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	1. 3242 Accesses	Method Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Olivier Harismendy, Richard B Schwab, Lei Bao, Jeff Olson, Sophie Rozenzhak, Steve K Kotsopoulos, Stephanie Pond, Brian Crain, Mark S Chee, Karen Messer, Darren R Link, Kelly A Frazer Genome Biology 2011, 12:R124 (20 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An ultra-deep targeted sequencing assay detects low prevalence mutations in Illumina MiSeq and GAII clinical datasets generated from heterogeneous tumor samples
	2. 2903 Accesses	Opinion Genomics in 2011: challenges and opportunities David Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X Shirley Liu, Chad Myers, Alicia Oshlack, John Rinn, Marian Walhout Genome Biology 2011, 12:137 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Several members of the Genome Biology Editorial Board give their views on the state of play in genomics
	3. 2493 Accesses	Research MicroRNAs and their isomiRs function cooperatively to target common biological pathways Nicole Cloonan, Shivangi Wani, Qinying Xu, Jian Gu, Kristi Lea, Sheila Heater, Catalin Barbacioru, Anita L Steptoe, Hilary C Martin, Ehsan Nourbakhsh, Keerthana Krishnan, Brooke Gardiner, Xiaohui Wang, Katia Nones, Jason A Steen, Nick Matigan, David L Wood, Karin S Kassahn, Nic Waddell, Jill Shepherd, Clarence Lee, Jeff Ichikawa, Kevin McKernan, Kelli Bramlett, Scott Kuersten, Sean M Grimmond Genome Biology 2011, 12:R126 (30 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary IsomiRs act cooperatively with canonical miRNAs to regulate gene expression
	4. 2288 Accesses	Research Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman Genome Biology 2002, 3:research0034-research0034.11 (18 June 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary Using real-time reverse transcription PCR ten housekeeping genes from different abundance and functional classes in various human tissues were evaluated. The conventional use of a single gene for normalization leads to relatively large errors in a significant proportion of samples tested.
	5. 2245 Accesses	Software Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R25 (4 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
	6. 2194 Accesses	Research Genetic adaptation to high altitude in the Ethiopian highlands Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Wolde Meskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff Genome Biology 2012, 13:R1 (20 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genetics of hypoxia selection in an Ethiopian high-altitude population are distinct from Andean and Tibetan genotypes, suggestive of convergent evolution
	7. 1986 Accesses	Method Differential expression analysis for sequence count data Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| F1000 Biology \| Editor’s summary DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
	8. 1800 Accesses	Review Evolution of biological interaction networks: from models to real data Mark GF Sun, Philip M Kim Genome Biology 2011, 12:235 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sun and Kim review progress in the study of biological network evolution, with a focus on the protein-protein interaction network
	9. 1704 Accesses	Research The draft genome and transcriptome of Cannabis sativa Harm van Bakel, Jake M Stout, Atina G Cote, Carling M Tallon, Andrew G Sharpe, Timothy R Hughes, Jonathan E Page Genome Biology 2011, 12:R102 (20 October 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	10. 1649 Accesses	Review Alu elements: know the SINEs Prescott Deininger Genome Biology 2011, 12:236 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Prescott Deininger reviews the contribution of Alu elements to genome evolution, gene regulation and disease
	11. 1504 Accesses	Research highlight Games with a scientific purpose Benjamin M Good, Andrew I Su Genome Biology 2011, 12:135 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Potent algorithms and solved "unsolvable" structures: are the 230,000 players of the protein folding game Foldit the scientists of the future?
	12. 1466 Accesses	Research Implications for health and disease in the genetic signature of the Ashkenazi Jewish population Saurav Guha, Jeffrey A Rosenfeld, Anil K Malhotra, Annette T Lee, Peter K Gregersen, John M Kane, Itsik Pe'er, Ariel Darvasi, Todd Lencz Genome Biology 2012, 13:R2 (25 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A population-specific genetic signature, derived from a large genotyping study, helps explain why some diseases are overrepresented in the Ashkenazi population
	13. 1442 Accesses	Open letter Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes John A St John, Edward L Braun, Sally R Isberg, Lee G Miles, Amanda Y Chong, Jaime Gongora, Pauline Dalzell, Christopher Moran, Bertrand Bed'Hom, Arkhat Abzhanov, Shane C Burgess, Amanda M Cooksey, Todd A Castoe, Nicholas G Crawford, Llewellyn D Densmore, Jennifer C Drew, Scott V Edwards, Brant C Faircloth, Matthew K Fujita, Matthew J Greenwold, Federico G Hoffmann, Jonathan M Howard, Taisen Iguchi, Daniel E Janes, Shahid Khan, Satomi Kohno, AP Jason de Koning, Stacey L Lance, Fiona M McCarthy, John E McCormack Genome Biology 2012, 13:415 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An Open Letter describing the project to sequence the genomes of the saltwater crocodile, the American alligator and the Indian gharial
	14. 1430 Accesses	Research Evaluation of next generation sequencing platforms for population targeted sequencing studies Olivier Harismendy, Pauline C Ng, Robert L Strausberg, Xiaoyun Wang, Timothy B Stockwell, Karen Y Beeson, Nicholas J Schork, Sarah S Murray, Eric J Topol, Samuel Levy, Kelly A Frazer Genome Biology 2009, 10:R32 (27 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.
	15. 1415 Accesses	Comment A Faustian bargain Gregory A Petsko Genome Biology 2010, 11:138 (31 October 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| 1 comment \| Editor’s summary An open letter to George M Philip, President of the State University of New York At Albany.
	16. 1396 Accesses	Opinion What is complex about complex disorders? Kevin J Mitchell Genome Biology 2012, 13:237 (23 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Complex disorders such as diabetes and schizophrenia are really groups of many distinct genetic disorders caused by rare, recent deleterious mutations
	17. 1390 Accesses	Research highlight DNA-protein interactions in high definition Eric M Mendenhall, Bradley E Bernstein Genome Biology 2012, 13:139 (27 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mendenhall and Bernstein highlight ChIP-exo, which is an elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors
	18. 1251 Accesses	Method A scaling normalization method for differential expression analysis of RNA-seq data Mark D Robinson, Alicia Oshlack Genome Biology 2010, 11:R25 (2 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A novel and empirical method for normalization of RNA-seq data is presented
	19. 1214 Accesses	Research Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera Tom A Mendum, Jane Newcombe, Ahmad A Mannan, Andrzej A Kierzek, Johnjoe McFadden Genome Biology 2011, 12:R127 (30 December 2011) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A global screen of mutant fitness in Neisseria meningitidis was used to construct a genome-scale metabolic network
	20. 1211 Accesses	Method Improving RNA-Seq expression estimates by correcting for fragment bias Adam Roberts, Cole Trapnell, Julie Donaghey, John L Rinn, Lior Pachter Genome Biology 2011, 12:R22 (16 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An extension to Cufflinks corrects bias in RNA-seq datasets
	21. 1208 Accesses	Research highlight Making enhancers from spare parts of the genome David Fredman, Xianjun Dong, Boris Lenhard Genome Biology 2011, 12:138 (29 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Boris Lenhard and colleagues on how developmental enhancers form in genomes by the recycling of existing functional elements
	22. 1172 Accesses	Research Dissecting the regulatory architecture of gene expression QTLs Daniel J Gaffney, Jean-Baptiste Veyrieras, Jacob F Degner, Pique-Regi Roger, Athma A Pai, Gregory E Crawford, Matthew Stephens, Yoav Gilad, Jonathan K Pritchard Genome Biology 2012, 13:R7 (31 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of eQTLs located in regulatory elements in the human genome
	23. 1102 Accesses	Meeting report Opening sequence: computational genomics in the era of high-throughput sequencing Emily V Chambers, Alida S Kindt, Colin AM Semple Genome Biology 2011, 12:310 (28 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, November 2011.
	24. 1079 Accesses	Method SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data Mark F Rogers, Julie Thomas, Anireddy SN Reddy, Asa Ben-Hur Genome Biology 2012, 13:R4 (31 January 2012) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A tool that uses a priori information to optimize alternative splicing prediction from RNA-seq data
	25. 1056 Accesses	Review Transcriptional enhancers in development and disease Noboru Sakabe, Daniel Savic, Marcelo A Nobrega Genome Biology 2012, 13:238 (23 January 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Distal enhancers are important in development and disease, and genome-wide analyses are now giving greater insights into their function