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Volume 10(10);  2009
Protein family review
The SR protein family
Peter J Shepard and Klemens J Hertel
Genome Biol. 2009; 10(10): 242. Published online 2009 October 27. doi: 10.1186/gb-2009-10-10-242.
PMCID: PMC2784316
| Free in PMC on 2010/10/27 |
Comment
The dog days of autumn
Gregory A Petsko
Genome Biol. 2009; 10(10): 112. Published online 2009 November 4. doi: 10.1186/gb-2009-10-10-112.
PMCID: PMC2784313
| Free in PMC on 2010/11/04 |
Minireviews
Comparing cellular proteomes by mass spectrometry
Florian Fröhlich and Tobias C Walther
Genome Biol. 2009; 10(10): 240. Published online 2009 October 28. doi: 10.1186/gb-2009-10-10-240.
PMCID: PMC2784314
| Free in PMC on 2010/10/28 |
Runaway repeats force expansion of the Phytophthora infestans genome
Mark Gijzen
Genome Biol. 2009; 10(10): 241. Published online 2009 October 27. doi: 10.1186/gb-2009-10-10-241.
PMCID: PMC2784315
| Free in PMC on 2010/10/27 |
Meeting Report
Watching proteins in motion
Mary Munson and Daniel N Bolon
Genome Biol. 2009; 10(10): 316. Published online 2009 October 27. doi: 10.1186/gb-2009-10-10-316.
PMCID: PMC2784317
| Free in PMC on 2010/10/27 |
Method
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, and David B Jaffe
Genome Biol. 2009; 10(10): R103. Published online 2009 October 1. doi: 10.1186/gb-2009-10-10-r103.
PMCID: PMC2784318
Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
Ian Sudbery, Jim Stalker, Jared T Simpson, Thomas Keane, Alistair G Rust, Matthew E Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve D Brown, Heng Li, Zemin Ning, Joseph H Nadeau, Colleen M Croniger, Richard Durbin, and David J Adams
Genome Biol. 2009; 10(10): R112. Published online 2009 October 13. doi: 10.1186/gb-2009-10-10-r112.
PMCID: PMC2784327
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov, Alexandre Melnikov, Timothy Fennell, Chad Nusbaum, Levi A Garraway, and Andreas Gnirke
Genome Biol. 2009; 10(10): R115. Published online 2009 October 16. doi: 10.1186/gb-2009-10-10-r115.
PMCID: PMC2784330
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, and Kelly A Frazer
Genome Biol. 2009; 10(10): R116. Published online 2009 October 16. doi: 10.1186/gb-2009-10-10-r116.
PMCID: PMC2784331
An optimization framework for unsupervised identification of rare copy number variation from SNP array data
Gökhan Yavaş, Mehmet Koyutürk, Meral Özsoyoğlu, Meetha P Gould, and Thomas LaFramboise
Genome Biol. 2009; 10(10): R119. Published online 2009 October 23. doi: 10.1186/gb-2009-10-10-r119.
PMCID: PMC2784334
Software
MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays
Peter Schüffler, Thomas Mikeska, Andreas Waha, Thomas Lengauer, and Christoph Bock
Genome Biol. 2009; 10(10): R105. Published online 2009 October 5. doi: 10.1186/gb-2009-10-10-r105.
PMCID: PMC2784320
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genome
Cizhong Jiang and B Franklin Pugh
Genome Biol. 2009; 10(10): R109. Published online 2009 October 8. doi: 10.1186/gb-2009-10-10-r109.
PMCID: PMC2784324
Research
Molecular networks involved in mouse cerebral corticogenesis and spatio-temporal regulation of Sox4 and Sox11 novel antisense transcripts revealed by transcriptome profiling
King-Hwa Ling, Chelsee A Hewitt, Tim Beissbarth, Lavinia Hyde, Kakoli Banerjee, Pike-See Cheah, Ping Z Cannon, Christopher N Hahn, Paul Q Thomas, Gordon K Smyth, Seong-Seng Tan, Tim Thomas, and Hamish S Scott
Genome Biol. 2009; 10(10): R104. Published online 2009 October 2. doi: 10.1186/gb-2009-10-10-r104.
PMCID: PMC2784319
Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions
Nicolas Corradi, Karen L Haag, Jean-François Pombert, Dieter Ebert, and Patrick J Keeling
Genome Biol. 2009; 10(10): R106. Published online 2009 October 6. doi: 10.1186/gb-2009-10-10-r106.
PMCID: PMC2784321
Defining the chromatin signature of inducible genes in T cells
Pek S Lim, Kristine Hardy, Karen L Bunting, Lina Ma, Kaiman Peng, Xinxin Chen, and Mary F Shannon
Genome Biol. 2009; 10(10): R107. Published online 2009 October 6. doi: 10.1186/gb-2009-10-10-r107.
PMCID: PMC2784322
Genomic DNA k-mer spectra: models and modalities
Benny Chor, David Horn, Nick Goldman, Yaron Levy, and Tim Massingham
Genome Biol. 2009; 10(10): R108. Published online 2009 October 8. doi: 10.1186/gb-2009-10-10-r108.
PMCID: PMC2784323
NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis
Christophe Rusniok, David Vallenet, Stéphanie Floquet, Helen Ewles, Coralie Mouzé-Soulama, Daniel Brown, Aurélie Lajus, Carmen Buchrieser, Claudine Médigue, Philippe Glaser, and Vladimir Pelicic
Genome Biol. 2009; 10(10): R110. Published online 2009 October 9. doi: 10.1186/gb-2009-10-10-r110.
PMCID: PMC2784325
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication
Jeong-Hwan Mun, Soo-Jin Kwon, Tae-Jin Yang, Young-Joo Seol, Mina Jin, Jin-A Kim, Myung-Ho Lim, Jung Sun Kim, Seunghoon Baek, Beom-Soon Choi, Hee-Ju Yu, Dae-Soo Kim, Namshin Kim, Ki-Byung Lim, Soo-In Lee, Jang-Ho Hahn, Yong Pyo Lim, Ian Bancroft, and Beom-Seok Park
Genome Biol. 2009; 10(10): R111. Published online 2009 October 12. doi: 10.1186/gb-2009-10-10-r111.
PMCID: PMC2784326
Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia
Xiaobo Xia and Andrew L Kung
Genome Biol. 2009; 10(10): R113. Published online 2009 October 14. doi: 10.1186/gb-2009-10-10-r113.
PMCID: PMC2784328
Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell
Peter von Dassow, Hiroyuki Ogata, Ian Probert, Patrick Wincker, Corinne Da Silva, Stéphane Audic, Jean-Michel Claverie, and Colomban de Vargas
Genome Biol. 2009; 10(10): R114. Published online 2009 October 15. doi: 10.1186/gb-2009-10-10-r114.
PMCID: PMC2784329
Simultaneous transcription of duplicated var2csa gene copies in individual Plasmodium falciparum parasites
Kim JM Brolin, Ulf Ribacke, Sandra Nilsson, Johan Ankarklev, Kirsten Moll, Mats Wahlgren, and Qijun Chen
Genome Biol. 2009; 10(10): R117. Published online 2009 October 22. doi: 10.1186/gb-2009-10-10-r117.
PMCID: PMC2784332
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
Tom M Conrad, Andrew R Joyce, M Kenyon Applebee, Christian L Barrett, Bin Xie, Yuan Gao, and Bernhard Ø Palsson
Genome Biol. 2009; 10(10): R118. Published online 2009 October 22. doi: 10.1186/gb-2009-10-10-r118.
PMCID: PMC2784333
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