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2X genomes - depth does matter
Michel C Milinkovitch, Raphael Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldon
Genome Biology 2010, 11: R16    
(9 February 2010)

The use of low coverage genomes in comparative evolutionary analyses to determine gene gain and loss events skews genome estimates.

[Abstract] [Provisional PDF]

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 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 Biology 2010, 11: R15    
(5 February 2010)

An automated method for constructing libraries for 454 sequencing significantly reduces the cost and time required.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack
Genome Biology 2010, 11: R14    
(4 February 2010)

GOseq is a method for Gene Ontology analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging
Kristen Fortney, Max Kotlyar, Igor Jurisica
Genome Biology 2010, 11: R13    
(3 February 2010)

An algorithm for determining networks from gene expression data enables the identification of genes potentially linked to aging in worms.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses
Kankshita Swaminathan, Magdy Alabady, Kranthi Varala, Emanuele De Paoli, Isaac Ho, Dan S Rokhsar, Aru K Arumuganathan, Ray Ming, Pamela J Green, Blake C Meyers, Stephen P Moose, Matthew E Hudson
Genome Biology 2010, 11: R12    
(3 February 2010)

Genomic data together with sequencing of tissue specific small RNA libraries reveals insights into the genome content, small RNA repertoire and evolutionary origins of the grass Miscanthus x giganteus.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats
Tiebing Liang, Mark W Kimpel, Jeanette N McClintick, Ashley R Skillman, Kevin McCall, Howard J Edenberg, Lucinda G Carr
Genome Biology 2010, 11: R11    
(3 February 2010)

Transcriptional profiling of specific regions of inbred rat brains reveals genes associated with alcohol preference in a known QTL locus on chromosome 4

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Rising in the East
Gregory A Petsko
Genome Biology 2010, 11(1):102   
(29 January 2010)

The genome sequence of the giant panda using next- generation sequencing marks a watershed in genome sequencing - in more ways than one.

[Abstract] [Full text] [PDF]

Ten years of Genome Biology
Clare Garvey
Genome Biology 2010, 11(1):101    
(29 January 2010)

Huge advances in the field of genomics along with the continued rise of open access has made the past ten years an exciting time to be a biologist.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

Characterization of X-Linked SNP genotypic variation in globally-distributed human populations
Amanda M Casto, Jun Z Li, Devin Absher, Richard Myers, Sohini Ramachandran, Marcus W Feldman
Genome Biology 2010, 11: R10    
(28 January 2010)

An analysis of X-linked genetic variation in human populations provides insights into population structure and demographic patterns.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Assembling genomes using short-read sequencing technology
Shaun D Jackman, nanç Birol
Genome Biology 2010, 11(1):202   
(28 January 2010)

Short-read sequencing technology can bring gigabase genome assemblies in under a million dollars.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

Looking for signatures of sex-specific demography and local adaptation on the X chromosome
Evelyne Heyer, Laure Segurel
Genome Biology 2010, 11(1):203   
(28 January 2010)

A genome-wide study of X chromosome genetic diversity in human populations shows the impact of social organization and local adaptation.

[Abstract] [Full text] [PDF]

Expressed Alu repeats as a novel, reliable tool for normalization of real-time quantitative RT-PCR data
Manuela Marullo, Chiara Zuccato, Caterina Mariotti, Nayana Lahiri, Sarah J Tabrizi, Stefano Di Donato, Elena Cattaneo
Genome Biology 2010, 11: R9    
(28 January 2010)

Expressed Alu repeats are a reliable, accurate and universal reference for use in RT-qPCR normalization of human genes

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Targeting viral infection by microRNA inhibition
Ashley PE Roberts, Catherine L Jopling
Genome Biology 2010, 11(1):201   
(26 January 2010)

An inhibitor of microRNA-122 reduces viral load in chimpanzees that are chronically infected with hepatitis C virus, suggesting that such an approach might have therapeutic potential in humans.

[Abstract] [Full text] [PDF] [PubMed] [Related articles]

Genome-wide prediction of transcription factor binding sites using an integrated model
Kyoung-Jae Won, Bing Ren, Wei Wang
Genome Biology 2010, 11: R7    
(22 January 2010)

A new approach for genome-wide transcription factor binding site prediction is presented that integrates sequence and chromatin modification data.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies
Shaolin Wang, Eric Peatman, Jason Abernathy, Geoff Waldbieser, Erika Lindquist, Paul Richardson, Susan Lucas, Mei Wang, Ping Li, Jyothi Thimmapuram, Lei Liu, Deepika Vullaganti, Huseyin Kucuktas, Christopher Murdock, Brian C Small, Melanie Wilson, Hong Liu, Yanliang Jiang, Yoona Lee, Fei Chen, et al.
Genome Biology 2010, 11: R8    
(22 January 2010)

Twelve cDNA libraries from two species of catfish have been sequenced, resulting in the generation of nearly 500,000 ESTs.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes
Andreas Ruepp, Andreas Kowarsch, Daniel Schmidl, Felix Buggenthin, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Fabian J Theis
Genome Biology 2010, 11: R6    
(20 January 2010)

PhenomiR is a comprehensive database of 542 studies reporting deregulation of miRNAs allowing large-scale statistical analysis of miRNA expression changes.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Rapid chromosome territory relocation by nuclear motor activity in response to serum removal in primary human fibroblasts
Ishita S Mehta, Manelle Amira, Amanda J Harvey, Joanna M Bridger
Genome Biology 2010, 11: R5    
(13 January 2010)

Nuclear myosin 1-dependent repositioning of chromosome territories occurs within 15 minutes of serum starvation in human cells.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays
Luca Santuari, Sylvain Pradervand, Amelia-Maria Amiguet-Vercher, Jerôme Thomas, Eavan Dorcey, Keith Harshman, Ioannis Xenarios, Thomas E Juenger, Christian S Hardtke
Genome Biology 2010, 11: R4    
(12 January 2010)

A new approach to detect deletions in divergentgenomes combines short read sequencing and tilling array data. Its utility is demonstrated on Arabidopsis strains.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

NetPath: a public resource of curated signal transduction pathways
Kumaran Kandasamy, S Sujatha Mohan, Rajesh Raju, Shivakumar Keerthikumar, Ghantasala S Sameer Kumar, Abhilash K Venugopal, Deepthi Telikicherla, J Daniel Navarro, Suresh Mathivanan, Christian Pecquet, Sashi Kanth Gollapudi, Sudhir Gopal Tattikota, Shyam Mohan, Hariprasad Padhukasahasram, Yashwanth Subbannayya, Renu Goel, Harrys KC Jacob, Jun Zhong, Raja Sekhar, Vishalakshi Nanjappa, et al.
Genome Biology 2010, 11: R3    
(12 January 2010)

NetPath, a novel community resource of curated human signaling pathways is presented and its utility demonstrated using immune signaling data.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

Integrating phenotype ontologies across multiple species
Christopher J Mungall, Georgios V Gkoutos, Cynthia L Smith, Melissa A Haendel, Suzanna E Lewis, Michael Ashburner
Genome Biology 2010, 11: R2    
(8 January 2010)

A phenotypic ontology that can be used for the analysis of phenotype-genotype data across multiple species, paving the way for truly cross species translational research.

[Abstract] [Provisional PDF] [PubMed] [Related articles]

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