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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

Is Cited by the Following 634 Articles in this Archive:

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
Julia Heisig, David Weber, Eva Englberger, Anja Winkler, Susanne Kneitz, Wing-Kin Sung, Elmar Wolf, Martin Eilers, Chia-Lin Wei, Manfred Gessler
PLoS Genet. 2012 May; 8(5): e1002728. Published online 2012 May 17. doi: 10.1371/journal.pgen.1002728
PMCID:
PMC3355086
Abstract Full Text PDF–1.4M Supplementary Material
Escape from Preferential Retention Following Repeated Whole Genome Duplications in Plants
James C. Schnable, Xiaowu Wang, J. Chris Pires, Michael Freeling
Front Plant Sci. 2012; 3: 94. Prepublished online 2012 March 12. Published online 2012 May 15. doi: 10.3389/fpls.2012.00094
PMCID:
PMC3355610
Abstract Full Text PDF–1.4M
Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Leopold Parts, Åsa K. Hedman, Sarah Keildson, Andrew J. Knights, Cei Abreu-Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartonicek, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C. Nica, Michael A. Quail, Kerrin S. Small, Daniel Glass, Anton J. Enright, John Winn, MuTHER Consortium, Panos Deloukas, Emmanouil T. Dermitzakis, Mark I. McCarthy, Timothy D. Spector, Richard Durbin, Cecilia M. Lindgren
PLoS Genet. 2012 May; 8(5): e1002704. Published online 2012 May 10. doi: 10.1371/journal.pgen.1002704
PMCID:
PMC3349731
Abstract Full Text PDF–960K Supplementary Material
On the Analysis of the Illumina 450k Array Data: Probes Ambiguously Mapped to the Human Genome
Xu Zhang, Wenbo Mu, Wei Zhang
Front Genet. 2012; 3: 73. Published online 2012 May 4. doi: 10.3389/fgene.2012.00073
PMCID:
PMC3343275
Full Text PDF–221K
GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics
Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama
PLoS One. 2012; 7(5): e36060. Published online 2012 May 4. doi: 10.1371/journal.pone.0036060
PMCID:
PMC3344842
Abstract Full Text PDF–1.5M
Dynamic Deposition of Histone Variant H3.3 Accompanies Developmental Remodeling of the Arabidopsis Transcriptome
Heike Wollmann, Sarah Holec, Keith Alden, Neil D. Clarke, Pierre-Étienne Jacques, Frédéric Berger
PLoS Genet. 2012 May; 8(5): e1002658. Published online 2012 May 3. doi: 10.1371/journal.pgen.1002658
PMCID:
PMC3342937
Abstract Full Text PDF–805K Supplementary Material
LINT, a Novel dL(3)mbt-Containing Complex, Represses Malignant Brain Tumour Signature Genes
Karin Meier, Eve-Lyne Mathieu, Florian Finkernagel, L. Maximilian Reuter, Maren Scharfe, Gunther Doehlemann, Michael Jarek, Alexander Brehm
PLoS Genet. 2012 May; 8(5): e1002676. Published online 2012 May 3. doi: 10.1371/journal.pgen.1002676
PMCID:
PMC3342951
Abstract Full Text PDF–1.0M Supplementary Material
Transcriptome-wide analysis of small RNA expression in early zebrafish development
Chunyao Wei, Leonidas Salichos, Carli M. Wittgrove, Antonis Rokas, James G. Patton
RNA. 2012 May; 18(5): 915–929. doi: 10.1261/rna.029090.111
PMCID:
PMC3334700
Abstract Full Text PDF–2.2M
Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming
Heike Berndt, Christiane Harnisch, Christiane Rammelt, Nadine Stöhr, Anne Zirkel, Juliane C. Dohm, Heinz Himmelbauer, Joao-Paulo Tavanez, Stefan Hüttelmaier, Elmar Wahle
RNA. 2012 May; 18(5): 958–972. doi: 10.1261/rna.032292.112
PMCID:
PMC3334704
Free in PMC on 2013/05/01
A DNA hypermethylation module for the stem/progenitor cell signature of cancer
Hariharan Easwaran, Sarah E. Johnstone, Leander Van Neste, Joyce Ohm, Tim Mosbruger, Qiuju Wang, Martin J. Aryee, Patrick Joyce, Nita Ahuja, Dan Weisenberger, Eric Collisson, Jingchun Zhu, Srinivasan Yegnasubramanian, William Matsui, Stephen B. Baylin
