Use
of Low-Coverage, Large-Insert, Short-Read Data for Rapid and Accurate
Generation of Enhanced-Quality Draft Pseudomonas Genome Sequences
Heath E. O'Brien, Yunchen Gong, Pauline Fung, Pauline W.
Wang, David S. Guttman
PLoS One. 2011; 6(11): e27199. Published online 2011 November 2. doi: 10.1371/journal.pone.0027199
PMCID: PMC3206934
Salmonella
Typhimurium-specific bacteriophage ΦSH19 and the origins of species
specificity in the Vi01-like phage family
Steven PT Hooton, Andrew R Timms, Joanna Rowsell, Ray
Wilson, Ian F Connerton
Virol J. 2011; 8: 498. Published online 2011 November 2. doi: 10.1186/1743-422X-8-498
PMCID: PMC3220722
An
Evaluation of Different Target Enrichment Methods in Pooled Sequencing Designs
for Complex Disease Association Studies
Aaron G. Day-Williams, Kirsten McLay, Eleanor Drury, Sarah
Edkins, Alison J. Coffey, Aarno Palotie, Eleftheria Zeggini
PLoS One. 2011; 6(11): e26279. Published online 2011 November 1. doi: 10.1371/journal.pone.0026279
PMCID: PMC3206031
Decontamination of MDA Reagents for
Single Cell Whole Genome Amplification
Tanja Woyke, Alexander Sczyrba, Janey Lee, Christian Rinke,
Damon Tighe, Scott Clingenpeel, Rex Malmstrom, Ramunas Stepanauskas, Jan-Fang
Cheng
PLoS One. 2011; 6(10): e26161. Published online 2011 October 20. doi: 10.1371/journal.pone.0026161
PMCID: PMC3197606
AGO6
Functions in RNA-Mediated Transcriptional Gene Silencing in Shoot and Root
Meristems in Arabidopsis thaliana
Changho Eun, Zdravko J. Lorkovic, Ulf Naumann, Quan Long,
Ericka R. Havecker, Stacey A. Simon, Blake C. Meyers, Antonius J. M. Matzke,
Marjori Matzke
PLoS One. 2011; 6(10): e25730. Published online 2011 October 5. doi: 10.1371/journal.pone.0025730
PMCID: PMC3187791
ESRRA-C11orf20
Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma
Julia Salzman, Robert J. Marinelli, Peter L. Wang, Ann E.
Green, Julie S. Nielsen, Brad H. Nelson, Charles W. Drescher, Patrick O. Brown
PLoS Biol. 2011 September; 9(9): e1001156. Published online 2011 September
20. doi: 10.1371/journal.pbio.1001156
PMCID: PMC3176749
Accurate
and comprehensive sequencing of personal genomes
Subramanian S. Ajay, Stephen C.J. Parker, Hatice Ozel Abaan,
Karin V. Fuentes Fajardo, Elliott H. Margulies
Genome Res. 2011 September; 21(9): 1498-1505. doi: 10.1101/gr.123638.111
PMCID: PMC3166834
Targeted
isolation of cloned genomic regions by recombineering for haplotype phasing and
isogenic targeting
Marta Nedelkova, Marcello Maresca, Jun Fu, Maria
Rostovskaya, Ramu Chenna, Christian Thiede, Konstantinos Anastassiadis, Mihail
Sarov, A. Francis Stewart
Nucleic Acids Res. 2011 November; 39(20): e137. Published online 2011 August
18. doi: 10.1093/nar/gkr668
PMCID: PMC3203589
Identification
of RNF213 as a Susceptibility Gene for Moyamoya Disease and Its Possible Role
in Vascular Development
Wanyang Liu, Daisuke Morito, Seiji Takashima, Yohei
Mineharu, Hatasu Kobayashi, Toshiaki Hitomi, Hirokuni Hashikata, Norio
Matsuura, Satoru Yamazaki, Atsushi Toyoda, Ken-ichiro Kikuta, Yasushi Takagi,
Kouji H. Harada, Asao Fujiyama, Roman Herzig, Boris Krischek, Liping Zou, Jeong
Eun Kim, Masafumi Kitakaze, Susumu Miyamoto, Kazuhiro Nagata, Nobuo Hashimoto,
Akio Koizumi
PLoS One. 2011; 6(7): e22542. Published online 2011 July 20. doi: 10.1371/journal.pone.0022542
PMCID: PMC3140517
High
Resolution Detection and Analysis of CpG Dinucleotides Methylation Using
MBD-Seq Technology
Xun Lan, Christopher Adams, Mark Landers, Miroslav Dudas,
Daniel Krissinger, George Marnellos, Russell Bonneville, Maoxiong Xu, Junbai
Wang, Tim H.-M. Huang, Gavin Meredith, Victor X. Jin
PLoS One. 2011; 6(7): e22226. Published online 2011 July 11. doi: 10.1371/journal.pone.0022226
PMCID: PMC3136941
Comprehensive
Genomic Analysis of a BRCA2 Deficient Human Pancreatic Cancer
Louise J. Barber, Juan M. Rosa Rosa, Iwanka Kozarewa, Kerry
Fenwick, Ioannis Assiotis, Costas Mitsopoulos, David Sims, Jarle Hakas, Marketa
Zvelebil, Christopher J. Lord, Alan Ashworth
PLoS One. 2011; 6(7): e21639. Published online 2011 July 5. doi: 10.1371/journal.pone.0021639
PMCID: PMC3130048
RET
Germline Mutations Identified by Exome Sequencing in a Chinese Multiple
Endocrine Neoplasia Type 2A/Familial Medullary Thyroid Carcinoma Family
Xiao-Ping Qi, Ju-Ming Ma, Zhen-Fang Du, Rong-Biao Ying, Jun
Fei, Hang-Yang Jin, Jian-Shan Han, Jin-Quan Wang, Xiao-Ling Chen, Chun-Yue
Chen, Wen-Ting Liu, Jia-Jun Lu, Jian-Guo Zhang, Xian-Ning Zhang
PLoS One. 2011; 6(5): e20353. Published online 2011 May 31. doi: 10.1371/journal.pone.0020353
PMCID: PMC3105051
Identification
of factors required for meristem function in Arabidopsis using a novel next
generation sequencing fast forward genetics approach
Michal Mokry, Isaäc J Nijman, Anja van Dijken, Rene
Benjamins, Renze Heidstra, Ben Scheres, Edwin Cuppen
BMC Genomics. 2011; 12: 256. Published online 2011 May 20. doi: 10.1186/1471-2164-12-256
PMCID: PMC3114748
Sequence-specific
error profile of Illumina sequencers
Kensuke Nakamura, Taku Oshima, Takuya Morimoto, Shun Ikeda,
Hirofumi Yoshikawa, Yuh Shiwa, Shu Ishikawa, Margaret C. Linak, Aki Hirai,
Hiroki Takahashi, Md. Altaf-Ul-Amin, Naotake Ogasawara, Shigehiko Kanaya
Nucleic Acids Res. 2011 July; 39(13): e90. Published online 2011 May
14. doi: 10.1093/nar/gkr344
PMCID: PMC3141275
Exome
Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in
Infantile Mitochondrial Cardiomyopathy
Alexandra Götz, Henna Tyynismaa, Liliya Euro, Pekka
Ellonen, Tuulia Hyötyläinen, Tiina Ojala, Riikka H. Hämäläinen,
Johanna Tommiska, Taneli Raivio, Matej Oresic, Riitta Karikoski, Outi Tammela,
Kalle O.J. Simola, Anders Paetau, Tiina Tyni, Anu Suomalainen
Am J Hum Genet. 2011 May 13; 88(5): 635-642.
