Subject: Bioinformatics Table of Contents for 01 January 2019 ------=_Part_994411511.1545414998617 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_994411511.1545414998617 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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New issue alert
 
 
 
 
 
 
Bioinformatics  
Volume 35 Issue 1
 
01 January 2019
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies 
 
Nilotpal Sanyal; Min-Tzu Lo; Karolina Kauppi; Srdjan Djurovic; Ole A Andreassen ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis 
 
Nelson Gil; Andras Fiser
 
 
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data 
 
Ehsan Haghshenas; S Cenk Sahinalp; Faraz Hach
 
 
 
GENE EXPRESSION
 
 
 
A descriptive marker gene approach to single-cell pseudotime inference border=  
 
Kieran R Campbell; Christopher Yau
 
 
Unraveling the role of low-frequency mutated genes in breast cancer 
 
Eleonora Lusito; Barbara Felice; Giovanni D'Ario; Alessandro Ogier ; Francesca Montani ...
 
 
GrandPrix: scaling up the Bayesian GPLVM for single-cell data border=  
 
Sumon Ahmed; Magnus Rattray; Alexis Boukouvalas
 
 
Differential coexpression in human tissues and the confounding effect of mean expression levels border=  
 
Marjan Farahbod; Paul Pavlidis
 
 
Exploring drivers of gene expression in the Cancer Genome Atlas 
 
Andrea Rau; Michael Flister; Hallgeir Rui; Paul L Auer
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Comparative assessment of different familial aggregation methods in the context of large and unstructured pedigrees border= 
 
Christian X Weichenberger ; Johannes Rainer; Cristian Pattaro; Peter P Pramstaller; Francisco S Domingues
 
 
 
SYSTEMS BIOLOGY
 
 
 
Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus 
 
Lei Han; Lei Li; Feng Wen; Lei Zhong ; Tong Zhang ...
 
 
A network-based zoning for parallel whole-cell simulation 
 
Barnali Das; Abhijeet Rajendra Patil; Pralay Mitra
 
 
Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy border= 
 
Mohammad Sajjad Ghaemi ; Daniel B DiGiulio; Kévin Contrepois; Benjamin Callahan; Thuy T M Ngo ...
 
 
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug'target interactions 
 
Fangping Wan; Lixiang Hong; An Xiao; Tao Jiang ; Jianyang Zeng
 
 
 
DATA AND TEXT MINING
 
 
 
Tightly integrated genomic and epigenomic data mining using tensor decomposition 
 
Jianwen Fang
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
htsget: a protocol for securely streaming genomic data border=  
 
Jerome Kelleher; Mike Lin; C H Albach ; Ewan Birney; Robert Davies ...
 
 
Seave: a comprehensive web platform for storing and interrogating human genomic variation border=  
 
Velimir Gayevskiy; Tony Roscioli; Marcel E Dinger ; Mark J Cowley
 
 
ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations 
 
Zhaohui Gu; Charles G Mullighan
 
 
Matt: Unix tools for alternative splicing analysis 
 
André Gohr; Manuel Irimia
 
 
Kmer-db: instant evolutionary distance estimation 
 
Sebastian Deorowicz; Adam GudyÅ›; Maciej DÅ‚ugosz; Marek Kokot ; Agnieszka Danek
 
 
Reproducible and replicable comparisons using SummarizedBenchmark 
 
Patrick K Kimes; Alejandro Reyes
 
 
WAVES: a web application for versatile enhanced bioinformatic services 
 
Marc Chakiachvili; Sylvain Milanesi; Anne-Muriel Arigon Chifolleau; Vincent Lefort
 
 
 
SEQUENCE ANALYSIS
 
 
 
Broom: application for non-redundant storage of high throughput sequencing data 
 
Levent Albayrak; Kamil Khanipov; George Golovko; Yuriy Fofanov
 
 
Cryfa: a secure encryption tool for genomic data border= 
 
Morteza Hosseini; Diogo Pratas; Armando J Pinho
 
 
 
PHYLOGENETICS
 
 
 
SonicParanoid: fast, accurate and easy orthology inference border=  
 
Salvatore Cosentino; Wataru Iwasaki
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs border= 
 
Maciej Antczak; Marcin Zablocki ; Tomasz Zok; Agnieszka Rybarczyk; Jacek Blazewicz ...
 
 
 
GENE EXPRESSION
 
 
 
GECO: gene expression correlation analysis after genetic algorithm-driven deconvolution 
 
Jamil Najafov; Ayaz Najafov
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data 
 
Shijia Zhu; Tongqi Qian; Yujin Hoshida; Yuan Shen ; Jing Yu ...
 
 
emeraLD: rapid linkage disequilibrium estimation with massive datasets 
 
Corbin Quick; Christian Fuchsberger; Daniel Taliun; Gonçalo Abecasis ; Michael Boehnke ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis border= 
 
Pierre Salvy; Georgios Fengos ; Meric Ataman; Thomas Pathier; Keng C Soh ...
 
 
 
DATA AND TEXT MINING
 
 
 
ACDtool: a web-server for the generic analysis of large data sets of counts 
 
Jean-Michel Claverie; Thi Ngan Ta
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains 
 
Chuan Jiao; Pengpeng Yan; Cuihua Xia; Zhaoming Shen; Zexi Tan ...
 
 
PepBDB: a comprehensive structural database of biological peptide'protein interactions 
 
Zeyu Wen; Jiahua He; Huanyu Tao; Sheng-You Huang
 
 
 
BIOIMAGE INFORMATICS
 
 
 
SPUTNIK: an R package for filtering of spatially related peaks in mass spectrometry imaging data border= 
 
Paolo Inglese; Gonçalo Correia; Zoltan Takats; Jeremy K Nicholson; Robert C Glen
 
 
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