Subject: Bioinformatics Table of Contents for 1 May 2017 Oxford Academic
 
 
 
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New issue alert
 
Bioinformatics  
Volume 33 Issue 9
 
1 May 2017
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
The null hypothesis of GSEA, and a novel statistical model for competitive gene set analysis 
 
Birgit Debrabant
 
 
A general framework for association analysis of microbial communities on a taxonomic tree border= 
 
Zheng-Zheng Tang; Guanhua Chen; Alexander V. Alekseyenko; Hongzhe Li
 
 
An informative approach on differential abundance analysis for time-course metagenomic sequencing data 
 
Dan Luo; Sara Ziebell; Lingling An
 
 
 
SEQUENCE ANALYSIS
 
 
 
A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm 
 
Joël Lafond-Lapalme; Marc-Olivier Duceppe; Shengrui Wang ; Peter Moffett; Benjamin Mimee
 
 
VarMatch: robust matching of small variant datasets using flexible scoring schemes 
 
Chen Sun; Paul Medvedev
 
 
 
 
A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra 
 
Qiang Kou ; Si Wu; Nikola Tolić; Ljiljana Paša-Tolić; Yunlong Liu ...
 
 
Development and application of an algorithm to compute weighted multiple glycan alignments border= 
 
Masae Hosoda; Yukie Akune ; Kiyoko F. Aoki-Kinoshita
 
 
ntCard: a streaming algorithm for cardinality estimation in genomics data border= 
 
Hamid Mohamadi; Hamza Khan; Inanc Birol
 
 
Protein multiple sequence alignment benchmarking through secondary structure prediction border= 
 
Quan Le; Fabian Sievers; Desmond G. Higgins
 
 
 
PHYLOGENETICS
 
 
 
Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function 
 
Jeremy Adams ; Michael J. Mansfield; Daniel J. Richard; Andrew C. Doxey
 
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction border= 
 
Claire Marks; Jaroslaw Nowak ; Stefan Klostermann; Guy Georges; James Dunbar ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Linearity of network proximity measures: implications for set-based queries and significance testing 
 
Sean Maxwell; Mark R. Chance; Mehmet Koyutürk
 
 
Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies 
 
Olga Nikolova; Russell Moser ; Christopher Kemp; Mehmet Gönen; Adam A. Margolin
 
 
 
DATA AND TEXT MINING
 
 
 
PhenoCurve: capturing dynamic phenotype-environment relationships using phenomics data 
 
Yifan Yang; Lei Xu; Zheyun Feng ; Jeffrey A. Cruz; Linda J. Savage ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Image-based correction of continuous and discontinuous non-planar axial distortion in serial section microscopy border= 
 
Philipp Hanslovsky; John A. Bogovic; Stephan Saalfeld
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
The genetic map comparator: a user-friendly application to display and compare genetic maps 
 
Yan Holtz; Jacques Léon David; Vincent Ranwez
 
 
VEXOR: an integrative environment for prioritization of functional variants in fine-mapping analysis 
 
Audrey Lemaçon; Charles Joly Beauparlant; Penny Soucy ; Jamie Allen; Douglas Easton ...
 
 
CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files 
 
E. Drori; D. Levy; P. Smirin-Yosef; O. Rahimi; M. Salmon-Divon
 
 
 
SEQUENCE ANALYSIS
 
 
 
Edlib: a C/C++ library for fast, exact sequence alignment using edit distance border= 
 
Martin Šošić; Mile Šikić
 
 
AFS: identification and quantification of species composition by metagenomic sequencing 
 
Yongchao Liu; Fabian Ripp; Rene Koeppel; Hanno Schmidt; Sören Lukas Hellmann ...
 
 
fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences 
 
Yong Qian; Thomas J. Butler; Krista Opsahl-Ong; Nicholas S. Giroux; Carlo Sidore ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
MobiDB-lite: fast and highly specific consensus prediction of intrinsic disorder in proteins 
 
Marco Necci; Damiano Piovesan; Zsuzsanna Dosztányi; Silvio C.E. Tosatto
 
 
Primerize-2D: automated primer design for RNA multidimensional chemical mapping 
 
Siqi Tian ; Rhiju Das
 
 
 
GENE EXPRESSION
 
 
 
IntegratedMRF: random forest-based framework for integrating prediction from different data types 
 
Raziur Rahman; John Otridge; Ranadip Pal
 
 
Chainy: an universal tool for standardized relative quantification in real-time PCR 
 
Izaskun Mallona; Anna Díez-Villanueva; Berta Martín; Miguel A. Peinado
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GppFst: genomic posterior predictive simulations of FST and dXY for identifying outlier loci from population genomic data 
 
Richard H. Adams; Drew R Schield; Daren C. Card; Heath Blackmon; Todd A. Castoe
 
 
Wright'Fisher exact solver (WFES): scalable analysis of population genetic models without simulation or diffusion theory border= 
 
Ivan Krukov ; Bianca de Sanctis; A.P. Jason de Koning
 
 
 
SYSTEMS BIOLOGY
 
 
 
BioPAXViz: a cytoscape application for the visual exploration of metabolic pathway evolution 
 
Fotis E. Psomopoulos; Dimitrios M. Vitsios; Shakuntala Baichoo; Christos A. Ouzounis
 
 
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia border= 
 
Laurent Heirendt ; Ines Thiele; Ronan M. T. Fleming
 
 
MAPPI-DAT: data management and analysis for protein'protein interaction data from the high-throughput MAPPIT cell microarray platform border= 
 
Surya Gupta; Veronic De Puysseleyr; José Van der Heyden; Davy Maddelein ; Irma Lemmens ...
 
 
 
DATA AND TEXT MINING
 
 
 
GDISC: a web portal for integrative analysis of gene'drug interaction for survival in cancer 
 
John Christian Givhan Spainhour; Juho Lim; Peng Qiu
 
 
CORRIGENDUM
 
 
 
Chainy: an universal tool for standardized relative quantification in real-time PCR 
 
Izaskun Mallona; Anna Díez-Villanueva ; Berta Martín; Miguel A. Peinado
 
 
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