doi: 10.1016/j.ajhg.2011.04.006
PMCID: PMC3146718
Mitochondrial
DNA polymerase editing mutation, PolgD257A, reduces the diabetic phenotype of
Akita male mice by suppressing appetite
Raymond Fox, Hyung-Suk Kim, Robert L. Reddick, Gregory C.
Kujoth, Tomas A. Prolla, Shuichi Tsutsumi, Youichiro Wada, Oliver Smithies,
Nobuyo Maeda
Proc Natl Acad Sci U S A. 2011 May 24; 108(21):
8779-8784. Published online
2011 May 9.
doi: 10.1073/pnas.1106344108
PMCID: PMC3102415
Exhaustive
T-cell repertoire sequencing of human peripheral blood samples reveals
signatures of antigen selection and a directly measured repertoire size of at
least 1 million clonotypes
René L. Warren, J. Douglas Freeman, Thomas Zeng, Gina Choe,
Sarah Munro, Richard Moore, John R. Webb, Robert A. Holt
Genome Res. 2011 May; 21(5): 790-797. doi: 10.1101/gr.115428.110
PMCID: PMC3083096
Neurons
show distinctive DNA methylation profile and higher interindividual variations
compared with non-neurons
Kazuya Iwamoto, Miki Bundo, Junko Ueda, Michael C. Oldham,
Wataru Ukai, Eri Hashimoto, Toshikazu Saito, Daniel H. Geschwind, Tadafumi Kato
Genome Res. 2011 May; 21(5): 688-696. doi: 10.1101/gr.112755.110
PMCID: PMC3083085
Comparison
of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform
Dale J. Hedges, Toumy Guettouche, Shan Yang, Guney Bademci,
Ashley Diaz, Ashley Andersen, William F. Hulme, Sara Linker, Arpit Mehta,
Yvonne J. K. Edwards, Gary W. Beecham, Eden R. Martin, Margaret A.
Pericak-Vance, Stephan Zuchner, Jeffery M. Vance, John R. Gilbert
PLoS One. 2011; 6(4): e18595. Published online 2011 April 29. doi: 10.1371/journal.pone.0018595
PMCID: PMC3084696
Large
Scale Library Generation for High Throughput Sequencing
Erik Borgström, Sverker Lundin, Joakim Lundeberg
PLoS One. 2011; 6(4): e19119. Published online 2011 April 27. doi: 10.1371/journal.pone.0019119
PMCID: PMC3083417
Loss-of-Function
Mutations in PTPN11 Cause Metachondromatosis, but Not Ollier Disease or
Maffucci Syndrome
Margot E. Bowen, Eric D. Boyden, Ingrid A. Holm, Belinda
Campos-Xavier, Luisa Bonafé, Andrea Superti-Furga, Shiro Ikegawa, Valerie
Cormier-Daire, Judith V. Bovée, Twinkal C. Pansuriya, Sérgio B. de Sousa,
Ravi Savarirayan, Elena Andreucci, Miikka Vikkula, Livia Garavelli, Caroline
Pottinger, Toshihiko Ogino, Akinori Sakai, Bianca M. Regazzoni, Wim Wuyts, Luca
Sangiorgi, Elena Pedrini, Mei Zhu, Harry P. Kozakewich, James R. Kasser, Jon G.
Seidman, Kyle C. Kurek, Matthew L. Warman
PLoS Genet. 2011 April; 7(4): e1002050. Published online 2011 April
14.
doi: 10.1371/journal.pgen.1002050
PMCID: PMC3077396
Accurate
and exact CNV identification from targeted high-throughput sequence data
Alex S Nord, Ming Lee, Mary-Claire King, Tom Walsh
BMC Genomics. 2011; 12: 184. Published online 2011 April 12. doi: 10.1186/1471-2164-12-184
PMCID: PMC3088570
Genetic
correction and analysis of induced pluripotent stem cells from a patient with
gyrate atrophy
Sara E. Howden, Athurva Gore, Zhe Li, Ho-Lim Fung, Benjamin
S. Nisler, Jeff Nie, Goukai Chen, Brian E. McIntosh, Daniel R. Gulbranson,
Nicole R. Diol, Seth M. Taapken, David T. Vereide, Karen Dyer Montgomery, Kun
Zhang, David M. Gamm, James A. Thomson
Proc Natl Acad Sci U S A. 2011 April 19; 108(16):
6537-6542. Published online
2011 April 4.
doi: 10.1073/pnas.1103388108
PMCID: PMC3080993
Efficient
and Cost Effective Population Resequencing by Pooling and In-Solution
Hybridization
Vikas Bansal, Ryan Tewhey, Emily M. LeProust, Nicholas J.