Genome Res. 2012 May; 22(5): 837–849. doi: 10.1101/gr.131169.111
PMCID:
PMC3337430
Abstract Full Text PDF–1.6M
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
Timothy E. Reddy, Jason Gertz, Florencia Pauli, Katerina S. Kucera, Katherine E. Varley, Kimberly M. Newberry, Georgi K. Marinov, Ali Mortazavi, Brian A. Williams, Lingyun Song, Gregory E. Crawford, Barbara Wold, Huntington F. Willard, Richard M. Myers
Genome Res. 2012 May; 22(5): 860–869. doi: 10.1101/gr.131201.111
PMCID:
PMC3337432
Free in PMC on 2012/11/01
Transcriptome Mapping of pAR060302, a blaCMY-2-Positive Broad-Host-Range IncA/C Plasmid
Kevin S. Lang, Jessica L. Danzeisen, Wayne Xu, Timothy J. Johnson
Appl Environ Microbiol. 2012 May; 78(9): 3379–3386. doi: 10.1128/AEM.07199-11
PMCID:
PMC3346456
Free in PMC on 2012/11/01
Long-Range Transcriptional Control of an Operon Necessary for Virulence-Critical ESX-1 Secretion in Mycobacterium tuberculosis
Debbie M. Hunt, Nathan P. Sweeney, Luisa Mori, Rachael H. Whalan, Iñaki Comas, Laura Norman, Teresa Cortes, Kristine B. Arnvig, Elaine O. Davis, Melanie R. Stapleton, Jeffrey Green, Roger S. Buxton
J Bacteriol. 2012 May; 194(9): 2307–2320. doi: 10.1128/JB.00142-12
PMCID:
PMC3347062
Free in PMC on 2012/11/01
Polycomb Repressive Complex 2-Dependent and -Independent Functions of Jarid2 in Transcriptional Regulation in Drosophila
Hans-Martin Herz, Man Mohan, Alexander S. Garrett, Caitlynn Miller, David Casto, Ying Zhang, Christopher Seidel, Jeffrey S. Haug, Laurence Florens, Michael P. Washburn, Masamitsu Yamaguchi, Ramin Shiekhattar, Ali Shilatifard
Mol Cell Biol. 2012 May; 32(9): 1683–1693. doi: 10.1128/MCB.06503-11
PMCID:
PMC3347239
Free in PMC on 2012/11/01
Dynamic Changes in Nucleosome Occupancy Are Not Predictive of Gene Expression Dynamics but Are Linked to Transcription and Chromatin Regulators
Dana J. Huebert, Pei-Fen Kuan, Sündüz Keleş, Audrey P. Gasch
Mol Cell Biol. 2012 May; 32(9): 1645–1653. doi: 10.1128/MCB.06170-11
PMCID:
PMC3347246
Free in PMC on 2012/11/01
Identification of Host-Chromosome Binding Sites and Candidate Gene Targets for Kaposi's Sarcoma-Associated Herpesvirus LANA
Fang Lu, Kevin Tsai, Horng-Shen Chen, Priyankara Wikramasinghe, Ramana V. Davuluri, Louise Showe, John Domsic, Ronen Marmorstein, Paul M. Lieberman
J Virol. 2012 May; 86(10): 5752–5762. doi: 10.1128/JVI.07216-11
PMCID:
PMC3347294
Free in PMC on 2012/11/01
Analysis of Chromatin Dynamics during Glucocorticoid Receptor Activation
Craig J. Burd, James M. Ward, Valerie J. Crusselle-Davis, Grace E. Kissling, Dhiral Phadke, Ruchir R. Shah, Trevor K. Archer
Mol Cell Biol. 2012 May; 32(10): 1805–1817. doi: 10.1128/MCB.06206-11
PMCID:
PMC3347412
Free in PMC on 2012/11/01
Codependency of H2B monoubiquitination and nucleosome reassembly on Chd1
Jung-Shin Lee, Alexander S. Garrett, Kuangyu Yen, Yoh-Hei Takahashi, Deqing Hu, Jessica Jackson, Christopher Seidel, B. Franklin Pugh, Ali Shilatifard
Genes Dev. 2012 May 1; 26(9): 914–919. doi: 10.1101/gad.186841.112
PMCID:
PMC3347789
Free in PMC on 2012/11/01
Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis
Frédéric Pontvianne, Todd Blevins, Chinmayi Chandrasekhara, Wei Feng, Hume Stroud, Steven E. Jacobsen, Scott D. Michaels, Craig S. Pikaard
Genes Dev. 2012 May 1; 26(9): 945–957. doi: 10.1101/gad.182865.111
PMCID:
PMC3347792
Abstract Full Text PDF–2.4M
Transcriptome Sequencing Revealed Significant Alteration of Cortical Promoter Usage and Splicing in Schizophrenia
Jing Qin Wu, Xi Wang, Natalie J. Beveridge, Paul A. Tooney, Rodney J. Scott, Vaughan J. Carr, Murray J. Cairns
PLoS One. 2012; 7(4): e36351. Published online 2012 April 27. doi: 10.1371/journal.pone.0036351
PMCID:
PMC3338678
