1.
Discovery and validation of cell cycle arrest biomarkers in human acute kidney injury
Kianoush
Kashani,
Ali
Al-Khafaji,
Thomas
Ardiles,
Antonio
Artigas,
Sean
M
Bagshaw,
Max
Bell,
Azra
Bihorac,
Robert
Birkhahn,
Cynthia
M
Cely,
Lakhmir
S
Chawla,
Danielle
L
Davison,
Thorsten
Feldkamp,
Lui
G
Forni,
Michelle
Gong,
Kyle
J
Gunnerson,
Michael
Haase,
James
Hackett,
Patrick
M
Honore,
Eric
AJ
Hoste,
Olivier
Joannes-Boyau,
Michael
Joannidis,
Patrick
Kim,
Jay
L
Koyner,
Daniel
T
Laskowitz,
Matthew
E
Lissauer,
Gernot
Marx,
Peter
A
McCullough,
Scott
Mullaney,
Marlies
Ostermann,
Thomas
Rimmelé,
Nathan
I
Shapiro,
Andrew
D
Shaw,
Jing
Shi,
Amy
M
Sprague,
Jean-Louis
Vincent,
Christophe
Vinsonneau
et al.
Critical Care 2013, 17 :R25 (6 February 2013)
Abstract | Provisional PDF
| PubMed | Cited on BioMed Central | F1000 Biology
|
Editor’s summary
Urine TIMP-2, and IGFBP7, two novel biomarkers for risk stratification of acute kidney injury, have been discovered and validated in more than 1000 critically ill patients.
2.
Open questions - in brief: Beyond -omics, missing motor proteins, and getting from molecules to organisms
Stephen
J
Benkovic,
Julie
Theriot,
Dagmar
Ringe
BMC Biology 2013, 11 :8 (31 January 2013)
Abstract | Full text | PDF | PubMed
3.
Modeling gene expression using chromatin features in various cellular contexts
Xianjun
Dong,
Melissa
C
Greven,
Anshul
Kundaje,
Sarah
Djebali,
James
B
Brown,
Chao
Cheng,
Thomas
R
Gingeras,
Mark
Gerstein,
Roderic
Guigó,
Ewan
Birney,
Zhiping
Weng
Genome Biology 2012, 13 :R53 (5 September 2012)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
4.
Small RNA pyrosequencing in the protozoan parasite Entamoeba histolytica reveals strain-specific small RNAs that target virulence genes
Hanbang
Zhang,
Gretchen
M
Ehrenkaufer,
Neil
Hall,
Upinder
Singh
BMC Genomics 2013, 14 :53 (25 January 2013)
Abstract | Provisional PDF
| PubMed
5.
FLI-1 Flightless-1 and LET-60 Ras control germ line morphogenesis in C. elegans
Jiamiao
Lu,
William
L
Dentler,
Erik
A
Lundquist
BMC Developmental Biology 2008, 8 :54 (16 May 2008)
Abstract | Full text | PDF | PubMed
6.
Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes
Walter
L
Eckalbar,
Elizabeth
D
Hutchins,
Glenn
J
Markov,
April
N
Allen,
Jason
J
Corneveaux,
Kerstin
Lindblad-Toh,
Federica
Di Palma,
Jessica
Alföldi,
Matthew
J
Huentelman,
Kenro
Kusumi
BMC Genomics 2013, 14 :49 (23 January 2013)
Abstract | Full text | PDF | PubMed
7.
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
Kevin
Y
Yip,
Chao
Cheng,
Nitin
Bhardwaj,
James
B
Brown,
Jing
Leng,
Anshul
Kundaje,
Joel
Rozowsky,
Ewan
Birney,
Peter
Bickel,
Michael
Snyder,
Mark
Gerstein
Genome Biology 2012, 13 :R48 (5 September 2012)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
Machine learning analysis of ENCODE data for 100 transcription factors reveals six classes of genomic regions
8.
Integration and publication of heterogeneous text-mined relationships on the Semantic Web
Adrien
Coulet,
Yael
Garten,
Michel
Dumontier,
Russ
B
Altman,
Mark
A
Musen,
Nigam
H
Shah
Journal of Biomedical Semantics 2011, 2 (Suppl 2):S10 (17 May 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
9.
Mapping between the OBO and OWL ontology languages
Syed
Tirmizi,
Stuart
Aitken,
Dilvan
A
Moreira,
Chris
Mungall,
Juan
Sequeda,
Nigam
H
Shah,
Daniel
P
Miranker
Journal of Biomedical Semantics 2011, 2 (Suppl 1):S3 (7 March 2011)
Abstract | Full text | PDF | PubMed
10.