Schork
PLoS One. 2011; 6(3): e18353. Published online 2011 March 30. doi: 10.1371/journal.pone.0018353
PMCID: PMC3068187
Universal
noninvasive detection of solid organ transplant rejection
Thomas M. Snyder, Kiran K. Khush, Hannah A. Valantine,
Stephen R. Quake
Proc Natl Acad Sci U S A. 2011 April 12; 108(15):
6229-6234. Published online
2011 March 28.
doi: 10.1073/pnas.1013924108
PMCID: PMC3076856
Evolution
combined with genomic study elucidates genetic bases of isobutanol tolerance in
Escherichia coli
Jeremy J Minty, Ann A Lesnefsky, Fengming Lin, Yu Chen, Ted
A Zaroff, Artur B Veloso, Bin Xie, Catie A McConnell, Rebecca J Ward, Donald R
Schwartz, Jean-Marie Rouillard, Yuan Gao, Erdogan Gulari, Xiaoxia Nina Lin
Microb Cell Fact. 2011; 10: 18. Published online 2011 March 25. doi: 10.1186/1475-2859-10-18
PMCID: PMC3071312
An
Effective Personalized Approach to a Rare Tumor: Prolonged Survival in
Metastatic Pancreatic Acinar Cell Carcinoma Based on Genetic Analysis and Cell
Line Development
Matthew D. Armstrong, Daniel Von Hoff, Bruce Barber, Laura
A. Marlow, Christina von Roemeling, Simon J. Cooper, Patrick Travis, Elizabeth
Campbell, Ricardo Paz-Fumagalli, John A. Copland, Gerardo Colon-Otero
J Cancer. 2011; 2: 142-152. Published online 2011 March 8.
PMCID: PMC3053537
The
GENCODE exome: sequencing the complete human exome
Alison J Coffey, Felix Kokocinski, Maria S Calafato, Carol E
Scott, Priit Palta, Eleanor Drury, Christopher J Joyce, Emily M LeProust, Jen
Harrow, Sarah Hunt, Anna-Elina Lehesjoki, Daniel J Turner, Tim J Hubbard, Aarno
Palotie
Eur J Hum Genet. 2011 July; 19(7): 827-831. Published online 2011 March
2. doi: 10.1038/ejhg.2011.28
PMCID: PMC3137498
Integrated
Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in
Breast Cancer Cells by Deep Sequencing
Zhifu Sun, Yan W. Asmann, Krishna R. Kalari, Brian Bot,
Jeanette E. Eckel-Passow, Tiffany R. Baker, Jennifer M. Carr, Irina
Khrebtukova, Shujun Luo, Lu Zhang, Gary P. Schroth, Edith A. Perez, E. Aubrey
Thompson
PLoS One. 2011; 6(2): e17490. Published online 2011 February 25. doi: 10.1371/journal.pone.0017490
PMCID: PMC3045451
Analyzing
and minimizing PCR amplification bias in Illumina sequencing libraries
Daniel Aird, Michael G Ross, Wei-Sheng Chen, Maxwell
Danielsson, Timothy Fennell, Carsten Russ, David B Jaffe, Chad Nusbaum, Andreas
Gnirke
Genome Biol. 2011; 12(2): R18. Published online 2011 February 21. doi: 10.1186/gb-2011-12-2-r18
PMCID: PMC3188800
Whole-genome
resequencing shows numerous genes with nonsynonymous SNPs in the Japanese
native cattle Kuchinoshima-Ushi
Ryouka Kawahara-Miki, Kaoru Tsuda, Yuh Shiwa, Yuko
Arai-Kichise, Takashi Matsumoto, Yu Kanesaki, Sen-ichi Oda, Shizufumi Ebihara,
Shunsuke Yajima, Hirofumi Yoshikawa, Tomohiro Kono
BMC Genomics. 2011; 12: 103. Published online 2011 February 10. doi: 10.1186/1471-2164-12-103
PMCID: PMC3048544
Performance
of Microarray and Liquid Based Capture Methods for Target Enrichment for
Massively Parallel Sequencing and SNP Discovery
Anna Kiialainen, Olof Karlberg, Annika Ahlford, Snaevar
Sigurdsson, Kerstin Lindblad-Toh, Ann-Christine Syvänen
PLoS One. 2011; 6(2): e16486. Published online 2011 February 9. doi: 10.1371/journal.pone.0016486
PMCID: PMC3036585
Hotspots
of aberrant epigenomic reprogramming in human induced pluripotent stem cells
Ryan Lister, Mattia Pelizzola, Yasuyuki S. Kida, R. David
Hawkins, Joseph R. Nery, Gary Hon, Jessica Antosiewicz-Bourget, Ronan O'Malley,
Rosa Castanon, Sarit Klugman, Michael Downes, Ruth Yu, Ron Stewart, Bing Ren,
James A. Thomson, Ronald M. Evans, Joseph R. Ecker
Nature. Author
manuscript; available in PMC 2011 September 3. Published in final edited form
as: Nature. 2011 March 3; 471 (7336) : 68-73.
Published online 2011 February 2.
doi: 10.1038/nature09798
PMCID: PMC3100360
Retrospective
Application of Transposon-Directed Insertion Site Sequencing to a Library of
Signature-Tagged Mini-Tn5Km2 Mutants of Escherichia coli O157:H7 Screened in
Cattle
Sabine E. Eckert, Francis Dziva, Roy R. Chaudhuri, Gemma C.
Langridge, Daniel J. Turner, Derek J. Pickard, Duncan J. Maskell, Nicholas R.
Thomson, Mark P. Stevens
J Bacteriol. 2011 April; 193(7): 1771-1776. Published online 2011 January
28. doi: 10.1128/JB.01292-10
PMCID: PMC3067669
Aberrant
Promoter CpG Methylation Is a Mechanism for Impaired PHD3 Expression in a
Diverse Set of Malignant Cells
Trenton L. Place, Matthew P. Fitzgerald, Sujatha
Venkataraman, Sabine U. Vorrink, Adam J. Case, Melissa L. T. Teoh, Frederick E.
