Content-Type: text/html; Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Biology Methods and Protocols is now included in the Emerging Sources Citation Index, making it the perfect home for your research.
Read our Instructions to Authors page and submit your research today
 
 
 
 
 
 
Bioinformatics  
Volume 37 Issue 22
 
15 November 2021
 
button-issue.png
 
 
ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
TIGER: inferring DNA replication timing from whole-genome sequence data 
 
Amnon Koren; Dashiell J Massey; Alexa N Bracci
 
 
Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs border= 
 
Joachim Wolff; Rolf Backofen; Björn Grüning
 
 
Methylation-eQTL analysis in cancer research 
 
Yusha Liu; Keith A Baggerly; Elias Orouji; Ganiraju Manyam; Huiqin Chen ...
 
 
Detecting copy number alterations in RNA-Seq using SuperFreq 
 
Christoffer Flensburg; Alicia Oshlack; Ian J Majewski
 
 
 
SEQUENCE ANALYSIS
 
 
 
Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family border= 
 
Chen Wang; Daniel M Konecki; David C Marciano ; Harikumar Govindarajan; Amanda M Williams ...
 
 
 
Humanization of antibodies using a machine learning approach on large-scale repertoire data 
 
Claire Marks; Alissa M Hummer; Mark Chin; Charlotte M Deane
 
 
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index border= 
 
Fatemeh Almodaresi; Mohsen Zakeri; Rob Patro
 
 
 
PHYLOGENETICS
 
 
 
Exploring parallel MPI fault tolerance mechanisms for phylogenetic inference with RAxML-NG border= 
 
Lukas Hübner; Alexey M Kozlov; Demian Hespe ; Peter Sanders; Alexandros Stamatakis
 
 
Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model 
 
Alexey Markin; Oliver Eulenstein
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
SAMF: a self-adaptive protein modeling framework 
 
Wenze Ding; Qijiang Xu; Siyuan Liu; Tong Wang; Bin Shao ...
 
 
 
Improving sequence-based modeling of protein families using secondary-structure quality assessment border= 
 
Cyril Malbranke; David Bikard; Simona Cocco ; Rémi Monasson
 
 
 
GENE EXPRESSION
 
 
 
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data 
 
Chunman Zuo; Hao Dai; Luonan Chen
 
 
Interfacing Seurat with the R tidy universe border= 
 
Stefano Mangiola; Maria A Doyle; Anthony T Papenfuss
 
 
Peel learning for pathway-related outcome prediction 
 
Yuantong Li; Fei Wang; Mengying Yan; Edward Cantu III ; Fan Nils Yang ...
 
 
scDetect: a rank-based ensemble learning algorithm for cell type identification of single-cell RNA sequencing in cancer 
 
Yifei Shen; Qinjie Chu; Michael P Timko; Longjiang Fan
 
 
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data border= 
 
Jared Brown; Zijian Ni; Chitrasen Mohanty ; Rhonda Bacher; Christina Kendziorski
 
 
Bayesian modeling of spatial molecular profiling data via Gaussian process 
 
Qiwei Li; Minzhe Zhang; Yang Xie; Guanghua Xiao
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
A framework to decipher the genetic architecture of combinations of complex diseases: applications in cardiovascular medicine 
 
Liangying Yin; Carlos Kwan-Long Chau; Yu-Ping Lin; Shitao Rao ; Yong Xiang ...
 
 
Fast numerical optimization for genome sequencing data in population biobanks 
 
Ruilin Li; Christopher Chang; Yosuke Tanigawa; Balasubramanian Narasimhan ; Trevor Hastie ...
 
 
 
SYSTEMS BIOLOGY
 
 
 
Bistability in cell signalling and its significance in identifying potential drug-targets 
 
Suvankar Halder; Sumana Ghosh; Joydev Chattopadhyay; Samrat Chatterjee
 
 
CyAnno: a semi-automated approach for cell type annotation of mass cytometry datasets 
 
Abhinav Kaushik; Diane Dunham; Ziyuan He; Monali Manohar ; Manisha Desai ...
 
 
BERTMHC: improved MHC'peptide class II interaction prediction with transformer and multiple instance learning border= 
 
Jun Cheng; Kaïdre Bendjama; Karola Rittner ; Brandon Malone
 
 
MecCog: a knowledge representation framework for genetic disease mechanism 
 
Kunal Kundu; Lindley Darden; John Moult
 
 
 
DATA AND TEXT MINING
 
 
 
Super LeArner Prediction of NAb Panels (SLAPNAP): a containerized tool for predicting combination monoclonal broadly neutralizing antibody sensitivity 
 
Brian D Williamson; Craig A Magaret; Peter B Gilbert; Sohail Nizam ; Courtney Simmons ...
 
 
AutoCCS: automated collision cross-section calculation software for ion mobility spectrometry'mass spectrometry border= 
 
Joon-Yong Lee; Aivett Bilbao; Christopher R Conant ; Kent J Bloodsworth; Daniel J Orton ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
efam: an expanded, metaproteome-supported HMM profile database of viral protein families border= 
 
Ahmed A Zayed; Dominik Lücking; Mohamed Mohssen ; Dylan Cronin; Ben Bolduc ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
MorphoScript: a dedicated analysis to assess the morphology and contractile structures of cardiomyocytes derived from stem cells 
 
Tess Homan; Hélène Delanoë-Ayari; Albano C Meli; Olivier Cazorla ; Csilla Gergely ...
 
 
A convolutional neural network for common coordinate registration of high-resolution histology images border= 
 
Aidan C Daly; Krzysztof J Geras; Richard Bonneau
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools border= 
 
José Marcos Moreno-Cabrera; Jesús del Valle; Elisabeth Castellanos ; Lidia Feliubadaló; Marta Pineda ...
 
