Volume 35, Issue 20, 15 October 2019

REVIEW

SEQUENCE ANALYSIS

EPIP: a novel approach for condition-specific enhancer–promoter interaction prediction

Amlan Talukder, Samaneh Saadat, Xiaoman Li, Haiyan Hu

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3877–3883, https://doi.org/10.1093/bioinformatics/btz641

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DISCOVERY NOTE

SEQUENCE ANALYSIS

Sub-dominant principal components inform new vaccine targets for HIV Gag

Syed Faraz Ahmed, Ahmed A Quadeer, David Morales-Jimenez, Matthew R McKay

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3884–3889, https://doi.org/10.1093/bioinformatics/btz524

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ORIGINAL PAPERS

GENOME ANALYSIS

Multiresolution correction of GC bias and application to identification of copy number alterations

Ho Jang, Hyunju Lee

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3890–3897, https://doi.org/10.1093/bioinformatics/btz174

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Dissecting differential signals in high-throughput data from complex tissues

Ziyi Li, Zhijin Wu, Peng Jin, Hao Wu

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3898–3905, https://doi.org/10.1093/bioinformatics/btz196

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ORE identifies extreme expression effects enriched for rare variants

F Richter, G E Hoffman, K B Manheimer, N Patel, A J Sharp ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3906–3912, https://doi.org/10.1093/bioinformatics/btz202

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ERVcaller: identifying polymorphic endogenous retrovirus and other transposable element insertions using whole-genome sequencing data

Xun Chen, Dawei Li

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3913–3922, https://doi.org/10.1093/bioinformatics/btz205

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Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

Arda Soylev, Thong Minh Le, Hajar Amini, Can Alkan, Fereydoun Hormozdiari

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3923–3930, https://doi.org/10.1093/bioinformatics/btz237

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Stable H3K4me3 is associated with transcription initiation during early embryo development

Xin Huang, Xudong Gao, Wanying Li, Shuai Jiang, Ruijiang Li ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3931–3936, https://doi.org/10.1093/bioinformatics/btz173

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SEQUENCE ANALYSIS

Neural networks with circular filters enable data efficient inference of sequence motifs

Christopher F Blum, Markus Kollmann

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3937–3943, https://doi.org/10.1093/bioinformatics/btz194

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SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing

Dennis C Wylie, Hans A Hofmann, Boris V Zemelman

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3944–3952, https://doi.org/10.1093/bioinformatics/btz198

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FLAS: fast and high-throughput algorithm for PacBio long-read self-correction

Ergude Bao, Fei Xie, Changjin Song, Dandan Song

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3953–3960, https://doi.org/10.1093/bioinformatics/btz206

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PHYLOGENETICS

ASTRAL-MP: scaling ASTRAL to very large datasets using randomization and parallelization

John Yin, Chao Zhang, Siavash Mirarab

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3961–3969, https://doi.org/10.1093/bioinformatics/btz211

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STRUCTURAL BIOINFORMATICS

Protein multiple alignments: sequence-based versus structure-based programs

Mathilde Carpentier, Jacques Chomilier

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3970–3980, https://doi.org/10.1093/bioinformatics/btz236

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SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data

Hao Zhu, Zheng Wang

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3981–3988, https://doi.org/10.1093/bioinformatics/btz181

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Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data

Hongjian Li, Jiangjun Peng, Pavel Sidorov, Yee Leung, Kwong-Sak Leung ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3989–3995, https://doi.org/10.1093/bioinformatics/btz183

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Significance tests for analyzing gene expression data with small sample sizes

Insha Ullah, Sudhir Paul, Zhenjie Hong, You-Gan Wang

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 3996–4003, https://doi.org/10.1093/bioinformatics/btz189

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Developing structural profile matrices for protein secondary structure and solvent accessibility prediction

Zafer Aydin, Nuh Azginoglu, Halil Ibrahim Bilgin, Mete Celik

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4004–4010, https://doi.org/10.1093/bioinformatics/btz238

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GENE EXPRESSION

Probabilistic count matrix factorization for single cell expression data analysis

Ghislain Durif, Laurent Modolo, Jeff E Mold, Sophie Lambert-Lacroix, Franck Picard

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4011–4019, https://doi.org/10.1093/bioinformatics/btz177