Domann
PLoS One. 2011; 6(1): e14617. Published online 2011 January 28. doi: 10.1371/journal.pone.0014617
PMCID: PMC3030558
Annotation-based
genome-wide SNP discovery in the large and complex Aegilops tauschii genome
using next-generation sequencing without a reference genome sequence
Frank M You, Naxin Huo, Karin R Deal, Yong Q Gu, Ming-Cheng
Luo, Patrick E McGuire, Jan Dvorak, Olin D Anderson
BMC Genomics. 2011; 12: 59. Published online 2011 January 25. doi: 10.1186/1471-2164-12-59
PMCID: PMC3041743
Experimental
selection of hypoxia-tolerant Drosophila melanogaster
Dan Zhou, Nitin Udpa, Merril Gersten, DeeAnn W. Visk, Ali
Bashir, Jin Xue, Kelly A. Frazer, James W. Posakony, Shankar Subramaniam,
Vineet Bafna, Gabriel G. Haddad
Proc Natl Acad Sci U S A. 2011 February 8; 108(6):
2349-2354. Published online
2011 January 24.
doi: 10.1073/pnas.1010643108
PMCID: PMC3038716
Genome-Scale
Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn-seq
Larry A. Gallagher, Jay Shendure, Colin Manoil
mBio. 2011 Jan-Feb; 2(1): e00315-10. Published online 2011 January
18. doi: 10.1128/mBio.00315-10
PMCID: PMC3023915
The
host genomic environment of the provirus determines the abundance of
HTLV-1-infected T-cell clones
Nicolas A. Gillet, Nirav Malani, Anat Melamed, Niall
Gormley, Richard Carter, David Bentley, Charles Berry, Frederic D. Bushman,
Graham P. Taylor, Charles R. M. Bangham
Blood. 2011 March 17; 117(11): 3113-3122. Prepublished online 2011 January
12.
doi: 10.1182/blood-2010-10-312926
PMCID: PMC3062313
A
scalable, fully automated process for construction of sequence-ready human
exome targeted capture libraries
Sheila Fisher, Andrew Barry, Justin Abreu, Brian Minie,
Jillian Nolan, Toni M Delorey, Geneva Young, Timothy J Fennell, Alexander
Allen, Lauren Ambrogio, Aaron M Berlin, Brendan Blumenstiel, Kristian
Cibulskis, Dennis Friedrich, Ryan Johnson, Frank Juhn, Brian Reilly, Ramy
Shammas, John Stalker, Sean M Sykes, Jon Thompson, John Walsh, Andrew Zimmer,
Zac Zwirko, Stacey Gabriel, Robert Nicol, Chad Nusbaum
Genome Biol. 2011; 12(1): R1. Published online 2011 January 4. doi: 10.1186/gb-2011-12-1-r1
PMCID: PMC3091298
Multiplex
Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection
Elaine M. Kenny, Paul Cormican, William P. Gilks, Amy S.
Gates, Colm T. O'Dushlaine, Carlos Pinto, Aiden P. Corvin, Michael Gill, Derek
W. Morris
DNA Res. 2011 February; 18(1): 31-38. Published online 2010 December
16.
doi: 10.1093/dnares/dsq029
PMCID: PMC3041504
Sequence
Analysis of the Genome of an Oil-Bearing Tree, Jatropha curcas L.
Shusei Sato, Hideki Hirakawa, Sachiko Isobe, Eigo Fukai,
Akiko Watanabe, Midori Kato, Kumiko Kawashima, Chiharu Minami, Akiko Muraki,
Naomi Nakazaki, Chika Takahashi, Shinobu Nakayama, Yoshie Kishida, Mitsuyo
Kohara, Manabu Yamada, Hisano Tsuruoka, Shigemi Sasamoto, Satoshi Tabata,
Tomoyuki Aizu, Atsushi Toyoda, Tadasu Shin-i, Yohei Minakuchi, Yuji Kohara,
Asao Fujiyama, Suguru Tsuchimoto, Shin'ichiro Kajiyama, Eri Makigano, Nobuko
Ohmido, Nakako Shibagaki, Joyce A. Cartagena, Naoki Wada, Tsutomu Kohinata,
Alipour Atefeh, Shota Yuasa, Sachihiro Matsunaga, Kiichi Fukui
DNA Res. 2011 February; 18(1): 65-76. Published online 2010 December
13.
doi: 10.1093/dnares/dsq030
PMCID: PMC3041505
Combining
target enrichment with barcode multiplexing for high throughput SNP discovery
Nik Cummings, Rob King, Andre Rickers, Antony Kaspi,
Sebastian Lunke, Izhak Haviv, Jeremy BM Jowett
BMC Genomics. 2010; 11: 641. Published online 2010 November 18. doi: 10.1186/1471-2164-11-641
PMCID: PMC3012606
Whole
Genome Sequencing Highlights Genetic Changes Associated with Laboratory
Domestication of C. elegans
Katherine P. Weber, Subhajyoti De, Iwanka Kozarewa, Daniel
J. Turner, M. Madan Babu, Mario de Bono
PLoS One. 2010; 5(11): e13922. Published online 2010 November 11. doi: 10.1371/journal.pone.0013922
PMCID: PMC2978686
Targeted
resequencing of candidate genes using selector probes
H. Johansson, M. Isaksson, E. Falk Sörqvist, F. Roos, J.
Stenberg, T. Sjöblom, J. Botling, P. Micke, K. Edlund, S. Fredriksson, H.
Göransson Kultima, Olle Ericsson, Mats Nilsson
Nucleic Acids Res. 2011 January; 39(2): e8. Published online 2010 November
8. doi: 10.1093/nar/gkq1005
PMCID: PMC3025563
The
Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and
Workers
Frank Lyko, Sylvain Foret, Robert Kucharski, Stephan Wolf,
Cassandra Falckenhayn, Ryszard Maleszka
PLoS Biol. 2010 November; 8(11): e1000506. Published online 2010 November
2.
doi: 10.1371/journal.pbio.1000506 Correction in:
Correction in:
PLoS Biol. 2011
January; 9 (1) :
10.1371/annotation/2db9ee19-faa4-43f2-af7a-c8aeacca8037.
