76.
Estimating enrichment of repetitive elements from high-throughput sequence data
Daniel
S
Day,
Lovelace
J
Luquette,
Peter
J
Park,
Peter
V
Kharchenko
Genome Biology 2010, 11 :R69 (28 June 2010)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
|
Editor’s summary
The authors present a method for estimating repetitive sequence content in high-throughput sequencing data, including from ChIP-seq experiments
77.
Ankyrin 3: genetic association with bipolar disorder and relevance to disease pathophysiology
Melanie
P
Leussis,
Jon
M
Madison,
Tracey
L
Petryshen
Biology of Mood & Anxiety Disorders 2012, 2 :18 (1 October 2012)
Abstract | Full text | PDF | PubMed
78.
Community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities
Frank
J
Stewart,
Adrian
K
Sharma,
Jessica
A
Bryant,
John
M
Eppley,
Edward
F
DeLong
Genome Biology 2011, 12 :R26 (22 March 2011)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
Analysis of several metagenomic datasets reveals that highly expressed genes are more conserved than less highly expressed ones
79.
Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)
Mingxiong
Pang,
Andrew
W
Woodward,
Vikram
Agarwal,
Xueying
Guan,
Misook
Ha,
Vanitharani
Ramachandran,
Xuemei
Chen,
Barbara
A
Triplett,
David
M
Stelly,
Z Jeffrey
Chen
Genome Biology 2009, 10 :R122 (4 November 2009)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
|
Editor’s summary
Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.
80.
The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs
Jill
R
Stewart,
Rebecca
J
Gast,
Roger
S
Fujioka,
Helena
M
Solo-Gabriele,
J Scott
Meschke,
Linda
A
Amaral-Zettler,
Erika
del Castillo,
Martin
F
Polz,
Tracy
K
Collier,
Mark
S
Strom,
Christopher
D
Sinigalliano,
Peter
DR
Moeller,
A Fredrick
Holland
Environmental Health 2008, 7 (Suppl 2):S3 (7 November 2008)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
81.
Echocardiographic AV-interval optimization in patients with reduced left ventricular function
C
Melzer,
AC
Borges,
F
Knebel,
WS
Richter,
W
Combs,
G
Baumann,
H
Theres
Cardiovascular Ultrasound 2004, 2 :30 (17 December 2004)
Abstract | Full text | PDF | PubMed
82.
Combined dietary folate, vitamin B-12, and vitamin B-6 intake influences plasma docosahexaenoic acid concentration in rats
Nick
van Wijk,
Carol
J
Watkins,
Robert J
J
Hageman,
John C
W
Sijben,
Patrick G H
J
Kamphuis,
Richard
J
Wurtman,
Laus
M
Broersen
Nutrition & Metabolism 2012, 9 :49 (30 May 2012)
Abstract | Full text | PDF | PubMed
83.
Transfer Entropy Estimation and Directional Coupling Change Detection in Biomedical Time Series
Joon
Lee,
Shamim
Nemati,
Ikaro
Silva,
Bradley
A
Edwards,
James
P
Butler,
Atul
Malhotra
BioMedical Engineering OnLine 2012, 11 :19 (13 April 2012)
Abstract | Full text | PDF | PubMed
84.
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
Daniel
E
Neafsey,
Stephen
F
Schaffner,
Sarah
K
Volkman,
Daniel
Park,
Philip
Montgomery,
Danny
A
Milner,
Amanda
Lukens,
David
Rosen,
Rachel
Daniels,
Nathan
Houde,
Joseph
F
Cortese,
Erin
Tyndall,
Casey
Gates,
Nicole
Stange-Thomann,
Ousmane
Sarr,
Daouda
Ndiaye,
Omar
Ndir,
Soulyemane
Mboup,
Marcelo
U
Ferreira,
Sandra
Moraes,
Aditya
P
Dash,
Chetan
E
Chitnis,
Roger
C
Wiegand,
Daniel
L
Hartl,
Bruce
W
Birren,
Eric
S
Lander,
Pardis
C
Sabeti,
Dyann
F
Wirth
Genome Biology 2008, 9 :R171 (15 December 2008)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
|
Editor’s summary
An array-based SNP genotyping platform for Plasmodium falciparum is reported together with an analysis of SNP diversity in global population samples.
