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1.
7882 Accesses
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Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Franck Rapaport, Raya Khanin, Yupu Liang, Mono Pirun, Azra Krek, Paul Zumbo, Christopher E Mason, Nicholas D Socci, Doron Betel Genome Biology 2013, 14:R95 (10 September 2013)
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Editor’s summary
An evaluation of differential gene expression analysis methods for RNA-seq data using the SEQC gold standard dataset
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2.
5156 Accesses
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Reducing assembly complexity of microbial genomes with single-molecule sequencing
Sergey Koren, Gregory P Harhay, Timothy PL Smith, James L Bono, Dayna M Harhay, Scott D Mcvey, Diana Radune, Nicholas H Bergman, Adam M Phillippy Genome Biology 2013, 14:R101 (13 September 2013)
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Editor’s summary
PacBio sequencing alone is capable of generating finished bacterial genomes in the majority of cases at reasonably low cost
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3.
5051 Accesses
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Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark Genome Biology 2011, 12:R100 (17 October 2011)
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Editor’s summary
The genome of the pathogenic ciliate Ichthyophthirius multifiliis, which causes white spot disease in fish, is presented
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4.
4021 Accesses
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Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2
Oskar Marin-Bejar, Francesco P Marchese, Alejandro Athie, Yolanda Sanchez, Jovanna Gonzalez, Victor Segura, Lulu Huang, Isabel Moreno, Alfons Navarro, Mariano Monzo, Jesus Garcia-Foncillas, John L Rinn, Shuling Guo, Maite Huarte Genome Biology 2013, 14:R104 (26 September 2013)
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Editor’s summary
A novel lincRNA, PINT, connects p53 activation with epigenetic silencing by PRC2 and is identified as a candidate tumor suppressor
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5.
3520 Accesses
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Crowdfunding genomics and bioinformatics
Pamela Cameron, David W Corne, Christopher E Mason, Jeffrey Rosenfeld Genome Biology 2013, 14:134 (30 September 2013)
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Editor’s summary
How to bypass traditional research funding routes and seek pennies from the people
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6.
3401 Accesses
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Differential expression analysis for sequence count data
Simon Anders, Wolfgang Huber Genome Biology 2010, 11:R106 (27 October 2010)
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Editor’s summary
DEseq allows the determination of differential expression of read count data from RNA-seq or ChIP-seq experiments
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7.
3062 Accesses
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The non-coding snRNA 7SK controls transcriptional termination, poising and bidirectionality in embryonic stem cells
Gonçalo Castelo-Branco, Paulo P Amaral, Pär G Engström, Samuel C Robson, Sueli C Marques, Paul Bertone, Tony Kouzarides Genome Biology 2013, 14:r98 (17 September 2013)
Abstract | Provisional PDF
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Editor’s summary
A study in ESCs finds that 7SK promotes transcriptional termination and poising, and regulates bidirectional transcription
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8.
3026 Accesses
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The mutational landscape of chromatin regulatory factors across 4623 tumor samples
Abel Gonzalez-Perez, Alba Jene-Sanz, Nuria Lopez-Bigas Genome Biology 2013, 14:r106 (24 September 2013)
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Identification of mutations in chromatin regulatory factors and their potential role in tumorigenesis
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9.
2847 Accesses
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Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape
Kenneth Day, Lindsay L Waite, Anna Thalacker-Mercer, Andrew West, Marcas M Bamman, James D Brooks, Richard M Myers, Devin Absher Genome Biology 2013, 14:R102 (13 September 2013)
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Editor’s summary
A study of DNA methylation changes in four tissues during aging finds both tissue-specific and universal age-associated methylation changes
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10.
2801 Accesses
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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)
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Editor’s summary
Bowtie: a new ultrafast memory-efficient tool for the alignment of short DNA sequence reads to large genomes.
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11.
2768 Accesses
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Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
Jessica Nordlund, Christofer L Bäcklin, Per Wahlberg, Stephan Busche, Eva C Berglund, Maija-Leena Eloranta, Trond Flaegstad, Erik Forestier, Britt-Marie Frost, Arja Harila-Saari, Mats Heyman, Ólafur G Jónsson, Rolf Larsson, Josefine Palle, Lars Rönnblom, Kjeld Schmiegelow, Daniel Sinnett, Stefan Söderhäll, Tomi Pastinen, Mats G Gustafsson, Gudmar Lönnerholm, Ann-Christine Syvänen Genome Biology 2013, 14:r105 (24 September 2013)
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Editor’s summary
DNA methylation signatures associated with subtype, relapse and gene expression in pediatric acute lymphoblastic leukemia
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12.
2480 Accesses
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The advantages of SMRT sequencing
Richard J Roberts, Mauricio O Carneiro, Michael C Schatz Genome Biology 2013, 14:405 (3 July 2013)
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Editor’s summary
Rich Roberts, Mauricio Carneiro and Michael Schatz argue for a greater uptake of the impressive PacBio SMRT sequencing platform
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13.
2406 Accesses
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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)
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Editor’s summary
A major update to TopHat, the popular Bowtie-based spliced aligner
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14.
2206 Accesses
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Characterizing and measuring bias in sequence data
Michael G Ross, Carsten Russ, Maura Costello, Andrew Hollinger, Niall J Lennon, Ryan Hegarty, Chad Nusbaum, David B Jaffe Genome Biology 2013, 14:R51 (29 May 2013)
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Editor’s summary
A comparison of the bias in sequencing data from four different platforms reveals that some human promoters are completelymissed
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15.