PMCID: PMC2970541
Genomic
analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses
from diverse hosts and environments
Matthew B Sullivan, Katherine H Huang, Julio C
Ignacio-Espinoza, Aaron M Berlin, Libusha Kelly, Peter R Weigele, Alicia S
DeFrancesco, Suzanne E Kern, Luke R Thompson, Sarah Young, Chandri Yandava,
Ross Fu, Bryan Krastins, Michael Chase, David Sarracino, Marcia S Osburne,
Matthew R Henn, Sallie W Chisholm
Environ Microbiol. 2010 November; 12(11): 3035-3056.
doi: 10.1111/j.1462-2920.2010.02280.x
PMCID: PMC3037559
Evaluation
of Second-Generation Sequencing of 19 Dilated Cardiomyopathy Genes for Clinical
Applications
Sivakumar Gowrisankar, Jordan P. Lerner-Ellis, Stephanie
Cox, Emily T. White, Megan Manion, Kevin LeVan, Jonathan Liu, Lisa M. Farwell,
Oleg Iartchouk, Heidi L. Rehm, Birgit H. Funke
J Mol Diagn. 2010 November; 12(6): 818-827.
doi: 10.2353/jmoldx.2010.100014
PMCID: PMC2963910
Massively
parallel sequencing for monitoring genetic consistency and quality control of
live viral vaccines
Alexander Neverov, Konstantin Chumakov
Proc Natl Acad Sci U S A. 2010 November 16; 107(46):
20063-20068. Published
online 2010 November 1.
doi: 10.1073/pnas.1012537107
PMCID: PMC2993378
Molecular
Diagnosis of Neonatal Diabetes Mellitus Using Next-Generation Sequencing of the
Whole Exome
Amélie Bonnefond, Emmanuelle Durand, Olivier Sand, Franck
De Graeve, Sophie Gallina, Kanetee Busiah, Stéphane Lobbens, Albane Simon,
Christine Bellanné-Chantelot, Louis Létourneau, Raphael Scharfmann, Jérôme
Delplanque, Robert Sladek, Michel Polak, Martine Vaxillaire, Philippe Froguel
PLoS One. 2010; 5(10): e13630. Published online 2010 October 26. doi: 10.1371/journal.pone.0013630
PMCID: PMC2964316
Whole-exome
sequencing-based discovery of STIM1 deficiency in a child with fatal classic
Kaposi sarcoma
Minji Byun, Avinash Abhyankar, Virginie Lelarge, Sabine
Plancoulaine, Ayse Palanduz, Leyla Telhan, Bertrand Boisson, Capucine Picard,
Scott Dewell, Connie Zhao, Emmanuelle Jouanguy, Stefan Feske, Laurent Abel,
Jean-Laurent Casanova
J Exp Med. 2010 October 25; 207(11): 2307-2312. doi: 10.1084/jem.20101597
PMCID: PMC2964585
Somatic
structural rearrangements in genetically engineered mouse mammary tumors
Ignacio Varela, Christiaan Klijn, Phillip J Stephens, Laura
J Mudie, Lucy Stebbings, Danushka Galappaththige, Hanneke van der Gulden, Eva
Schut, Sjoerd Klarenbeek, Peter J Campbell, Lodewyk FA Wessels, Michael R
Stratton, Jos Jonkers, P Andrew Futreal, David J Adams
Genome Biol. 2010; 11(10): R100. Published online 2010 October 13. doi: 10.1186/gb-2010-11-10-r100
PMCID: PMC3218656
Mutations
in WDR62, encoding a centrosome-associated protein, cause microcephaly with
simplified gyri and abnormal cortical architecture
Timothy W. Yu, Ganeshwaran H. Mochida, David J. Tischfield,
Sema K. Sgaier, Laura Flores-Sarnat, Consolato M. Sergi, Meral Topçu, Marie T.
McDonald, Brenda J. Barry, Jillian Felie, Christine Sunu, William B. Dobyns,
Rebecca D. Folkerth, A. James Barkovich, Christopher A. Walsh
Nat Genet.
Author manuscript; available in PMC 2011 May 1. Published in final
edited form as: Nat
Genet. 2010 November; 42 (11) : 1015-1020. Published online 2010 October 3. doi: 10.1038/ng.683
PMCID: PMC2969850
Single
Molecule Sequencing with a HeliScope Genetic Analysis System
John F. Thompson, Kathleen E. Steinmann
Curr Protoc Mol Biol.
Author manuscript; available in PMC 2011 October 1. Published in final
edited form as: Curr Protoc
Mol Biol. 2010 October; CHAPTER : Unit7.10.
doi: 10.1002/0471142727.mb0710s92
PMCID: PMC2954431
Systematic
comparison of three genomic enrichment methods for massively parallel DNA
sequencing
Jamie K. Teer, Lori L. Bonnycastle, Peter S. Chines, Nancy
F. Hansen, Natsuyo Aoyama, Amy J. Swift, Hatice Ozel Abaan, Thomas J. Albert,
NISC Comparative Sequencing Program, Elliott H. Margulies, Eric D. Green,
Francis S. Collins, James C. Mullikin, Leslie G. Biesecker
Genome Res. 2010 October; 20(10): 1420-1431. doi: 10.1101/gr.106716.110
PMCID: PMC2945191
Comparison
of sequencing-based methods to profile DNA methylation and identification of
monoallelic epigenetic modifications
R. Alan Harris, Ting Wang, Cristian Coarfa, Raman P.
Nagarajan, Chibo Hong, Sara L. Downey, Brett E. Johnson, Shaun D. Fouse, Allen
Delaney, Yongjun Zhao, Adam Olshen, Tracy Ballinger, Xin Zhou, Kevin J.