Abstract Full Text PDF–1.0M Supplementary Material
Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]
Xiang Tao, Ying-Hong Gu, Hai-Yan Wang, Wen Zheng, Xiao Li, Chuan-Wu Zhao, Yi-Zheng Zhang
PLoS One. 2012; 7(4): e36234. Published online 2012 April 27. doi: 10.1371/journal.pone.0036234
PMCID:
PMC3338685
Abstract Full Text PDF–602K Supplementary Material
Sequence-Specific Targeting of Dosage Compensation in Drosophila Favors an Active Chromatin Context
Artyom A. Alekseyenko, Joshua W. K. Ho, Shouyong Peng, Marnie Gelbart, Michael Y. Tolstorukov, Annette Plachetka, Peter V. Kharchenko, Youngsook L. Jung, Andrey A. Gorchakov, Erica Larschan, Tingting Gu, Aki Minoda, Nicole C. Riddle, Yuri B. Schwartz, Sarah C. R. Elgin, Gary H. Karpen, Vincenzo Pirrotta, Mitzi I. Kuroda, Peter J. Park
PLoS Genet. 2012 April; 8(4): e1002646. Published online 2012 April 26. doi: 10.1371/journal.pgen.1002646
PMCID:
PMC3343056
Abstract Full Text PDF–1.6M Supplementary Material
mRNA-Seq Analysis of the Pseudoperonospora cubensis Transcriptome During Cucumber (Cucumis sativus L.) Infection
Elizabeth A. Savory, Bishwo N. Adhikari, John P. Hamilton, Brieanne Vaillancourt, C. Robin Buell, Brad Day
PLoS One. 2012; 7(4): e35796. Published online 2012 April 24. doi: 10.1371/journal.pone.0035796
PMCID:
PMC3335787
Abstract Full Text PDF–1.1M Supplementary Material
Non-Overlapping Progesterone Receptor Cistromes Contribute to Cell-Specific Transcriptional Outcomes
Christine L. Clarke, J. Dinny Graham
PLoS One. 2012; 7(4): e35859. Published online 2012 April 24. doi: 10.1371/journal.pone.0035859
PMCID:
PMC3335806
Abstract Full Text PDF–931K Supplementary Material
Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens
Lihong Xiao, Liechi Zhang, Ge Yang, Honglin Zhu, Yikun He
PLoS One. 2012; 7(4): e35961. Published online 2012 April 24. doi: 10.1371/journal.pone.0035961
PMCID:
PMC3335808
Abstract Full Text PDF–1.0M Supplementary Material
Expression Profiling of Cucumis sativus in Response to Infection by Pseudoperonospora cubensis
Bishwo N. Adhikari, Elizabeth A. Savory, Brieanne Vaillancourt, Kevin L. Childs, John P. Hamilton, Brad Day, C. Robin Buell
PLoS One. 2012; 7(4): e34954. Published online 2012 April 24. doi: 10.1371/journal.pone.0034954
PMCID:
PMC3335828
Abstract Full Text PDF–708K Supplementary Material
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy
Kankshita Swaminathan, Won Byoung Chae, Therese Mitros, Kranthi Varala, Liang Xie, Adam Barling, Katarzyna Glowacka, Megan Hall, Stanislaw Jezowski, Ray Ming, Matthew Hudson, John A Juvik, Daniel S Rokhsar, Stephen P Moose
BMC Genomics. 2012; 13: 142. Published online 2012 April 24. doi: 10.1186/1471-2164-13-142
PMCID:
PMC3355032
Abstract Full Text PDF–2.8M Supplementary Material
Conserved and essential transcription factors for cellulase gene expression in ascomycete fungi
Samuel T. Coradetti, James P. Craig, Yi Xiong, Teresa Shock, Chaoguang Tian, N. Louise Glass
Proc Natl Acad Sci U S A. 2012 May 8; 109(19): 7397–7402. Published online 2012 April 24. doi: 10.1073/pnas.1200785109
PMCID:
PMC3358856
Free in PMC on 2012/11/08
Worm Burden-Dependent Disruption of the Porcine Colon Microbiota by Trichuris suis Infection
Sitao Wu, Robert W. Li, Weizhong Li, Ethiopia Beshah, Harry D. Dawson, Joseph F. Urban, Jr
PLoS One. 2012; 7(4): e35470. Published online 2012 April 20. doi: 10.1371/journal.pone.0035470
PMCID:
PMC3332011
Abstract Full Text PDF–776K
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data
Jin Zhang, Jiayin Wang, Yufeng Wu
BMC Bioinformatics. 2012; 13(Suppl 6): S6. Published online 2012 April 19. doi: 10.1186/1471-2105-13-S6-S6
PMCID:
PMC3358659
Abstract Full Text PDF–906K
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