85.
Assessing statistical significance in causal graphs
Leonid
Chindelevitch,
Po-Ru
Loh,
Ahmed
Enayetallah,
Bonnie
Berger,
Daniel
Ziemek
BMC Bioinformatics 2012, 13 :35 (20 February 2012)
Abstract | Full text | PDF | PubMed
86.
BglBricks: A flexible standard for biological part assembly
J Christopher
Anderson,
John
E
Dueber,
Mariana
Leguia,
Gabriel
C
Wu,
Jonathan
A
Goler,
Adam
P
Arkin,
Jay
D
Keasling
Journal of Biological Engineering 2010, 4 :1 (20 January 2010)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
87.
Assisted assembly: how to improve a de novo genome assembly by using related species
Sante
Gnerre,
Eric
S
Lander,
Kerstin
Lindblad-Toh,
David
B
Jaffe
Genome Biology 2009, 10 :R88 (27 August 2009)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
|
Editor’s summary
A method is described for improving low sequence coverage genome assemblies
88.
Mechanistic studies of Gemcitabine-loaded nanoplatforms in resistant pancreatic cancer cells
Anne-Laure
Papa,
Sudipta
Basu,
Poulomi
Sengupta,
Deboshri
Banerjee,
Shiladitya
Sengupta,
Rania
Harfouche
BMC Cancer 2012, 12 :419 (22 September 2012)
Abstract | Full text | PDF | PubMed
89.
Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
Kang
Zhou,
Lihan
Zhou,
Qing
Lim,
Ruiyang
Zou,
Gregory
Stephanopoulos,
Heng-Phon
Too
BMC Molecular Biology 2011, 12 :18 (23 April 2011)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
A suite of novel reference genes that are more reliable than commonly used rRNAs, have been selected from a meta-analysis of microarray data for use in quantitative Real-Time PCR experiments in E. coli over-expressing recombinant proteins.
90.
Uncertainty in techno-economic estimates of cellulosic ethanol production due to experimental measurement uncertainty
Kristin
J
Vicari,
Sai
Tallam,
Tatyana
Shatova,
Koh
Joo,
Christopher
J
Scarlata,
David
Humbird,
Edward
J
Wolfrum,
Gregg
T
Beckham
Biotechnology for Biofuels 2012, 5 :23 (17 April 2012)
Abstract | Full text | PDF | PubMed
91.
Authentic teaching and learning through synthetic biology
Natalie
Kuldell
Journal of Biological Engineering 2007, 1 :8 (27 December 2007)
Abstract | Full text | PDF | PubMed |
92.
Serum protein profiles predict coronary artery disease in symptomatic patients referred for coronary angiography
William
A
LaFramboise,
Rajiv
Dhir,
Lori
A
Kelly,
Patricia
Petrosko,
John
M
Krill-Burger,
Christin
M
Sciulli,
Maureen
A
Lyons-Weiler,
Uma
R
Chandran,
Aleksey
Lomakin,
Robert
V
Masterson,
Oscar
C
Marroquin,
Suresh
R
Mulukutla,
Dennis
M
McNamara
BMC Medicine 2012, 10 :157 (5 December 2012)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
Protein biomarkers discriminate between patients lacking significant coronary artery disease from those with the disease and requiring angiography, with long-term benefits including reduced patient exposure to ionization and lower healthcare costs.
93.
Epigenomics and chromatin dynamics
Veronika
Akopian,
Michelle
M
Chan,
Kendell
Clement,
Christina
Galonska,
Casey
A
Gifford,
Elizabeth
Lehtola,
Jing
Liao,
Payman
Samavarchi-Tehrani,
Camille
Sindhu,
Zachary
D
Smith,
Alexander
M
Tsankov,
Jamie
Webster,
Yingying
Zhang,
Michael
J
Ziller,
Alexander
Meissner
Genome Biology 2012, 13 :313 (24 February 2012)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
A report on the Joint Keystone Symposium on Epigenomics and Chromatin Dynamics, Keystone, Colorado, 17-22 January 2012
94.
Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data
Joanne
H
Wang,
Derek
Pappas,
Philip
L
De Jager,
Daniel
Pelletier,
Paul
IW
de Bakker,
Ludwig
Kappos,
Chris
H
Polman,
Lori
B
Chibnik,
David
A
Hafler,
Paul
M
Matthews,
Stephen
L
Hauser,
Sergio
E
Baranzini,
Jorge
R
Oksenberg
Genome Medicine 2011, 3 :3 (18 January 2011)
Abstract | Full text | PDF | PubMed
|
Editor’s summary
A novel genetic profile for multiple sclerosis is enriched for genes involved in such pathways as immune response and nervous system development, providing insights into disease heterogeneity and genetic risk.
95.
JNER: a forum to discuss how neuroscience and biomedical engineering are reshaping physical medicine & rehabilitation
Paolo
Bonato
Journal of NeuroEngineering and Rehabilitation 2004, 1 :1 (13 October 2004)
Abstract | Full text | PDF | PubMed
96.
Interplay between neural-cadherin and vascular endothelial-cadherin in breast cancer progression
Maryam
Rezaei,
Katrin
Friedrich,
Ben
Wielockx,
Aleksandar
Kuzmanov,
Antje
Kettelhake,
Myriam
Labelle,
Hans
Schnittler,
Gustavo
Baretton,
Georg
Breier
Breast Cancer Research 2012, 14 :R154 (6 December 2012)
Abstract | Full text | PDF | PubMed
97.
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian
J
Haas,
Steven
L
Salzberg,
Wei
Zhu,
Mihaela
Pertea,
Jonathan
E
Allen,
Joshua
Orvis,
Owen
White,
C Robin
Buell,
Jennifer
R
Wortman
Genome Biology 2008, 9 :R7 (11 January 2008)
Abstract | Full text | PDF | PubMed | Cited on BioMed Central
|
Editor’s summary
EVidenceModeler (EVM) is an automated annotation tool that predicts protein-coding regions, alternatively spliced transcripts and untranslated regions of eukaryotic genes.
98.
Improving the performance of true single molecule sequencing for ancient DNA
Aurelien
Ginolhac,
Julia
Vilstrup,
Jesper
Stenderup,
Morten
Rasmussen,
Mathias
Stiller,
Beth
Shapiro,
Grant
Zazula,
Duane
Froese,
Kathleen
E
Steinmann,
John
F
Thompson,
Khaled
AS
AL-Rasheid,
Thomas
MP
Gilbert,
Eske
Willerslev,
Ludovic
Orlando
BMC Genomics 2012, 13 :177 (10 May 2012)
Abstract | Full text | PDF | PubMed
99.
Modeling formalisms in Systems Biology
Daniel
Machado,
Rafael
S
Costa,
Miguel
Rocha,
Eugénio
C
Ferreira,
Bruce
Tidor,
Isabel
Rocha
AMB Express 2011, 1 :45 (5 December 2011)
Abstract | Full text | PDF | PubMed
100.
Sterol regulatory element binding protein-dependent regulation of lipid synthesis supports cell survival and tumor growth
Beatrice
Griffiths,
Caroline
A
Lewis,
Karim
Bensaad,
Susana
Ros,
Qifeng
Zhang,
Emma
C
Ferber,
Sofia
Konisti,
Barrie
Peck,
Heike
Miess,
Philip
East,
Michael
Wakelam,
Adrian
L
Harris,
Almut
Schulze
Cancer & Metabolism 2013, 1 :3 (23 January 2013)
Abstract | Full text | PDF
|
Editor’s summary
Akt/mTORC1 signalling via SREBP was shown to coordinate lipid and protein biosynthesis in both normal and cancer cells, while ablation of this pathway caused ER stress, apoptosis and cell death and prevented tumor growth in a mouse model.