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maTE: discovering expressed interactions between microRNAs and their targets

Malik Yousef, Loai Abdallah, Jens Allmer

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4020–4028, https://doi.org/10.1093/bioinformatics/btz204

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Simultaneous clustering of multiview biomedical data using manifold optimization

Yun Yu, Lei-Hong Zhang, Shuqin Zhang

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4029–4037, https://doi.org/10.1093/bioinformatics/btz217

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GENETICS AND POPULATION ANALYSIS

SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics

Lei Song, Aiyi Liu, Jianxin Shi, Molecular Genetics of Schizophrenia Consortium

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4038–4044, https://doi.org/10.1093/bioinformatics/btz176

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Modelling $G×E$ with historical weather information improves genomic prediction in new environments

Jussi Gillberg, Pekka Marttinen, Hiroshi Mamitsuka, Samuel Kaski

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4045–4052, https://doi.org/10.1093/bioinformatics/btz197

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SYSTEMS BIOLOGY

SodaPop: a forward simulation suite for the evolutionary dynamics of asexual populations on protein fitness landscapes

Louis Gauthier, Rémicia Di Franco, Adrian W R Serohijos

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4053–4062, https://doi.org/10.1093/bioinformatics/btz175

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CyTOFmerge: integrating mass cytometry data across multiple panels

Tamim Abdelaal, Thomas Höllt, Vincent van Unen, Boudewijn P F Lelieveldt, Frits Koning ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4063–4071, https://doi.org/10.1093/bioinformatics/btz180

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Simulation-assisted machine learning

Timo M Deist, Andrew Patti, Zhaoqi Wang, David Krane, Taylor Sorenson ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4072–4080, https://doi.org/10.1093/bioinformatics/btz199

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Enhanced Waddington landscape model with cell–cell communication can explain molecular mechanisms of self-organization

Hosein Fooladi, Parsa Moradi, Ali Sharifi-Zarchi, Babak Hosein Khalaj

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4081–4088, https://doi.org/10.1093/bioinformatics/btz201

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CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network

Oriol Senan, Antoni Aguilar-Mogas, Miriam Navarro, Jordi Capellades, Luke Noon ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4089–4097, https://doi.org/10.1093/bioinformatics/btz207

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Differential proteostatic regulation of insoluble and abundant proteins

Reshmi Ramakrishnan, Bert Houben, Frederic Rousseau, Joost Schymkowitz

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4098–4107, https://doi.org/10.1093/bioinformatics/btz214

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DATA AND TEXT MINING

Drug repositioning through integration of prior knowledge and projections of drugs and diseases

Ping Xuan, Yangkun Cao, Tiangang Zhang, Xiao Wang, Shuxiang Pan ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4108–4119, https://doi.org/10.1093/bioinformatics/btz182

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Compressed filesystem for managing large genome collections

Gonzalo Navarro, Víctor Sepúlveda, Mauricio Marín, Senén González

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4120–4128, https://doi.org/10.1093/bioinformatics/btz192

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Health assistant: answering your questions anytime from biomedical literature

Zan-Xia Jin, Bo-Wen Zhang, Fan Fang, Le-Le Zhang, Xu-Cheng Yin

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4129–4139, https://doi.org/10.1093/bioinformatics/btz195

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SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties

Ghazaleh Taherzadeh, Abdollah Dehzangi, Maryam Golchin, Yaoqi Zhou, Matthew P Campbell

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4140–4146, https://doi.org/10.1093/bioinformatics/btz215

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DATABASES AND ONTOLOGIES

BrAPI—an application programming interface for plant breeding applications

Peter Selby, Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4147–4155, https://doi.org/10.1093/bioinformatics/btz190

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APPLICATIONS NOTES

GENOME ANALYSIS

ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline

Muhammad Tahir Ul Qamar, Xitong Zhu, Feng Xing, Ling-Ling Chen

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4156–4158, https://doi.org/10.1093/bioinformatics/btz168

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ScanNeo: identifying indel-derived neoantigens using RNA-Seq data

Ting-You Wang, Li Wang, Sk Kayum Alam, Luke H Hoeppner, Rendong Yang

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4159–4161, https://doi.org/10.1093/bioinformatics/btz193

