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Bioinformatics  
Volume 37 Issue 17
 
1 September 2021
 
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ORIGINAL PAPERS
 
 
 
 
GENOME ANALYSIS
 
 
 
CCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression 
 
Fan Yang; Kevin J. Gleason; Jiebiao Wang; Jubao Duan ; Xin He ...
 
 
NIBNA: a network-based node importance approach for identifying breast cancer drivers 
 
Mandar S. Chaudhary; Vu V.H. Pham; Thuc D. Le
 
 
ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements 
 
Manisha Panta; Avdesh Mishra; Md Tamjidul Hoque; Joel Atallah
 
 
Hummingbird: efficient performance prediction for executing genomic applications in the cloud 
 
Amir Bahmani; Ziye Xing; Vandhana Krishnan; Utsab Ray ; Frank Mueller ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
A modeling framework for embedding-based predictions for compound'viral protein activity 
 
Raghvendra Mall; Abdurrahman Elbasir; Hossam Almeer; Zeyaul Islam ; Prasanna R. Kolatkar ...
 
 
 
BERT4Bitter: a bidirectional encoder representations from transformers (BERT)-based model for improving the prediction of bitter peptides 
 
Phasit Charoenkwan; Chanin Nantasenamat; Md Mehedi Hasan; Balachandran Manavalan ; Watshara Shoombuatong
 
 
Compact and evenly distributed k-mer binning for genomic sequences border= 
 
Johan Nyström-Persson; Gabriel Keeble-Gagnère; Niamat Zawad
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
Proteo-chemometrics interaction fingerprints of protein'ligand complexes predict binding affinity 
 
Debby D. Wang; Haoran Xie; Hong Yan
 
 
Protein interaction interface region prediction by geometric deep learning 
 
Bowen Dai; Chris Bailey-Kellogg
 
 
Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning 
 
Jaswinder Singh; Kuldip Paliwal; Tongchuan Zhang; Jaspreet Singh ; Thomas Litfin ...
 
 
 
 
 
GENE EXPRESSION
 
 
 
Integrative survival analysis of breast cancer with gene expression and DNA methylation data border= 
 
Isabelle Bichindaritz; Guanghui Liu; Christopher Bartlett
 
 
ASpli: integrative analysis of splicing landscapes through RNA-Seq assays 
 
Estefania Mancini; Andres Rabinovich; Javier Iserte; Marcelo Yanovsky ; Ariel Chernomoretz
 
 
Bipartite graph-based approach for clustering of cell lines by gene expression'drug response associations 
 
Calvin Chi; Yuting Ye; Bin Chen; Haiyan Huang
 
 
Super-delta2: an enhanced differential expression analysis procedure for multi-group comparisons of RNA-seq data 
 
Zihan Cui; Yuhang Liu; Jinfeng Zhang; Xing Qiu
 
 
MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing border= 
 
Zihao Zheng; Aisha M. Mergaert; Irene M. Ong; Miriam A. Shelef ; Michael A. Newton
 
 
sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling border= 
 
Alma Andersson; Joakim Lundeberg
 
 
MUFFIN: multi-scale feature fusion for drug'drug interaction prediction 
 
Yujie Chen; Tengfei Ma; Xixi Yang; Jianmin Wang ; Bosheng Song ...
 
 
Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq border= 
 
Ferhat Alkan; Joana Silva; Eric Pintó Barberà ; William J. Faller
 
 
 
SYSTEMS BIOLOGY
 
 
 
Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy 
 
Abdullah Ça─člar Öksüz; Erman Ayday; U─čur Güdükbay
 
 
Using interpretable deep learning to model cancer dependencies border= 
 
Chih-Hsu Lin; Olivier Lichtarge
 
 
Biphasic regulation of transcriptional surge generated by the gene feedback loop in a two-component system 
 
Wen Liu; Xiang Li; Hong Qi; Yuning Wu ; