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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg
Genome Biol. 2009; 10(3): R25. Published online 2009 March 4. doi: 10.1186/gb-2009-10-3-r25
PMCID:
PMC2690996
Abstract Full Text PDF–538K Supplementary Material
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 Is Cited by the Following 422 Articles in this Archive:
Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes
Paul A. Hohenlohe, Susan Bassham, Mark Currey, William A. Cresko
Philos Trans R Soc Lond B Biol Sci. 2012 February 5; 367(1587): 395–408. doi: 10.1098/rstb.2011.0245
PMCID:
PMC3233713
Abstract Full Text PDF–976K
CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms
Arun Rawat, Mohamed O. Elasri, Kurt A. Gust, Glover George, Don Pham, Leona D. Scanlan, Chris Vulpe, Edward J. Perkins
PLoS One. 2012; 7(2): e30370. Published online 2012 February 3. doi: 10.1371/journal.pone.0030370
PMCID:
PMC3272009
Abstract Full Text PDF–696K Supplementary Material
The Pseudomonas aeruginosa Transcriptome in Planktonic Cultures and Static Biofilms Using RNA Sequencing
Andreas Dötsch, Denitsa Eckweiler, Monika Schniederjans, Ariane Zimmermann, Vanessa Jensen, Maren Scharfe, Robert Geffers, Susanne Häussler
PLoS One. 2012; 7(2): e31092. Published online 2012 February 3. doi: 10.1371/journal.pone.0031092
PMCID:
PMC3272035
Abstract Full Text PDF–513K Supplementary Material
Tissue-Specific Whole Transcriptome Sequencing in Castor, Directed at Understanding Triacylglycerol Lipid Biosynthetic Pathways
Adrian P. Brown, Johan T. M. Kroon, David Swarbreck, Melanie Febrer, Tony R. Larson, Ian A. Graham, Mario Caccamo, Antoni R. Slabas
PLoS One. 2012; 7(2): e30100. Published online 2012 February 3. doi: 10.1371/journal.pone.0030100
PMCID:
PMC3272049
Abstract Full Text PDF–1.0M Supplementary Material
A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
PLoS One. 2012; 7(1): e29685. Published online 2012 January 26. doi: 10.1371/journal.pone.0029685
PMCID:
PMC3266888
Abstract Full Text PDF–950K Supplementary Material
The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines
Rebecca L. Skalsky, David L. Corcoran, Eva Gottwein, Christopher L. Frank, Dong Kang, Markus Hafner, Jeffrey D. Nusbaum, Regina Feederle, Henri-Jacques Delecluse, Micah A. Luftig, Thomas Tuschl, Uwe Ohler, Bryan R. Cullen
PLoS Pathog. 2012 January; 8(1): e1002484. Published online 2012 January 26. doi: 10.1371/journal.ppat.1002484
PMCID:
PMC3266933
Abstract Full Text PDF–992K Supplementary Material
Characterization and Comparison of the Leukocyte Transcriptomes of Three Cattle Breeds
Wen Huang, Asif Nadeem, Bao Zhang, Masroor Babar, Morris Soller, Hasan Khatib
PLoS One. 2012; 7(1): e30244. Published online 2012 January 23. doi: 10.1371/journal.pone.0030244
PMCID:
PMC3264571
Abstract Full Text PDF–392K Supplementary Material
Pseudorabies Virus Infected Porcine Epithelial Cell Line Generates a Diverse Set of Host MicroRNAs and a Special Cluster of Viral MicroRNAs
Yi-Quan Wu, Di-Jun Chen, Hua-Bin He, Dong-Sheng Chen, Ling-Ling Chen, Huan-Chun Chen, Zheng-Fei Liu
PLoS One. 2012; 7(1): e30988. Published online 2012 January 23. doi: 10.1371/journal.pone.0030988
PMCID:
PMC3264653
Abstract Full Text PDF–2.0M Supplementary Material
RNA-Seq Based Transcriptional Map of Bovine Respiratory Disease Pathogen “Histophilus somni 2336”
Ranjit Kumar, Mark L. Lawrence, James Watt, Amanda M. Cooksey, Shane C. Burgess, Bindu Nanduri
PLoS One. 2012; 7(1): e29435. Published online 2012 January 20. doi: 10.1371/journal.pone.0029435
PMCID:
PMC3262788
Abstract Full Text PDF–581K Supplementary Material