Evaluation of lifestyle interventions to treat elevated cardiometabolic risk in primary care (E-LITE): a randomized controlled trial
Jun
Ma,
Abby
C
King,
Sandra
R
Wilson,
Lan
Xiao,
Randall
S
Stafford
BMC Family Practice 2009, 10 :71 (12 November 2009)
Abstract | Full text | PDF | PubMed
11.
An encyclopedia of mouse DNA elements (Mouse ENCODE)
John
A
Stamatoyannopoulos,
Michael
Snyder,
Ross
Hardison,
Bing
Ren,
Thomas
Gingeras,
David
M
Gilbert,
Mark
Groudine,
Michael
Bender,
Rajinder
Kaul,
Theresa
Canfield,
Erica
Giste,
Audra
Johnson,
Mia
Zhang,
Gayathri
Balasundaram,
Rachel
Byron,
Vaughan
Roach,
Peter
J
Sabo,
Richard
Sandstrom,
A Sandra
Stehling,
Robert
E
Thurman,
Sherman
M
Weissman,
Philip
Cayting,
Manoj
Hariharan,
Jin
Lian,
Yong
Cheng,
Stephen
G
Landt,
Zhihai
Ma,
Barbara
J
Wold,
Job
Dekker
et al.
Genome Biology 2012, 13 :418 (13 August 2012)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
The Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome
12.
The Transcription Factor Encyclopedia
Dimas
Yusuf,
Stefanie
L
Butland,
Magdalena
I
Swanson,
Eugene
Bolotin,
Amy
Ticoll,
Warren
A
Cheung,
Xiao
Cindy Zhang,
Christopher
TD
Dickman,
Debra
L
Fulton,
Jonathan
S
Lim,
Jake
M
Schnabl,
Oscar
HP
Ramos,
Mireille
Vasseur-Cognet,
Charles
N
de Leeuw,
Elizabeth
M
Simpson,
Gerhart
U
Ryffel,
Eric
W-F
Lam,
Ralf
Kist,
Miranda
SC
Wilson,
Raquel
Marco-Ferreres,
Jan
J
Brosens,
Leonardo
L
Beccari,
Paola
Bovolenta,
Bérénice
A
Benayoun,
Lara
J
Monteiro,
Helma
DC
Schwenen,
Lars
Grontved,
Elizabeth
Wederell,
Susanne
Mandrup,
Reiner
A
Veitia
et al.
Genome Biology 2012, 13 :R24 (29 March 2012)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central |
|
Editor’s summary
A high quality compendium of transcription factor data that allows researchers to add new data via a peer-review system
13.
Model-based Analysis of ChIP-Seq (MACS)
Yong
Zhang,
Tao
Liu,
Clifford
A
Meyer,
Jérôme
Eeckhoute,
David
S
Johnson,
Bradley
E
Bernstein,
Chad
Nusbaum,
Richard
M
Myers,
Myles
Brown,
Wei
Li,
X Shirley
Liu
Genome Biology 2008, 9 :R137 (17 September 2008)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
|
Editor’s summary
MACS performs model-based analysis of ChIP-Seq data generated by short read sequencers.
14.
The Stanford Health Assessment Questionnaire: Dimensions and Practical Applications
Bonnie
Bruce,
James
F
Fries
Health and Quality of Life Outcomes 2003, 1 :20 (9 June 2003)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
15.
Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes
Paea
LePendu,
Srinivasan
V
Iyer,
Cédrick
Fairon,
Nigam
H
Shah
Journal of Biomedical Semantics 2012, 3 (Suppl 1):S5 (24 April 2012)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
16.
What determines cell size?
Wallace
F
Marshall,
Kevin
D
Young,
Matthew
Swaffer,
Elizabeth
Wood,
Paul
Nurse,
Akatsuki
Kimura,
Joseph
Frankel,
John
Wallingford,
Virginia
Walbot,
Xian
Qu,
Adrienne
HK
Roeder
BMC Biology 2012, 10 :101 (14 December 2012)
Abstract | Full text | PDF | PubMed |
|
Editor’s summary
In a Forum article in the Cell geometry series, ten experts in ten different systems explain why it matters what size a cell is, and offer ten different answers on how it is controlled – probably all of them right.
17.
