 DOI: 10.1101/Pdb.Prot094672 |
0.372 |
|
| 2016 |
Mardis E, McCombie WR. Solution-Phase Exome Capture. Cold Spring Harbor Protocols. PMID 27803274 DOI: 10.1101/Pdb.Prot094680 |
0.437 |
|
| 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 |
0.382 |
|
| 2016 |
Mardis E, McCombie WR. Cycle-Sequencing Reactions. Cold Spring Harbor Protocols. PMID 27803269 DOI: 10.1101/Pdb.Prot094607 |
0.422 |
|
| 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 |
0.486 |
|
| 2016 |
Goes FS, Pirooznia M, Parla JS, Kramer M, Ghiban E, Mavruk S, Chen YC, Monson ET, Willour VL, Karchin R, Flickinger M, Locke AE, Levy SE, Scott LJ, Boehnke M, ... ... McCombie WR, et al. Exome Sequencing of Familial Bipolar Disorder. Jama Psychiatry. PMID 27120077 DOI: 10.1001/Jamapsychiatry.2016.0251 |
0.301 |
|
| 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 |
0.443 |
|
| 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 |
0.49 |
|
| 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 |
0.445 |
|
| 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 |
0.742 |
|
| 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 |
0.395 |
|
| 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 |
0.499 |
|
| 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 |
0.334 |
|
| 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 |
0.364 |
|
| 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 |
0.365 |
|
| 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 |
0.584 |
|
| 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 |
0.564 |
|
| 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 |
0.386 |
|
| 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 |
0.348 |
|
| 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 |
0.492 |
|
| 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 |
0.778 |
|
| 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 |
0.367 |
|
| 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 |
0.302 |
|
| 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 |
0.327 |
|
| 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 |
0.504 |
|
| 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 |
0.428 |
|
| 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 |
0.345 |
|
| 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 |
0.563 |
|
| 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 |
0.433 |
|
| 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 |
0.481 |
|
| 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 |
0.325 |
|
| 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 |
0.543 |
|
| 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 |
0.775 |
|
| 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 |
0.384 |
|
| 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 |
0.459 |
|
| 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 |
0.33 |
|
| 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 |
0.388 |
|
| 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 |
0.354 |
|
| 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 |
0.396 |
|
| 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 |
0.504 |
|
| 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 |
0.393 |
|
| 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 |
0.499 |
|
| 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 |
0.553 |
|
| 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 |
0.564 |
|
| 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 |
0.4 |
|
| 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 |
0.465 |
|
| 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 |
0.38 |
|
| 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 |
0.41 |
|
| 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 |
0.478 |
|
| 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 |
0.415 |
|
| 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 |
0.533 |
|
| 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 |
0.458 |
|
| 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 |
0.776 |
|
| 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 |
0.534 |
|
| 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 |
0.412 |
|
| 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 |
0.459 |
|
| 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 |
0.786 |
|
| 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 |
0.416 |
|
| 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 |
0.52 |
|
| 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 |
0.375 |
|
| 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 |
0.479 |
|
| 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 |
0.463 |
|
| 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 |
0.524 |
|
| 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 |
0.391 |
|
| 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 |
0.518 |
|
| 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 |
0.554 |
|
| 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 |
0.445 |
|
| 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 |
0.776 |
|
| 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 |
0.388 |
|
| 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 |
0.33 |
|
| 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 |
0.551 |
|
| 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 |
0.532 |
|
| 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 |
0.532 |
|
| 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 |
0.44 |
|
| 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 |
0.419 |
|
| 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 |
0.423 |
|
| 2001 |
Martienssen R, McCombie WR. The first plant genome. Cell. 105: 571-4. PMID 11389827 DOI: 10.1016/S0092-8674(01)00382-8 |
0.311 |
|
| 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 |
0.73 |
|
| 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 |
0.467 |
|
| 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 |
0.472 |
|
| 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 |
0.416 |
|
| 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 |
0.319 |
|
| 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 |
0.465 |
|
| 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 |
0.508 |
|
| 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 |
0.435 |
|
| 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 |
0.35 |
|
| 1994 |
McCombie WR, Kieleczawa J. Automated DNA sequencing using 4-color fluorescent detection of reactions primed with hexamer strings. Biotechniques. 17: 574-9. PMID 7818912 |
0.307 |
|
| 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 |
0.352 |
|
| 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 |
0.378 |
|
| 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 |
0.363 |
|
| 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 |
0.39 |
|
| 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 |
0.325 |
|
| 1990 |
Venter JC, McCombie WR, McConnell JB. Genome Sequencing Conference I: Summary Genomics. 8: 186-188. DOI: 10.1016/0888-7543(90)90245-P |
0.491 |
|
| 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 |
0.353 |
|
| Show low-probability matches. |