Rapid Sequencing of the Bamboo Mitochondrial Genome Using Illumina Technology and Parallel Episodic Evolution of Organelle Genomes in Grasses
Peng-Fei Ma, Zhen-Hua Guo, De-Zhu Li
PLoS One. 2012; 7(1): e30297. Published online 2012 January 17. doi: 10.1371/journal.pone.0030297
PMCID:
PMC3260276
Abstract Full Text PDF–742K Supplementary Material
Isoform Diversity and Regulation in Peripheral and Central Neurons Revealed through RNA-Seq
Jessica K. Lerch, Frank Kuo, Dario Motti, Richard Morris, John L. Bixby, Vance P. Lemmon
PLoS One. 2012; 7(1): e30417. Published online 2012 January 17. doi: 10.1371/journal.pone.0030417
PMCID:
PMC3260295
Abstract Full Text PDF–754K Supplementary Material
Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines
Philippe Chouvarine, Amanda M. Cooksey, Fiona M. McCarthy, David A. Ray, Brian S. Baldwin, Shane C. Burgess, Daniel G. Peterson
PLoS One. 2012; 7(1): e29850. Published online 2012 January 10. doi: 10.1371/journal.pone.0029850
PMCID:
PMC3254643
Abstract Full Text PDF–374K
Customisation of the Exome Data Analysis Pipeline Using a Combinatorial Approach
Swetansu Pattnaik, Srividya Vaidyanathan, Durgad G. Pooja, Sa Deepak, Binay Panda
PLoS One. 2012; 7(1): e30080. Published online 2012 January 6. doi: 10.1371/journal.pone.0030080
PMCID:
PMC3253117
Abstract Full Text PDF–488K Supplementary Material
Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma
Elaine M. Morazzani, Michael R. Wiley, Marta G. Murreddu, Zach N. Adelman, Kevin M. Myles
PLoS Pathog. 2012 January; 8(1): e1002470. Published online 2012 January 5. doi: 10.1371/journal.ppat.1002470
PMCID:
PMC3252369
Abstract Full Text PDF–1.1M Supplementary Material
Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Robert K. Bradley, Jason Merkin, Nicole J. Lambert, Christopher B. Burge
PLoS Biol. 2012 January; 10(1): e1001229. Published online 2012 January 3. doi: 10.1371/journal.pbio.1001229
PMCID:
PMC3250501
Abstract Full Text PDF–1.0M Supplementary Material
Rate of meristem maturation determines inflorescence architecture in tomato
Soon Ju Park, Ke Jiang, Michael C. Schatz, Zachary B. Lippman
Proc Natl Acad Sci U S A. 2012 January 10; 109(2): 639–644. Published online 2011 December 27. doi: 10.1073/pnas.1114963109
PMCID:
PMC3258637
Abstract Full Text PDF–1.1M Supplementary Material
Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology
Lesley Joan Collins
Front Genet. 2011; 2: 96. Prepublished online 2011 November 28. Published online 2011 December 27. doi: 10.3389/fgene.2011.00096
PMCID:
PMC3268645
Abstract Full Text PDF–952K
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing
Wanfei Liu, Yuhui Zhao, Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Xinyu Tan, Shuhui Song, Jun Yu, Songnian Hu
Front Genet. 2011; 2: 93. Published online 2011 December 26. doi: 10.3389/fgene.2011.00093
PMCID:
PMC3268642
Abstract Full Text PDF–1.3M Supplementary Material
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development
Jonathan Göke, Marc Jung, Sarah Behrens, Lukas Chavez, Sean O'Keeffe, Bernd Timmermann, Hans Lehrach, James Adjaye, Martin Vingron
PLoS Comput Biol. 2011 December; 7(12): e1002304. Published online 2011 December 22. doi: 10.1371/journal.pcbi.1002304
PMCID:
PMC3245296
Abstract Full Text PDF–1.1M Supplementary Material
Identification of Evolutionarily Conserved Exons as Regulated Targets for the Splicing Activator Tra2β in Development
Sushma Grellscheid, Caroline Dalgliesh, Markus Storbeck, Andrew Best, Yilei Liu, Miriam Jakubik, Ylva Mende, Ingrid Ehrmann, Tomaz Curk, Kristina Rossbach, Cyril F. Bourgeois, James Stévenin, David Grellscheid, Michael S. Jackson, Brunhilde Wirth, David J. Elliott
