Genome Biology | All articles

Submit a manuscript Register Contact us Follow us on Twitter

Explore Genome Biology

Advertisement

Articles

Supplements

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

Display options

Editor's summary Citation

Download options

Send
To

	All
		Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
		Research highlight New gene expression pipelines gush lncRNAs Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013) Abstract \| Full text \| PDF \| Editor’s summary The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts
		Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Jin Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Provisional PDF \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
		Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
		Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
		Research CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye Genome Biology 2013, 14:R40 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
		Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
		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
		Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
		Research Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
		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
		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
		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
		Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
		Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
		Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
		Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
		Meeting report Single-cell biology meeting marks rebirth of an old science Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
		Review Neurogenomics of speech and language disorders: the road ahead Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
		Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
		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
		Research highlight The fractured genome of HeLa cells David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
		Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
		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
		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

	All
		Meeting report Epigenetics and transgenerational inheritance Emilie Brasset, Séverine Chambeyron Genome Biology 2013, 14:306 (24 May 2013) Abstract \| Full text \| PDF \| Editor’s summary A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, held at Churchill College, Cambridge, UK, April 11-12, 2013.
		Research highlight New gene expression pipelines gush lncRNAs Jiashi Wang, Bronwyn A Lucas, Lynne E Maquat Genome Biology 2013, 14:117 (24 May 2013) Abstract \| Full text \| PDF \| Editor’s summary The characterization of lncRNA expression during neuronal development is a useful resource for elucidating the functions of non-coding transcripts
		Research Longitudinal, genome-scale analysis of DNA methylation in twins from birth to 18 months of age reveals rapid epigenetic change in early life and pair-specific effects of discordance David Martino, Yuk Jin Loke, Lavinia Gordon, Miina Ollikainen, Mark N Cruickshank, Richard Saffery, Jeffrey M Craig Genome Biology 2013, 14:R42 (22 May 2013) Abstract \| Provisional PDF \| Editor’s summary A longitudinal study of DNA methylation in twins at birth and 18 months finds that some loci drift in methylation status
		Research Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei-Ting Li, Qiong Zhang, Min-Jeong Kim, Michael C Schatz, Michael Campbell, Jingping Li, John E Bowers, Haibao Tang, Eric Lyons, Ann A Ferguson, Giuseppe Narzisi, David R Nelson, Crysten E Blaby-Haas, Andrea R Gschwend, Yuannian Jiao, Joshua P Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A Hudson, Ratnesh Singh, Aleel K Grennan, Steven J Karpowicz, Jennifer R Watling, Kikukatsu Ito et al. Genome Biology 2013, 14:R41 (10 May 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome of the long-living, slowly evolving sacred lotus reveals the genetic mechanisms underlying its adaptation to limited nutrient availability
		Comment After the gold rush Neil Hall Genome Biology 2013, 14:115 (7 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Neil Hall wonders whether genomics is ready for a plateau in sequencing costs
		Research CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes Quan Zhang, Mina Rho, Haixu Tang, Thomas G Doak, Yuzhen Ye Genome Biology 2013, 14:R40 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of CRISPR sequences contained in human metagenomic datasets reveals a variety of different targeted mobile genetic elements
		Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
		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
		Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
		Research Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis Srikanth Nagalla, Jeff W Chou, Mark C Willingham, Jimmy Ruiz, James P Vaughn, Purnima Dubey, Timothy L Lash, Stephen J Hamilton-Dutoit, Jonas Bergh, Christos Sotiriou, Michael A Black, Lance D Miller Genome Biology 2013, 14:R34 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary An analysis of nearly 2,000 breast cancer microarray samples reveals the presence of prognostic metagenes
		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
		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
		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
		Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
		Research DNA binding specificities of the long zinc-finger recombination protein PRDM9 Timothy Billings, Emil D Parvanov, Christopher L Baker, Michael Walker, Kenneth Paigen, Petko M Petkov Genome Biology 2013, 14:R35 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A detailed analysis of DNA binding by PRDM9, the zinc finger protein that determines recombination hotspots in mammals
		Research Systematic biases in DNA copy number originate from isolation procedures Sebastiaan van Heesch, Michal Mokry, Veronika Boskova, Wade Junker, Rajdeep Mehon, Pim Toonen, Ewart de Bruijn, James D Shull, Timothy J Aitman, Edwin Cuppen, Victor Guryev Genome Biology 2013, 14:R33 (24 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A new study pinpoints the sources of copy number variation biases, highlighting the important issue of sample preparation
		Research highlight The complex binding of PRDM9 Laure Ségurel Genome Biology 2013, 14:112 (24 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A Research Highlight by Laure Segurel offers a perspective on this issue's Research Article delineating the DNA-binding properties of PRDM9
		Meeting report Single-cell biology meeting marks rebirth of an old science Sten Linnarsson Genome Biology 2013, 14:305 (19 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report on the third Single Cell Analyses meeting, held at the Cold Spring Harbor Laboratory, New York, USA, March 6-9, 2013
		Review Neurogenomics of speech and language disorders: the road ahead Pelagia Deriziotis, Simon E Fisher Genome Biology 2013, 14:204 (18 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary From GWAS to Neanderthal genomes: Fisher and Deriziotis review what genomics can teach us about speech, language and their associated disorders
		Research p53 induces transcriptional and translational programs to suppress cell proliferation and growth Fabricio Loayza-Puch, Jarno Drost, Koos Rooijers, Rui Lopes, Ran Elkon, Reuven Agami Genome Biology 2013, 14:R32 (17 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary p53 activation results in mTOR inhibition and global repression of protein translation in response to oncogenic and energy stress
		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
		Research highlight The fractured genome of HeLa cells David Mittelman, John H Wilson Genome Biology 2013, 14:111 (17 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Mittelman and John Wilson steer clear of the controversy, and offer a scientific perspective on the HeLa cell genome
		Software CRAC: an integrated approach to the analysis of RNA-seq reads Nicolas Philippe, Mikaël Salson, Thérèse Commes, Eric Rivals Genome Biology 2013, 14:R30 (28 March 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Integrated analysis of mutations, indels and splice or chimeric junctions from RNA-seq data
		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
		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