Forsberg, Junchen Gu, Lorigail Echipare, Henriette O€™Geen, Ryan Lister, Mattia
Pelizzola, Yuanxin Xi, Charles B. Epstein, Bradley E. Bernstein, R. David
Hawkins, Bing Ren, Wen-Yu Chung, Hongcang Gu, Christoph Bock, Andreas Gnirke,
Michael Q. Zhang, David Haussler, Joseph Ecker, Wei Li, Peggy J. Farnham,
Robert A. Waterland, Alexander Meissner, Marco A. Marra, Martin Hirst,
Aleksandar Milosavljevic, Joseph F. Costello
Nat Biotechnol.
Author manuscript; available in PMC 2011 April 1. Published in final
edited form as: Nat
Biotechnol. 2010 October; 28 (10) : 1097-1105. Published online 2010 September
19. doi: 10.1038/nbt.1682
PMCID: PMC2955169
The
Baker's Yeast Diploid Genome Is Remarkably Stable in Vegetative Growth and
Meiosis
K. T. Nishant, Wu Wei, Eugenio Mancera, Juan Lucas Argueso,
Andreas Schlattl, Nicolas Delhomme, Xin Ma, Carlos D. Bustamante, Jan O.
Korbel, Zhenglong Gu, Lars M. Steinmetz, Eric Alani
PLoS Genet. 2010 September; 6(9): e1001109. Published online 2010 September
9.
doi: 10.1371/journal.pgen.1001109
PMCID: PMC2936533
Multi-Platform
Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome
Assembly and Analysis
Rami A. Dalloul, Julie A. Long, Aleksey V. Zimin, Luqman
Aslam, Kathryn Beal, Le Ann Blomberg, Pascal Bouffard, David W. Burt, Oswald
Crasta, Richard P. M. A. Crooijmans, Kristal Cooper, Roger A. Coulombe, Supriyo
De, Mary E. Delany, Jerry B. Dodgson, Jennifer J. Dong, Clive Evans, Karin M.
Frederickson, Paul Flicek, Liliana Florea, Otto Folkerts, Martien A. M.
Groenen, Tim T. Harkins, Javier Herrero, Steve Hoffmann, Hendrik-Jan Megens,
Andrew Jiang, Pieter de Jong, Pete Kaiser, Heebal Kim, Kyu-Won Kim, Sungwon
Kim, David Langenberger, Mi-Kyung Lee, Taeheon Lee, Shrinivasrao Mane,
Guillaume Marcais, Manja Marz, Audrey P. McElroy, Thero Modise, Mikhail
Nefedov, Cédric Notredame, Ian R. Paton, William S. Payne, Geo Pertea, Dennis
Prickett, Daniela Puiu, Dan Qioa, Emanuele Raineri, Magali Ruffier, Steven L.
Salzberg, Michael C. Schatz, Chantel Scheuring, Carl J. Schmidt, Steven
Schroeder, Stephen M. J. Searle, Edward J. Smith, Jacqueline Smith, Tad S.
Sonstegard, Peter F. Stadler, Hakim Tafer, Zhijian (Jake) Tu, Curtis P. Van
Tassell, Albert J. Vilella, Kelly P. Williams, James A. Yorke, Liqing Zhang,
Hong-Bin Zhang, Xiaojun Zhang, Yang Zhang, Kent M. Reed
PLoS Biol. 2010 September; 8(9): e1000475. Published online 2010 September
7. doi: 10.1371/journal.pbio.1000475
PMCID: PMC2935454
Bacterial
charity work leads to population-wide resistance
Henry H. Lee, Michael N. Molla, Charles R. Cantor, James J.
Collins
Nature. Author manuscript;
available in PMC 2011 March 1. Published in final edited form as: Nature. 2010 September 2;
467 (7311) : 82-85.
doi: 10.1038/nature09354
PMCID: PMC2936489
Next
Generation Sequencing for Clinical Diagnostics-Principles and Application to
Targeted Resequencing for Hypertrophic Cardiomyopathy: A Paper from the 2009
William Beaumont Hospital Symposium on Molecular Pathology
Karl V. Voelkerding, Shale Dames, Jacob D. Durtschi
J Mol Diagn. 2010 September; 12(5): 539-551.
doi: 10.2353/jmoldx.2010.100043
PMCID: PMC2928417
A
mixed community of actinomycetes produce multiple antibiotics for the fungus
farming ant Acromyrmex octospinosus
Jörg Barke, Ryan F Seipke, Sabine Grüschow, Darren
Heavens, Nizar Drou, Mervyn J Bibb, Rebecca JM Goss, Douglas W Yu, Matthew I
Hutchings
BMC Biol. 2010; 8: 109. Published online 2010 August 26. doi: 10.1186/1741-7007-8-109
PMCID: PMC2942817
Mitochondrial
DNA Variant Discovery and Evaluation in Human Cardiomyopathies through
Next-Generation Sequencing
Michael V. Zaragoza, Joseph Fass, Marta Diegoli, Dawei Lin,
Eloisa Arbustini
PLoS One. 2010; 5(8): e12295. Published online 2010 August 20. doi: 10.1371/journal.pone.0012295
PMCID: PMC2924892
Targeted
Enrichment of Specific Regions in the Human Genome by Array Hybridization
Catherine Igartua, Emily H. Turner, Sarah B. Ng, Emily
Hodges, Gregory J. Hannon, Arindam Bhattacharjee, Mark J. Rieder, Deborah A.
Nickerson, Jay Shendure
Curr Protoc Hum Genet.
Author manuscript; available in PMC 2011 July 1. Published in final
edited form as: Curr Protoc
Hum Genet. 2010 July; CHAPTER : Unit-18.3.
doi: 10.1002/0471142905.hg1803s66
PMCID: PMC2910258
Combining
Next-Generation Sequencing Strategies for Rapid Molecular Resource Development
from an Invasive Aphid Species, Aphis glycines
Xiaodong Bai, Wei Zhang, Lucia Orantes, Tae-Hwan Jun,
Omprakash Mittapalli, M. A. Rouf Mian, Andrew P. Michel
PLoS One. 2010; 5(6): e11370. Published online 2010 June 29. doi: 10.1371/journal.pone.0011370
PMCID: PMC2894077
Semi-Automated
Library Preparation for High-Throughput DNA Sequencing Platforms
Eveline Farias-Hesson, Jonathan Erikson, Alexander Atkins,
Peidong Shen, Ronald W. Davis, Curt Scharfe, Nader Pourmand
J Biomed Biotechnol. 2010; 2010: 617469. Published online 2010 June 8. doi: 10.1155/2010/617469
PMCID: PMC2896710
Using
next-generation sequencing for high resolution multiplex analysis of copy
number variation from nanogram quantities of DNA from formalin-fixed
paraffin-embedded specimens
Henry M. Wood, Ornella Belvedere, Caroline Conway, Catherine
Daly, Rebecca Chalkley, Melissa Bickerdike, Claire McKinley, Phil Egan, Lisa
Ross, Bruce Hayward, Joanne Morgan, Leslie Davidson, Ken MacLennan, Thian K.