PLoS Genet. 2011 December; 7(12): e1002390. Published online 2011 December 15. doi: 10.1371/journal.pgen.1002390
PMCID:
PMC3240583
Abstract Full Text PDF–5.5M Supplementary Material
The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs
Peter Arensburger, Robert H Hice, Jennifer A Wright, Nancy L Craig, Peter W Atkinson
BMC Genomics. 2011; 12: 606. Published online 2011 December 15. doi: 10.1186/1471-2164-12-606
PMCID:
PMC3259105
Abstract Full Text PDF–982K Supplementary Material
A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi
Young-Jun Choi, Elodie Ghedin, Matthew Berriman, Jacqueline McQuillan, Nancy Holroyd, George F. Mayhew, Bruce M. Christensen, Michelle L. Michalski
PLoS Negl Trop Dis. 2011 December; 5(12): e1409. Published online 2011 December 13. doi: 10.1371/journal.pntd.0001409
PMCID:
PMC3236722
Abstract Full Text PDF–375K Supplementary Material
Detection of microRNAs in color space
Antonio Marco, Sam Griffiths-Jones
Bioinformatics. 2012 February 1; 28(3): 318–323. Published online 2011 December 9. doi: 10.1093/bioinformatics/btr686
PMCID:
PMC3268249
Abstract Full Text PDF–284K Supplementary Material
Toward an Integrated Model of Capsule Regulation in Cryptococcus neoformans
Brian C. Haynes, Michael L. Skowyra, Sarah J. Spencer, Stacey R. Gish, Matthew Williams, Elizabeth P. Held, Michael R. Brent, Tamara L. Doering
PLoS Pathog. 2011 December; 7(12): e1002411. Published online 2011 December 8. doi: 10.1371/journal.ppat.1002411
PMCID:
PMC3234223
Abstract Full Text PDF–2.0M Supplementary Material
Changes in Gene Expression Associated with Reproductive Maturation in Wild Female Baboons
Courtney C. Babbitt, Jenny Tung, Gregory A. Wray, Susan C. Alberts
Genome Biol Evol. 2012; 4(2): 102–109. Published online 2011 December 8. doi: 10.1093/gbe/evr134
PMCID:
PMC3273164
Abstract Full Text PDF–871K
Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads
Li C. Xia, Jacob A. Cram, Ting Chen, Jed A. Fuhrman, Fengzhu Sun
PLoS One. 2011; 6(12): e27992. Published online 2011 December 6. doi: 10.1371/journal.pone.0027992
PMCID:
PMC3232206
Abstract Full Text PDF–1.3M Supplementary Material
B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data
Benjamin Kreck, George Marnellos, Julia Richter, Felix Krueger, Reiner Siebert, Andre Franke
Bioinformatics. 2012 February 1; 28(3): 428–429. Published online 2011 December 6. doi: 10.1093/bioinformatics/btr660
PMCID:
PMC3268236
Abstract Full Text PDF–63K Supplementary Material
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
Matthew B. Rogers, James D. Hilley, Nicholas J. Dickens, Jon Wilkes, Paul A. Bates, Daniel P. Depledge, David Harris, Yerim Her, Pawel Herzyk, Hideo Imamura, Thomas D. Otto, Mandy Sanders, Kathy Seeger, Jean-Claude Dujardin, Matthew Berriman, Deborah F. Smith, Christiane Hertz-Fowler, Jeremy C. Mottram
Genome Res. 2011 December; 21(12): 2129–2142. doi: 10.1101/gr.122945.111
PMCID:
PMC3227102
Abstract Full Text PDF–1.3M
Methods, Challenges, and Promise of Next-Generation Sequencing in Cancer Biology
Adrian D. Haimovich
Yale J Biol Med. 2011 December; 84(4): 439–446. Published online 2011 December.
PMCID:
PMC3238319
Abstract Full Text PDF–259K
AutismKB: an evidence-based knowledgebase of autism genetics
Li-Ming Xu, Jia-Rui Li, Yue Huang, Min Zhao, Xing Tang, Liping Wei
Nucleic Acids Res. 2012 January; 40(D1): D1016–D1022. Published online 2011 December 1. doi: 10.1093/nar/gkr1145
PMCID:
PMC3245106
Abstract Full Text PDF–6.6M
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