Genome Biology | Most Forwarded

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Display/download options Articles per page: 25 | 50 | 100

Display options

Editor's summary Citation

Download options

Send
To

	All
	1.	Method ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
	2.	Comment How to evaluate a graduate studentship, or choosing the right doctoral advisor Duncan T Odom Genome Biology 2013, 14:114 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Duncan Odom has some sage advice for those considering PhD options
	3.	Method TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley, Steven L Salzberg Genome Biology 2013, 14:R36 (25 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A major update to TopHat, the popular Bowtie-based spliced aligner
	4.	Editorial Raymond Gosling: the man who crystallized genes Naomi Attar Genome Biology 2013, 14:402 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary "The most wonderful thing!" - Genome Biology meets Raymond Gosling, a key player in the discovery of the double helix
	5.	Method Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda Genome Biology 2013, 14:R31 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
	6.	Method jMOSAiCS: joint analysis of multiple ChIP-seq datasets Xin Zeng, Rajendran Sanalkumar, Emery H Bresnick, Hongda Li, Qiang Chang, Sunduz Keles Genome Biology 2013, 14:R38 (29 April 2013) Abstract \| Provisional PDF \| Editor’s summary A novel probabilistic method for jointly analyzing multiple ChIP-seq datasets offers an improvement over chromHMM
	7.	Research Wound healing and inflammation genes revealed by array analysis of 'macrophageless' PU.1 null mice Lisa Cooper, Claire Johnson, Frank Burslem, Paul Martin Genome Biology 2004, 6:R5 (23 December 2004) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary To define the events in wound healing that are independent of inflammation, gene expression during wound healing was profiled in wild-type mice and PU.1 null mice, which cannot raise the standard inflammatory response but which can repair skin wounds rapidly.
	8.	Research Systematic analysis of gene expression in human brains before and after death Henriette Franz, Claudia Ullmann, Albert Becker, Margaret Ryan, Sabine Bahn, Thomas Arendt, Matthias Simon, Svante Pääbo, Philipp Khaitovich Genome Biology 2005, 6:R112 (30 December 2005) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Comparison of the gene expression profiles of pre- and post-mortem human brains suggests that post-mortem human brain samples are suitable for investigating general gene-expression patterns.
	9.	Research Genes regulated by estrogen in breast tumor cells in vitro are similarly regulated in vivo in tumor xenografts and human breast tumors Chad J Creighton, Kevin E Cordero, Jose M Larios, Rebecca S Miller, Michael D Johnson, Arul M Chinnaiyan, Marc E Lippman, James M Rae Genome Biology 2006, 7:R28 (7 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Estrogen-regulated gene expression profiles of in vivo breast tumor cell lines and in vitro xenografts and breast tumors are remarkably similar.
	10.	Research A genome-wide genetic signature of Jewish ancestry perfectly separates individuals with and without full Jewish ancestry in a large random sample of European Americans Anna C Need, Dalia Kasperavičiūtė, Elizabeth T Cirulli, David B Goldstein Genome Biology 2009, 10:R7 (22 January 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary A principal components analysis of genomic information showed that individuals with full Jewish ancestry formed a clearly distinct cluster from those individuals with no Jewish ancestry.
	11.	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 \| 1 comment \| F1000 Biology \| Editor’s summary The genome and transcriptome of marijuana, and comparative analysis with resequenced hemp, explains the genetic basis of psychoactivity
	12.	Research Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium Lara Rajeev, Eric G Luning, Paramvir S Dehal, Morgan N Price, Adam P Arkin, Aindrila Mukhopadhyay Genome Biology 2011, 12:R99 (12 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary All response regulators in the genome of Desulfovibrius vulgaris are identified, as are all their target genes
	13.	Review Unlocking Mendelian disease using exome sequencing Christian Gilissen, Alexander Hoischen, Han G Brunner, Joris A Veltman Genome Biology 2011, 12:228 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the past 2 years, exome sequencing has provided significant new insights into the causes of both Mendelian and sporadic genetic diseases
