Subject: Bioinformatics Table of Contents for 1 August 2019 ------=_Part_1347332140.1564701555185 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.mcmaster.ca. ------=_Part_1347332140.1564701555185 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Bioinformatics  
Volume 35 Issue 15
 
1 August 2019
 
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DISCOVERY NOTE
 
 
 
 
GENOME ANALYSIS
 
 
 
Deciphering the complexity of human non-coding promoter-proximal transcriptome border= 
 
Sarah N Mapelli; Sara Napoli ; Giuseppina Pisignano; Ramon Garcia-Escudero; Giuseppina M Carbone ...
 
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
DeepIsoFun: a deep domain adaptation approach to predict isoform functions 
 
Dipan Shaw; Hao Chen; Tao Jiang
 
 
 
SEQUENCE ANALYSIS
 
 
 
ModL: exploring and restoring regularity when testing for positive selection 
 
Joseph Mingrone; Edward Susko; Joseph P Bielawski
 
 
Very low-depth whole-genome sequencing in complex trait association studies border=  
 
Arthur Gilly; Lorraine Southam; Daniel Suveges ; Karoline Kuchenbaecker; Rachel Moore ...
 
 
 
PHYLOGENETICS
 
 
 
Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices 
 
Asher Moshe; Tal Pupko
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Insights on protein thermal stability: a graph representation of molecular interactions border= 
 
Mattia Miotto; Pier Paolo Olimpieri ; Lorenzo Di Rienzo; Francesco Ambrosetti; Pietro Corsi ...
 
 
Inter-residue interactions in alpha-helical transmembrane proteins 
 
Eduardo Mayol; Mercedes Campillo; Arnau Cordomí; Mireia Olivella
 
 
Increasing the accuracy of protein loop structure prediction with evolutionary constraints 
 
Claire Marks; Charlotte M Deane
 
 
 
GENE EXPRESSION
 
 
 
DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data 
 
Ziwei Chen; Shaokun An; Xiangqi Bai; Fuzhou Gong; Liang Ma ...
 
 
Optimal Gene Filtering for Single-Cell data (OGFSC)'a gene filtering algorithm for single-cell RNA-seq data 
 
Jie Hao; Wei Cao; Jian Huang; Xin Zou ; Ze-Guang Han
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Gene expression models based on transcription factor binding events confer insight into functional cis -regulatory variants border= 
 
Wenqiang Shi; Oriol Fornes ; Wyeth W Wasserman
 
 
 
SYSTEMS BIOLOGY
 
 
 
Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection 
 
Annika Röhl; Tanguy Riou; Alexander Bockmayr
 
 
Systematic characterization and prediction of post-translational modification cross-talk between proteins 
 
Rongting Huang; Yuanhua Huang; Yubin Guo; Shangwei Ji ; Ming Lu ...
 
 
Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions border=  
 
Meshari Alazmi; Hiroyuki Kuwahara; Othman Soufan ; Lizhong Ding; Xin Gao
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Fully unsupervised symmetry-based mitosis detection in time-lapse cell microscopy 
 
Topaz Gilad; Jose Reyes; Jia-Yun Chen; Galit Lahav ; Tammy Riklin Raviv
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
AStrap: identification of alternative splicing from transcript sequences without a reference genome 
 
Guoli Ji; Wenbin Ye; Yaru Su; Moliang Chen ; Guangzao Huang ...
 
 
atSNP Search: a web resource for statistically evaluating influence of human genetic variation on transcription factor binding 
 
Sunyoung Shin; Rebecca Hudson; Christopher Harrison ; Mark Craven; Sündüz KeleÅŸ
 
 
CNValidator: validating somatic copy-number inference border= 
 
Lucian P Smith; Jon A Yamato; Mary K Kuhner
 
 
 
SEQUENCE ANALYSIS
 
 
 
poreTally: run and publish de novo nanopore assembler benchmarks 
 
Carlos de Lannoy; Judith Risse; Dick de Ridder
 
 
Pathogen'Host Analysis Tool (PHAT): an integrative platform to analyze next-generation sequencing data 
 
Christopher M Gibb; Robert Jackson; Sabah Mohammed; Jinan Fiaidhi ; Ingeborg Zehbe
 
 
Implementation of a Stirling number estimator enables direct calculation of population genetics tests for large sequence datasets 
 
Swaine L Chen
 
 
MapOptics: a light-weight, cross-platform visualization tool for optical mapping alignment 
 
Josephine Burgin; Corentin Molitor; Fady Mohareb
 
 
SPRING: a next-generation compressor for FASTQ data 
 
Shubham Chandak; Kedar Tatwawadi; Idoia Ochoa; Mikel Hernaez ; Tsachy Weissman
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
PconsC4: fast, accurate and hassle-free contact predictions 
 
Mirco Michel; David Menéndez Hurtado; Arne Elofsson
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
CASMAP: detection of statistically significant combinations of SNPs in association mapping border= 
 
Felipe Llinares-López; Laetitia Papaxanthos; Damian Roqueiro; Dean Bodenham; Karsten Borgwardt
 
 
KinVis: a visualization tool to detect cryptic relatedness in genetic datasets 
 
Ehsan Ullah; Michaël Aupetit; Arun Das; Abhishek Patil ; Noora Al Muftah ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators border= 
 
Asa Thibodeau; Dong-Guk Shin
 
 
 
DATA AND TEXT MINING
 
 
 
DNABarcodeCompatibility: an R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments border= 
 
Céline Trébeau ; Jacques Boutet de Monvel; Fabienne Wong Jun Tai; Christine Petit; Raphaël Etournay
 
 
 
LETTERS TO THE EDITOR
 
 
 
 
GENOME ANALYSIS
 
 
 
Comment on: ˜Empirical comparison of web-based antimicrobial peptide prediction tools' 
 
Boris Vishnepolsky; Malak Pirtskhalava
 
 
Response to comments on ˜Empirical comparison of web-based antimicrobial peptide prediction tools' 
 
Musa Nur Gabere; William Stafford Noble
 
 
 
SEQUENCE ANALYSIS
 
 
 
Commonly misunderstood parameters of NCBI BLAST and important considerations for users 
 
Raúl A González-Pech; Timothy G Stephens; Cheong Xin Chan
 
 
Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows 
 
Thomas L Madden; Ben Busby; Jian Ye
 
 
 
DATA AND TEXT MINING
 
 
 
On what to permute in test-based approaches for variable importance measures in Random Forests 
 
Stefano Nembrini
 
 
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