Ong, Kostas Papagiannopoulos, Ian Cook, David J. Adams, Graham R. Taylor,
Pamela Rabbitts
Nucleic Acids Res. 2010 August; 38(14): e151. Published online 2010 June
4. doi: 10.1093/nar/gkq510
PMCID: PMC2919738
GC-Biased
Evolution Near Human Accelerated Regions
Sol Katzman, Andrew D. Kern, Katherine S. Pollard, Sofie R.
Salama, David Haussler
PLoS Genet. 2010 May; 6(5): e1000960. Published online 2010 May 20. doi: 10.1371/journal.pgen.1000960
PMCID: PMC2873926
Massively
Parallel Sequencing of Exons on the X Chromosome Identifies RBM10 as the Gene
that Causes a Syndromic Form of Cleft Palate
Jennifer J. Johnston, Jamie K. Teer, Praveen F. Cherukuri,
Nancy F. Hansen, Stacie K. Loftus, NIH Intramural Sequencing Center, Karen
Chong, James C. Mullikin, Leslie G. Biesecker
Am J Hum Genet. 2010 May 14; 86(5): 743-748. doi: 10.1016/j.ajhg.2010.04.007
PMCID: PMC2868995
Direct
detection of DNA methylation during single-molecule, real-time sequencing
Benjamin A. Flusberg, Dale Webster, Jessa Lee, Kevin
Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach, Stephen W. Turner
Nat Methods.
Author manuscript; available in PMC 2010 December 1. Published in final
edited form as: Nat
Methods. 2010 June; 7 (6) : 461-465. Published online 2010 May 9. doi: 10.1038/nmeth.1459
PMCID: PMC2879396
Hi-C:
A Method to Study the Three-dimensional Architecture of Genomes.
Nynke L. van Berkum, Erez Lieberman-Aiden, Louise Williams,
Maxim Imakaev, Andreas Gnirke, Leonid A. Mirny, Job Dekker, Eric S. Lander
J Vis Exp. 2010; (39): 1869. Published online 2010 May 6. doi: 10.3791/1869
PMCID: PMC3149993
The
Tandem Inversion Duplication in Salmonella enterica: Selection Drives Unstable
Precursors to Final Mutation Types
Elisabeth Kugelberg, Eric Kofoid, Dan I. Andersson, Yong Lu,
Joseph Mellor, Frederick P. Roth, John R. Roth
Genetics. 2010 May; 185(1): 65-80. doi: 10.1534/genetics.110.114074
PMCID: PMC2870977
Increased
Throughput by Parallelization of Library Preparation for Massive Sequencing
Sverker Lundin, Henrik Stranneheim, Erik Pettersson, Daniel
Klevebring, Joakim Lundeberg
PLoS One. 2010; 5(4): e10029. Published online 2010 April 6. doi: 10.1371/journal.pone.0010029
PMCID: PMC2850305
Whole
Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding
Christina A. Bormann Chung, Victoria L. Boyd, Kevin J.
McKernan, Yutao Fu, Cinna Monighetti, Heather E. Peckham, Melissa Barker
PLoS One. 2010; 5(2): e9320. Published online 2010 February 22. doi: 10.1371/journal.pone.0009320
PMCID: PMC2825269
Accurate
SNP and mutation detection by targeted custom microarray-based genomic
enrichment of short-fragment sequencing libraries
Michal Mokry, Harma Feitsma, Isaac J. Nijman, Ewart de
Bruijn, Pieter J. van der Zaag, Victor Guryev, Edwin Cuppen
Nucleic Acids Res. 2010 June; 38(10): e116. Published online 2010 February
17. doi: 10.1093/nar/gkq072
PMCID: PMC2879533
A
scalable, fully automated process for construction of sequence-ready barcoded
libraries for 454
Niall J Lennon, Robert E Lintner, Scott Anderson, Pablo
Alvarez, Andrew Barry, William Brockman, Riza Daza, Rachel L Erlich, Georgia
Giannoukos, Lisa Green, Andrew Hollinger, Cindi A Hoover, David B Jaffe, Frank
Juhn, Danielle McCarthy, Danielle Perrin, Karen Ponchner, Taryn L Powers,
Kamran Rizzolo, Dana Robbins, Elizabeth Ryan, Carsten Russ, Todd Sparrow, John
Stalker, Scott Steelman, Michael Weiand, Andrew Zimmer, Matthew R Henn, Chad
Nusbaum, Robert Nicol
Genome Biol. 2010; 11(2): R15. Published online 2010 February 5. doi: 10.1186/gb-2010-11-2-r15
PMCID: PMC2872875
Analysis
of High-Throughput Sequencing and Annotation Strategies for Phage Genomes
Matthew R. Henn, Matthew B. Sullivan, Nicole Stange-Thomann,
Marcia S. Osburne, Aaron M. Berlin, Libusha Kelly, Chandri Yandava, Chinnappa
Kodira, Qiandong Zeng, Michael Weiand, Todd Sparrow, Sakina Saif, Georgia
Giannoukos, Sarah K. Young, Chad Nusbaum, Bruce W. Birren, Sallie W. Chisholm
PLoS One. 2010; 5(2): e9083. Published online 2010 February 5. doi: 10.1371/journal.pone.0009083
PMCID: PMC2816706
Simultaneous
assay of every Salmonella Typhi gene using one million transposon mutants
Gemma C. Langridge, Minh-Duy Phan, Daniel J. Turner, Timothy
T. Perkins, Leopold Parts, Jana Haase, Ian Charles, Duncan J. Maskell, Sarah E.
Peters, Gordon Dougan, John Wain, Julian Parkhill, A. Keith Turner
Genome Res. 2009 December; 19(12): 2308-2316. doi: 10.1101/gr.097097.109
PMCID: PMC2792183
Microdroplet-based
PCR amplification for large scale targeted sequencing
Ryan Tewhey, Jason Warner, Masakazu Nakano, Brian Libby,
Martina Medkova, Patricia David, Steve Kotsopoulos, Michael Samuels, J. Brian
Hutchison, Jonathan W. Larson, Eric J. Topol, Michael P. Weiner, Olivier
Harismendy, Jeff Olson, Darren R. Link, Kelly A. Frazer
Nat Biotechnol.