	14.	Research Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families Zippora Brownstein, Lilach M Friedman, Hashem Shahin, Varda Oron-Karni, Nitzan Kol, Amal Rayyan, Thomas Parzefall, Dorit Lev, Stavit Shalev, Moshe Frydman, Bella Davidov, Mordechai Shohat, Michele Rahile, Sari Lieberman, Ephrat Levy-Lahad, Ming K Lee, Noam Shomron, Mary-Claire King, Tom Walsh, Moien Kanaan, Karen B Avraham Genome Biology 2011, 12:R89 (14 September 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Targeted capture and sequencing of genomic DNA from subjects with inherited hearing loss offers an effective screen for mutations
	15.	Research Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus Santiago Castillo-Ramírez, Jukka Corander, Pekka Marttinen, Mona Aldeljawi, William P Hanage, Henrik Westh, Kit Boye, Zeynep Gulay, Stephen D Bentley, Julian Parkhill, Matthew T Holden, Edward J Feil Genome Biology 2012, 13:R126 (27 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Different evolution rates of methicillin-resistant Staphylococcus aureus clone ST239 collected in different geographical locations are caused by fast global dissemination
	16.	Opinion Women in Science Genome Biology Genome Biology 2012, 13:148 (8 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Four leading scientists answer our questions on how being female can impact upon a scientific career
	17.	Research Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium Simen M Kristoffersen, Chad Haase, M Ryan Weil, Karla D Passalacqua, Faheem Niazi, Stephen K Hutchison, Brian Desany, Anne-Brit Kolstø, Nicolas J Tourasse, Timothy D Read, Ole Økstad Genome Biology 2012, 13:R30 (26 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary RNA-seq is used to determine mRNA decay rates to single nucleotide resolution in the Gram positive bacterium Bacillus cereus
	18.	Research A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers Nathan P Palmer, Patrick R Schmid, Bonnie Berger, Isaac S Kohane Genome Biology 2012, 13:R71 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comprehensive in silico analysis of mRNA expression profiles in human stem cells, cancers and normal tissues
	19.	Meeting report Food for thought from plant and animal genomes Emily Abrash Genome Biology 2013, 14:302 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Plant and Animal Genome XXI meeting, held in San Diego, USA, January 12-16, 2013.
	20.	Research A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration Mario Looso, Jens Preussner, Konstantinos Sousounis, Marc Bruckskotten, Christian S Michel, Ettore Lignelli, Richard Reinhardt, Sabrina Hoeffner, Marcus Krueger, Panagiotis A Tsonis, Thilo Borchardt, Thomas Braun Genome Biology 2013, 14:R16 (20 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A newt transcriptome, incorporating both undamaged and regenerating organs, reveals new protein families that may be involved in tissue regeneration
	21.	Research The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila Tobias Kockmann, Moritz Gerstung, Tommy Schlumpf, Zhu Xhinzhou, Daniel Hess, Niko Beerenwinkel, Christian Beisel, Renato Paro Genome Biology 2013, 14:R18 (25 February 2013) Abstract \| Provisional PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Trithorax group members ASH1 and FSH act as general coactivators of transcription rather than by blocking Polycomb group repression
	22.	Review Recent progress in the use of genetics to understand links between type 2 diabetes and related metabolic traits Hanieh Yaghootkar, Timothy M Frayling Genome Biology 2013, 14:203 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tim Frayling and Hanieh Yaghootkar review how modern genetics is informing our understanding of the mechanisms underlying type 2 diabetes
	23.	Meeting report Clinical applications of sequencing take center stage Gustavo Glusman Genome Biology 2013, 14:303 (28 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the Advances in Genome Biology and Technology (AGBT) meeting, Marco Island, Florida, USA, February 20-23, 2013
	24.	Research RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes Katie L Ayers, Nadia M Davidson, Diana Demiyah, Kelly N Roeszler, Frank Grutzner, Andrew H Sinclair, Alicia Oshlack, Craig A Smith Genome Biology 2013, 14:R26 (25 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A transcriptomic analysis of the chicken female-specific W sex chromosome sheds light on avian sex differentiation
	25.	Research The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage John Abramyan, Daleen Badenhorst, Kyle K Biggar, Glen M Borchert, Christopher W Botka, Rachel M Bowden, Edward L Braun, Anne M Bronikowski, Benoit G Bruneau, Leslie T Buck, Blanche Capel, Todd A Castoe, Mike Czerwinski, Kim D Delehaunty, Scott V Edwards, Catrina C Fronick, Matthew K Fujita, Lucinda Fulton, Tina A Graves, Richard E Green, Wilfried Haerty, Ramkumar Hariharan, LaDeana H Hillier, Alisha K Holloway, Daniel Janes, Fredric J Janzen, Cyriac Kandoth, Lesheng Kong, Jason de Koning, Yang Li et al. Genome Biology 2013, 14:R28 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the western painted turtle, Chrysemys picta bellii, reveals insights into its extreme tolerance to anoxia and freezing