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Bioinformatics  
Volume 37 Issue 20
 
15 October 2021
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
Determining optical mapping errors by simulations 
 
Michal Va┼íinek; Marek B─Ťhálek; Petr Gajdo┼í; Regina Fillerová; Eva Kriegová
 
 
Comparison of structural variants detected by optical mapping with long-read next-generation sequencing 
 
Jakub Savara; Tomá┼í Novosád; Petr Gajdo┼í; Eva Kriegová
 
 
DeepEBV: a deep learning model to predict Epstein'Barr virus (EBV) integration sites 
 
Jiuxing Liang; Zifeng Cui; Canbiao Wu; Yao Yu ; Rui Tian ...
 
 
ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs 
 
Abhijit Chakraborty; Ferhat Ay; Ramana V Davuluri
 
 
 
SEQUENCE ANALYSIS
 
 
 
SeRenDIP-CE: sequence-based interface prediction for conformational epitopes border= 
 
Qingzhen Hou; Bas Stringer; Katharina Waury; Henriette Capel ; Reza Haydarlou ...
 
 
 
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction border= 
 
QHwan Kim; Joon-Hyuk Ko; Sunghoon Kim ; Nojun Park; Wonho Jhe
 
 
CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks 
 
Jianwei Hong; Ruitian Gao; Yang Yang
 
 
Rapid T-cell receptor interaction grouping with ting 
 
Felix Mölder; Ulrik Stervbo; Lucie Loyal; Petra Bacher ; Nina Babel ...
 
 
Clustering FunFams using sequence embeddings improves EC purity border= 
 
Maria Littmann; Nicola Bordin; Michael Heinzinger; Konstantin Schütze ; Christian Dallago ...
 
 
eCOMPASS: evaluative comparison of multiple protein alignments by statistical score border= 
 
Andrew F Neuwald; Bryan D Kolaczkowski; Stephen F Altschul
 
 
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning 
 
Jaspreet Singh; Thomas Litfin; Kuldip Paliwal; Jaswinder Singh ; Anil Kumar Hanumanthappa ...
 
 
In silico prediction of in vitro protein liquid'liquid phase separation experiments outcomes with multi-head neural attention 
 
Daniele Raimondi; Gabriele Orlando; Emiel Michiels; Donya Pakravan ; Anna Bratek-Skicki ...
 
 
Full-length de novo protein structure determination from cryo-EM maps using deep learning 
 
Jiahua He; Sheng-You Huang
 
 
ProteoMill: efficient network-based functional analysis portal for proteomics data border= 
 
Martin Rydén; Martin Englund; Neserin Ali
 
 
RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis 
 
Tongchuan Zhang; Jaswinder Singh; Thomas Litfin; Jian Zhan ; Kuldip Paliwal ...
 
 
 
GENE EXPRESSION
 
 
 
scConnect: a method for exploratory analysis of cell'cell communication based on single-cell RNA-sequencing data border= 
 
Jon E T Jakobsson; Ola Spjuth; Malin C Lagerström
 
 
VeTra: a tool for trajectory inference based on RNA velocity border= 
 
Guangzheng Weng; Junil Kim; Kyoung Jae Won
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GEM: scalable and flexible gene'environment interaction analysis in millions of samples border= 
 
Kenneth E Westerman; Duy T Pham; Liang Hong ; Ye Chen; Magdalena Sevilla-González ...
 
 
Assessment of significance of conditionally independent GWAS signals 
 
Sahar Ghasemi; Alexander Teumer; Matthias Wuttke; Tim Becker
 
 
 
SYSTEMS BIOLOGY
 
 
 
Capturing dynamic relevance in Boolean networks using graph theoretical measures border= 
 
Felix M Weidner; Julian D Schwab; Silke D Werle ; Nensi Ikonomi; Ludwig Lausser ...
 
 
Evaluation of categorical matrix completion algorithms: toward improved active learning for drug discovery border= 
 
Huangqingbo Sun; Robert F Murphy
 
 
Multimodal regularized linear models with flux balance analysis for mechanistic integration of omics data 
 
Giuseppe Magazzù; Guido Zampieri; Claudio Angione
 
 
Inferring the experimental design for accurate gene regulatory network inference border= 
 
Deniz Seçilmi┼č; Thomas Hillerton; Sven Nelander ; Erik L L Sonnhammer
 
 
NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate'product pairs border= 
 
Jasmin Hafner; Vassily Hatzimanikatis
 
 
 
DATA AND TEXT MINING
 
 
 
MANIEA: a microbial association network inference method based on improved Eclat association rule mining algorithm 
 
Maidi Liu; Yanqing Ye; Jiang Jiang; Kewei Yang
 
 
Evaluating disease similarity based on gene network reconstruction and representation 
 
Yang Li; Wang Keqi; Guohua Wang
 
 
Omics community detection using multi-resolution clustering border= 
 
Ali Rahnavard; Suvo Chatterjee; Bahar Sayoldin; Keith A Crandall ; Fasil Tekola-Ayele ...
 