Author manuscript; available in PMC 2010 May 1. Published in final
edited form as: Nat
Biotechnol. 2009 November; 27 (11) : 1025-1031. Published online 2009 November 1. doi: 10.1038/nbt.1583
PMCID: PMC2779736
Enrichment
of sequencing targets from the human genome by solution hybridization
Ryan Tewhey, Masakazu Nakano, Xiaoyun Wang, Carlos
Pabón-Peña, Barbara Novak, Angelica Giuffre, Eric Lin, Scott Happe, Doug N
Roberts, Emily M LeProust, Eric J Topol, Olivier Harismendy, Kelly A Frazer
Genome Biol. 2009; 10(10): R116. Published online 2009 October 16. doi: 10.1186/gb-2009-10-10-r116
PMCID: PMC2784331
Quantitative
phenotyping via deep barcode sequencing
Andrew M. Smith, Lawrence E. Heisler, Joseph Mellor, Fiona
Kaper, Michael J. Thompson, Mark Chee, Frederick P. Roth, Guri Giaever, Corey
Nislow
Genome Res. 2009 October; 19(10): 1836-1842. doi: 10.1101/gr.093955.109
PMCID: PMC2765281
Tracking
insertion mutants within libraries by deep sequencing and a genome-wide screen
for Haemophilus genes required in the lung
Jeffrey D. Gawronski, Sandy M. S. Wong, Georgia Giannoukos,
Doyle V. Ward, Brian J. Akerley
Proc Natl Acad Sci U S A. 2009 September 22; 106(38):
16422-16427. Published
online 2009 September 4.
doi: 10.1073/pnas.0906627106
PMCID: PMC2752563
Whole
Genome Amplification and De novo Assembly of Single Bacterial Cells
Sébastien Rodrigue, Rex R. Malmstrom, Aaron M. Berlin,
Bruce W. Birren, Matthew R. Henn, Sallie W. Chisholm
PLoS One. 2009; 4(9): e6864. Published online 2009 September 2. doi: 10.1371/journal.pone.0006864
PMCID: PMC2731171
Sequence
and structural variation in a human genome uncovered by short-read, massively
parallel ligation sequencing using two-base encoding
Kevin Judd McKernan, Heather E. Peckham, Gina L. Costa,
Stephen F. McLaughlin, Yutao Fu, Eric F. Tsung, Christopher R. Clouser, Cisyla
Duncan, Jeffrey K. Ichikawa, Clarence C. Lee, Zheng Zhang, Swati S. Ranade,
Eileen T. Dimalanta, Fiona C. Hyland, Tanya D. Sokolsky, Lei Zhang, Andrew
Sheridan, Haoning Fu, Cynthia L. Hendrickson, Bin Li, Lev Kotler, Jeremy R.
Stuart, Joel A. Malek, Jonathan M. Manning, Alena A. Antipova, Damon S. Perez,
Michael P. Moore, Kathleen C. Hayashibara, Michael R. Lyons, Robert E.
Beaudoin, Brittany E. Coleman, Michael W. Laptewicz, Adam E. Sannicandro,
Michael D. Rhodes, Rajesh K. Gottimukkala, Shan Yang, Vineet Bafna, Ali Bashir,
Andrew MacBride, Can Alkan, Jeffrey M. Kidd, Evan E. Eichler, Martin G. Reese,
Francisco M. De La Vega, Alan P. Blanchard
Genome Res. 2009 September; 19(9): 1527-1541. doi: 10.1101/gr.091868.109
PMCID: PMC2752135
Hybrid
selection of discrete genomic intervals on custom-designed microarrays for
massively parallel sequencing
Emily Hodges, Michelle Rooks, Zhenyu Xuan, Arindam
Bhattacharjee, D Benjamin Gordon, Leonardo Brizuela, W Richard McCombie,
Gregory J Hannon
Nat Protoc.
Author manuscript; available in PMC 2010 November 23. Published in final
edited form as: Nat
Protoc. 2009; 4 (6) : 960-974. Published online 2009 May 28. doi: 10.1038/nprot.2009.68
PMCID: PMC2990409
Solution
Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel
Targeted Sequencing
Andreas Gnirke, Alexandre Melnikov, Jared Maguire, Peter
Rogov, Emily M. LeProust, William Brockman, Timothy Fennell, Georgia
Giannoukos, Sheila Fisher, Carsten Russ, Stacey Gabriel, David B. Jaffe, Eric
S. Lander, Chad Nusbaum
Nat Biotechnol.
Author manuscript; available in PMC 2009 August 1. Published in final
edited form as: Nat Biotechnol. 2009 February; 27 (2) : 182-189. Published online 2009 February 1. doi: 10.1038/nbt.1523
PMCID: PMC2663421
A
large genome centre’s improvements to the Illumina sequencing system
Michael A. Quail, Iwanka Kozarewa, Frances Smith, Aylwyn
Scally, Philip J. Stephens, Richard Durbin, Harold Swerdlow, Daniel J. Turner
Nat Methods.
Author manuscript; available in PMC 2009 June 1. Published in final
edited form as: Nat
Methods. 2008 December; 5 (12) : 1005-1010. doi: 10.1038/nmeth.1270
PMCID: PMC2610436
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