A novel bocavirus in canine liver
Linlin
Li,
Patricia
A
Pesavento,
Christian
M
Leutenegger,
Marko
Estrada,
Lark
L
Coffey,
Samia
N
Naccache,
Erik
Samayoa,
Charles
Chiu,
Jianming
Qiu,
Chunlin
Wang,
Xutao
Deng,
Eric
Delwart
Virology Journal 2013, 10 :54 (13 February 2013)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
A new species of bocavirus has been identified in the liver of a dog with haemorrhagic gastoenteritis and is highly genetically distinct from the two known canine bocaviruses.
18.
clusterMaker: a multi-algorithm clustering plugin for Cytoscape
John
H
Morris,
Leonard
Apeltsin,
Aaron
M
Newman,
Jan
Baumbach,
Tobias
Wittkop,
Gang
Su,
Gary
D
Bader,
Thomas
E
Ferrin
BMC Bioinformatics 2011, 12 :436 (9 November 2011)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
19.
Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers
Alayne
L
Brunner,
Andrew
H
Beck,
Badreddin
Edris,
Robert
T
Sweeney,
Shirley
X
Zhu,
Rui
Li,
Kelli
Montgomery,
Sushama
Varma,
Thea
Gilks,
Xiangqian
Guo,
Joseph
W
Foley,
Daniela
M
Witten,
Craig
P
Giacomini,
Ryan
A
Flynn,
Jonathan
R
Pollack,
Robert
Tibshirani,
Howard
Y
Chang,
Matt
van de Rijn,
Robert
B
West
Genome Biology 2012, 13 :R75 (28 August 2012)
Abstract | Provisional PDF
| PubMed | Cited on BioMed Central
|
Editor’s summary
Transcript sequencings from 64 solid tumours of 17 diagnostic classes reveals cancer-specific lncRNAs
20.
Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states
Aaron
L
Sarver,
Amy
J
French,
Pedro
M
Borralho,
Venugopal
Thayanithy,
Ann
L
Oberg,
Kevin
AT
Silverstein,
Bruce
W
Morlan,
Shaun
M
Riska,
Lisa
A
Boardman,
Julie
M
Cunningham,
Subbaya
Subramanian,
Liang
Wang,
Tom
C
Smyrk,
Cecilia
MP
Rodrigues,
Stephen
N
Thibodeau,
Clifford
J
Steer
BMC Cancer 2009, 9 :401 (18 November 2009)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
21.
Ablation of rat TRPV1-expressing Adelta/C-fibers with resiniferatoxin: analysis of withdrawal behaviors, recovery of function and molecular correlates
Kendall
Mitchell,
Brian
D
Bates,
Jason
M
Keller,
Matthew
Lopez,
Lindsey
Scholl,
Julia
Navarro,
Nicholas
Madian,
Gal
Haspel,
Michael
I
Nemenov,
Michael
J
Iadarola
Molecular Pain 2010, 6 :94 (17 December 2010)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
22.
Are we training pit bulls to review our manuscripts?
Virginia
Walbot
Journal of Biology 2009, 8 :24 (9 March 2009)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central |
|
Editor’s summary
Virginia Walbot accepts some of the blame for remorselessly negative reviewers, and suggests a training program for graduate students and post docs that will deliver a fairer assessment of manuscripts.
23.
The effect of a cold beverage during an exercise session combining both strength and energy systems development training on core temperature and markers of performance
Danielle
LaFata,
Amanda
Carlson-Phillips,
Stacy
T
Sims,
Elizabeth
M
Russell
Journal of the International Society of Sports Nutrition 2012, 9 :44 (19 September 2012)
Abstract | Full text | PDF | PubMed
24.
Identification of somatic and germline mutations using whole exome sequencing of congenital acute lymphoblastic leukemia
Vivian
Y
Chang,
Giuseppe
Basso,
Kathleen
M
Sakamoto,
Stanley
F
Nelson
BMC Cancer 2013, 13 :55 (4 February 2013)
Abstract | Full text | PDF | PubMed
25.
Anti-NMDA-receptor antibody detected in encephalitis, schizophrenia, and narcolepsy with psychotic features
Ko
Tsutsui,
Takashi
Kanbayashi,
Keiko
Tanaka,
Shuken
Boku,
Wakako
Ito,
Jun
Tokunaga,
Akane
Mori,
Yasuo
Hishikawa,
Tetsuo
Shimizu,
Seiji
Nishino
BMC Psychiatry 2012, 12 :37 (8 May 2012)
Abstract | Full text | PDF | PubMed