 
Target'Decoy MineR for determining the biological relevance of variables in noisy datasets 
 
Cesaré Ovando-Vázquez; Daniel Cázarez-García; Robert Winkler
 
 
TimiRGeN: R/Bioconductor package for time series microRNA'mRNA integration and analysis border= 
 
K Patel; S Chandrasegaran; I M Clark ; C J Proctor; D A Young ...
 
 
A combined recall and rank framework with online negative sampling for Chinese procedure terminology normalization 
 
Ming Liang; Kui Xue; Qi Ye; Tong Ruan
 
 
Autoencoder-based drug'target interaction prediction by preserving the consistency of chemical properties and functions of drugs 
 
Chang Sun; Yangkun Cao; Jin-Mao Wei; Jian Liu
 
 
Family Rank: a graphical domain knowledge informed feature ranking algorithm 
 
Michelle Saul; Valentin Dinu
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Towards an automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation 
 
Dominik Stallmann; Jan P Göpfert; Julian Schmitz; Alexander Grünberger ; Barbara Hammer
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
Customized de novo mutation detection for any variant calling pipeline: SynthDNM 
 
Aojie Lian; James Guevara; Kun Xia; Jonathan Sebat
 
 
interacCircos: an R package based on JavaScript libraries for the generation of interactive circos plots 
 
Zhe Cui; Ya Cui; Tianyi Zang; Yadong Wang
 
 
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST border= 
 
Zhemin Zhou; Jane Charlesworth; Mark Achtman
 
 
SKSV: ultrafast structural variation detection from circular consensus sequencing reads 
 
Yadong Liu; Tao Jiang; Junhao Su; Bo Liu ; Tianyi Zang ...
 
 
TieBrush: an efficient method for aggregating and summarizing mapped reads across large datasets 
 
Ales Varabyou; Geo Pertea; Christopher Pockrandt; Mihaela Pertea
 
 
 
SEQUENCE ANALYSIS
 
 
 
DamageProfiler: fast damage pattern calculation for ancient DNA 
 
Judith Neukamm; Alexander Peltzer; Kay Nieselt
 
 
tSFM 1.0: tRNA Structure'Function Mapper 
 
Travis J Lawrence; Fatemeh Hadi-Nezhad; Ivo Grosse; David H Ardell
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python border= 
 
She Zhang; James M Krieger; Yan Zhang ; Cihan Kaya; Burak Kaynak ...
 
 
RNAStructViz: graphical base pairing analysis 
 
Maxie Dion Schmidt; Anna Kirkpatrick; Christine Heitsch
 
 
VisuaLife: library for interactive visualization in rich web applications border= 
 
Justyna D Kry┼Ť; Dominik Gront
 
 
 
GENE EXPRESSION
 
 
 
NeuroCirc: an integrative resource of circular RNA expression in the human brain 
 
Kieran Walsh; Akira Gokool; Hamid Alinejad-Rokny; Irina Voineagu
 
 
COBRAC: a fast implementation of convex biclustering with compression 
 
Haidong Yi; Le Huang; Gal Mishne; Eric C Chi
 
 
Quickomics: exploring omics data in an intuitive, interactive and informative manner 
 
Benbo Gao; Jing Zhu; Soumya Negi; Xinmin Zhang ; Stefka Gyoneva ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
GSpace: an exact coalescence simulator of recombining genomes under isolation by distance 
 
Thimothée Virgoulay; François Rousset; Camille Noûs; Raphaël Leblois
 
 
 
SYSTEMS BIOLOGY
 
 
 
AMICI: high-performance sensitivity analysis for large ordinary differential equation models border= 
 
Fabian Fröhlich; Daniel Weindl; Yannik Schälte ; Dilan Pathirana; ┼ ukasz Paszkowski ...
 
 
mzRAPP: a tool for reliability assessment of data pre-processing in non-targeted metabolomics border= 
 
Yasin El Abiead; Maximilian Milford; Reza M Salek ; Gunda Koellensperger
 
 
TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures 
 
Mengyu Xie; Kyubum Lee; John H Lockhart; Scott D Cukras ; Rodrigo Carvajal ...
 
 
IntAct App: a Cytoscape application for molecular interaction network visualization and analysis border= 
 
Eliot Ragueneau; Anjali Shrivastava; John H Morris ; Noemi del-Toro; Henning Hermjakob ...
 
 
 
DATA AND TEXT MINING
 
 
 
SPDE: a multi-functional software for sequence processing and data extraction 
 
Dong Xu; Zhuchou Lu; Kangming Jin; Wenmin Qiu ; Guirong Qiao ...
 
 
MassExplorer: a computational tool for analyzing desorption electrospray ionization mass spectrometry data 
 
Vishnu Shankar; Robert Tibshirani; Richard N Zare
 
 
GEInter: an R package for robust gene'environment interaction analysis 
 
Mengyun Wu; Xing Qin; Shuangge Ma
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
A decoupled, modular and scriptable architecture for tools to curate data platforms border= 
 
Momo Langenstein; Henning Hermjakob; Manuel Bernal Llinares
 
 
 
BIOIMAGE INFORMATICS
 
 
 
FPM app: an open-source MATLAB application for simple and intuitive Fourier ptychographic reconstruction 
 
Miko┼éaj Rogalski; Piotr Zda┼"kowski; Maciej Trusiak
 
 
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