 
DetectIS: a pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data border= 
 
Luigi Grassi; Claire Harris; Jie Zhu ; Colin Hardman; Diane Hatton
 
 
Bathometer: lightning fast depth-of-reads query border= 
 
U Stenzel; S Horn
 
 
Semi-supervised peak calling with SPAN and JBR genome browser border= 
 
Oleg Shpynov; Aleksei Dievskii; Roman Chernyatchik; Petr Tsurinov ; Maxim N Artyomov
 
 
MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets 
 
Cerag Oguztuzun; Pelin Yasar; Kerim Yavuz; Mesut Muyan ; Tolga Can
 
 
UMI4Cats: an R package to analyze chromatin contact profiles obtained by UMI-4C border= 
 
Mireia Ramos-Rodríguez; Marc Subirana-Granés; Lorenzo Pasquali
 
 
LevioSAM: fast lift-over of variant-aware reference alignments border= 
 
Taher Mun; Nae-Chyun Chen; Ben Langmead
 
 
 
SEQUENCE ANALYSIS
 
 
 
NeoFox: annotating neoantigen candidates with neoantigen features border= 
 
Franziska Lang; Pablo Riesgo-Ferreiro; Martin Löwer; Ugur Sahin ; Barbara Schrörs
 
 
Sparse allele vectors and the savvy software suite 
 
Jonathon LeFaive; Albert V Smith; Hyun Min Kang; Gonçalo Abecasis
 
 
cfDNApipe: a comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data border= 
 
Wei Zhang; Lei Wei; Jiaqi Huang ; Bixi Zhong; Jiaqi Li ...
 
 
ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy border= 
 
Marco A Tangaro; Giuseppe Defazio; Bruno Fosso ; Vito Flavio Licciulli; Giorgio Grillo ...
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
DeepChargePredictor: a web server for predicting QM-based atomic charges via state-of-the-art machine-learning algorithms 
 
Jike Wang; Huiyong Sun; Jiawen Chen; Dejun Jiang ; Zhe Wang ...
 
 
3DBionotes COVID-19 edition border= 
 
Jose Ramon Macias; Ruben Sanchez-Garcia; Pablo Conesa; Erney Ramirez-Aportela ; Marta Martinez Gonzalez ...
 
 
Oligator: a flexible interface to draw oligosaccharide structures and generate their theoretical tandem mass spectra 
 
Virginie Lollier; Mathieu Fanuel; David Ropartz; Dominique Tessier ; Hélène Rogniaux
 
 
 
GENE EXPRESSION
 
 
 
CrossTalkeR: analysis and visualization of ligand'receptorne tworks border= 
 
James S Nagai; Nils B Leimkühler; Michael T Schaub; Rebekka K Schneider ; Ivan G Costa
 
 
FBA: feature barcoding analysis for single cell RNA-Seq 
 
Jialei Duan; Gary C Hon
 
 
powerEQTL: an R package and shiny application for sample size and power calculation of bulk tissue and single-cell eQTL analysis border= 
 
Xianjun Dong; Xiaoqi Li; Tzuu-Wang Chang ; Clemens R Scherzer; Scott T Weiss ...
 
 
Jutils: a visualization toolkit for differential alternative splicing events border= 
 
Guangyu Yang; Leslie Cope; Zitong He; Liliana Florea
 
 
 
SYSTEMS BIOLOGY
 
 
 
ChemHub: a knowledgebase of functional chemicals for synthetic biology studies 
 
Mengying Han; Dachuan Zhang; Shaozhen Ding; Yu Tian ; Xingxiang Cheng ...
 
 
Funm6AViewer: a web server and R package for functional analysis of context-specific m6A RNA methylation 
 
Song-Yao Zhang; Shao-Wu Zhang; Yujiao Tang; Xiao-Nan Fan ; Jia Meng
 
 
PaIntDB: network-based omics integration and visualization using protein'protein interactions in Pseudomonas aeruginosa 
 
Javier J Castillo-Arnemann; Olga Solodova; Bhavjinder K Dhillon; Robert E W Hancock
 
 
EnMCB: an R/bioconductor package for predicting disease progression based on methylation correlated blocks using ensemble models 
 
Xin Yu; De-Xin Kong
 
 
 
DATA AND TEXT MINING
 
 
 
SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities border= 
 
Marie Macnee; Eduardo Pérez-Palma; Sarah Schumacher-Bass ; Jarrod Dalton; Costin Leu ...
 
 
 
DATABASE AND ONTOLOGIES
 
 
 
Tfcancer: a manually curated database of transcription factors associated with human cancers 
 
Qingqing Huang; Zhengtang Tan; Yanjing Li; Wenzhu Wang ; Mei Lang ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
HEAL: an automated deep learning framework for cancer histopathology image analysis 
 
Yanan Wang; Nicolas Coudray; Yun Zhao; Fuyi Li ; Changyuan Hu ...
 
 
 
ERRATA
 
 
 
Erratum to: Assessing heterogeneity in spatial data using the HTA index with applications to spatial transcriptomics and imaging border= 
 
Alona Levy-Jurgenson; Xavier Tekpli; Zohar Yakhini
 
 
On the stability of log-rank test under labeling errors border= 
 
Ben Galili; Anat Samohi; Zohar Yakhini
 
 
 
CORRIGENDUM
 
 
 
CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome border= 
 
Mark F Rogers; Tom R Gaunt; Colin Campbell
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
Oxford University Press
 
 
                                 



This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_704239804.1637892495292--