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PHYLOGENETICS

GToTree: a user-friendly workflow for phylogenomics

Michael D Lee

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4162–4164, https://doi.org/10.1093/bioinformatics/btz188

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STRUCTURAL BIOINFORMATICS

Lemon: a framework for rapidly mining structural information from the Protein Data Bank

Jonathan Fine, Gaurav Chopra

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4165–4167, https://doi.org/10.1093/bioinformatics/btz178

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FoldX 5.0: working with RNA, small molecules and a new graphical interface

Javier Delgado, Leandro G Radusky, Damiano Cianferoni, Luis Serrano

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4168–4169, https://doi.org/10.1093/bioinformatics/btz184

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CABS-dock standalone: a toolbox for flexible protein–peptide docking

Mateusz Kurcinski, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E Badaczewska-Dawid ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4170–4172, https://doi.org/10.1093/bioinformatics/btz185

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GENE EXPRESSION

Holistic optimization of an RNA-seq workflow for multi-threaded environments

Ling-Hong Hung, Wes Lloyd, Radhika Agumbe Sridhar, Saranya Devi Athmalingam Ravishankar, Yuguang Xiong ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4173–4175, https://doi.org/10.1093/bioinformatics/btz169

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Pinetree: a step-wise gene expression simulator with codon-specific translation rates

Benjamin R Jack, Claus O Wilke

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4176–4178, https://doi.org/10.1093/bioinformatics/btz203

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GENETICS AND POPULATION ANALYSIS

PleioNet: a web-based visualization tool for exploring pleiotropy across complex traits

X Raymond Gao, Hua Huang

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4179–4180, https://doi.org/10.1093/bioinformatics/btz179

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ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices

Wen Yao, Fangfang Huang, Xuehai Zhang, Jihua Tang

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4181–4183, https://doi.org/10.1093/bioinformatics/btz186

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PedigreeNet: a web-based pedigree viewer for biological databases

Bremen L Braun, David A Schott, John L Portwood, Carson M Andorf, Taner Z Sen

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4184–4186, https://doi.org/10.1093/bioinformatics/btz208

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SYSTEMS BIOLOGY

CytoBackBone: an algorithm for merging of phenotypic information from different cytometric profiles

Adrien Leite Pereira, Olivier Lambotte, Roger Le Grand, Antonio Cosma, Nicolas Tchitchek

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4187–4189, https://doi.org/10.1093/bioinformatics/btz212

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DATA AND TEXT MINING

GladiaTOX: GLobal Assessment of Dose-IndicAtor in TOXicology

Vincenzo Belcastro, Stephane Cano, Diego Marescotti, Stefano Acali, Carine Poussin ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4190–4192, https://doi.org/10.1093/bioinformatics/btz187

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PgpRules: a decision tree based prediction server for P-glycoprotein substrates and inhibitors

Pei-Hua Wang, Yi-Shu Tu, Yufeng J Tseng

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4193–4195, https://doi.org/10.1093/bioinformatics/btz213

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DATABASES AND ONTOLOGIES

onlineFDR: an R package to control the false discovery rate for growing data repositories

David S Robertson, Jan Wildenhain, Adel Javanmard, Natasha A Karp

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4196–4199, https://doi.org/10.1093/bioinformatics/btz191

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TISIDB: an integrated repository portal for tumor–immune system interactions

Beibei Ru, Ching Ngar Wong, Yin Tong, Jia Yi Zhong, Sophia Shek Wa Zhong ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4200–4202, https://doi.org/10.1093/bioinformatics/btz210

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STRUCTURAL GENOMICS

The TMCrys server for supporting crystallization of transmembrane proteins

Julia K Varga, Gábor E Tusnády

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Pages 4203–4204, https://doi.org/10.1093/bioinformatics/btz108

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CORRIGENDA

relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data

Sébastien Morin, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary S Thompson ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Page 4205, https://doi.org/10.1093/bioinformatics/btz397

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Corrigendum to: A new cis-acting regulatory element driving gene expression in the zebrafish pineal gland

Shahar Alon, Eli Eisenberg, Jasmine Jacob-Hirsch, Gideon Rechavi, Gad Vatine ...

Bioinformatics, Volume 35, Issue 20, 15 October 2019, Page 4206, https://doi.org/10.1093/bioinformatics/btz410

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