2204 Accesses
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Intraspecific variation of recombination rate in maize
Eva Bauer, Matthieu Falque, Hildrun Walter, Cyril Bauland, Christian Camisan, Laura Campo, Nina Meyer, Nicolas Ranc, Renaud Rincent, Wolfgang Schipprack, Thomas Altmann, Pascal Flament, Albrecht E Melchinger, Monica Menz, Jesús Moreno-González, Milena Ouzunova, Pedro Revilla, Alain Charcosset, Olivier C Martin, Chris-Carolin Schön Genome Biology 2013, 14:R103 (19 September 2013)
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Editor’s summary
A large-scale analysis of recombination rates between 22 European maize inbred lines reveals significant differences in recombination between populations
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16.
2172 Accesses
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High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing
Zhaojie Zhang, Jerome E Lee, Kent Riemondy, Emily M Anderson, Rui Yi Genome Biology 2013, 14:R109 (7 October 2013)
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Editor’s summary
An efficient sRNA cloning method from Rui Yi's lab overcomes ligation biases and enables accurate quantification over a wide dynamic range
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17.
2152 Accesses
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Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus
Laurent AF Frantz, Joshua G Schraiber, Ole Madsen, Hendrik-Jan Megens, Mirte Bosse, Yogesh Paudel, Gono Semiadi, Erik Meijaard, Ning Li, Richard PMA Crooijmans, Alan L Archibald, Montgomery Slatkin, Lawrence B Schook, Greger Larson, Martien AM Groenen Genome Biology 2013, 14:R107 (26 September 2013)
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Editor’s summary
Genome sequencing points to climatic fluctuations and human mediated translocations as factors impacting upon Sus speciation in Southeast Asia
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18.
2145 Accesses
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A blood based 12-miRNA signature of Alzheimer disease patients
Petra Leidinger, Christina Backes, Stephanie Deutscher, Katja Schmitt, Sabine C Mueller, Karen Frese, Jan Haas, Klemens Ruprecht, Friedemann Paul, Cord Stähler, Christoph JG Lang, Benjamin Meder, Tamas Bartfai, Eckart Meese, Andreas Keller Genome Biology 2013, 14:R78 (29 July 2013)
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Editor’s summary
A 12-miRNA signature in blood samples can be used to detect Alzheimer’s disease and other neurological disorders
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19.
1955 Accesses
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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)
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Editor’s summary
A novel and empirical method for normalization of RNA-seq data is presented
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20.
1936 Accesses
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PU.1 target genes undergo Tet2-coupled demethylation and DNMT3b-mediated methylation in monocyte-to-osteoclast differentiation
Lorenzo de la Rica, Javier Rodríguez-Ubreva, Mireia García, Abul BMMK Islam, José M Urquiza, Henar Hernando, Jesper Christensen, Kristian Helin, Carmen Gómez-Vaquero, Esteban Ballestar Genome Biology 2013, 14:R99 (12 September 2013)
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Tet2 and DNMT3b act in concert with the transcription factor PU.1 to remodel the epigenome during monocyte-to-osteoclast differentiation
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21.
1913 Accesses
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Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene
Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brazma Genome Biology 2013, 14:R70 (1 July 2013)
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Editor’s summary
Analysis of RNA-seq data across different tissues and cell lines reveals that the majority of genes have a single dominant transcript
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22.
1828 Accesses
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A comparative phenotypic and genomic analysis of C57BL/6J and C57BL/6N mouse strains
Michelle M Simon, Simon Greenaway, Jacqueline K White, Helmut Fuchs, Valérie Gailus-Durner, Sara Wells, Tania Sorg, Kim Wong, Elodie Bedu, Elizabeth J Cartwright, Romain Dacquin, Sophia Djebali, Jeanne Estabel, Jochen Graw, Neil J Ingham, Ian J Jackson, Andreas Lengeling, Silvia Mandillo, Jacqueline Marvel, Hamid Meziane, Frédéric Preitner, Oliver Puk, Michel Roux, David J Adams, Sarah Atkins, Abdel Ayadi, Lore Becker, Andrew Blake, Debra Brooker, Heather Cater, Marie-France Champy, Roy Combe, Petr Danecek, Armida di Fenza, Hilary Gates, Anna-Karin Gerdin, Elisabetta Golini, John M Hancock et al.
Genome Biology 2013, 14:R82 (31 July 2013)
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Editor’s summary
A comprehensive genomic and phenotypic analysis identifies significant differences between the widely used C57BL/6J and C57BL/6N mouse strains
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23.
1815 Accesses
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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, 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)
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Editor’s summary
Quartz-Seq is a method for performing single cell RNA-seq which displays high reproducibility
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24.
1656 Accesses
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Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species
Claudio Donati, N Luisa Hiller, Hervé Tettelin, Alessandro Muzzi, Nicholas J Croucher, Samuel V Angiuoli, Marco Oggioni, Julie C Dunning Hotopp, Fen Z Hu, David R Riley, Antonello Covacci, Tim J Mitchell, Stephen D Bentley, Morgens Kilian, Garth D Ehrlich, Rino Rappuoli, E Richard Moxon, Vega Masignani Genome Biology 2010, 11:R107 (29 October 2010)
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Editor’s summary
Streptococcus pneumoniae genome analysis reveals that the presence of pathogenicity genes is not sufficient to determine virulence
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25.
1598 Accesses
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Web Apollo: a web-based genomic annotation editing platform
Eduardo Lee, Gregg A Helt, Justin T Reese, Monica C Munoz-Torres, Chris P Childers, Robert M Buels, Lincoln Stein, Ian H Holmes, Christine G Elsik, Suzanna E Lewis Genome Biology 2013, 14:R93 (30 August 2013)
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Editor’s summary
A new web-based tool for international collaborations on genome annotations
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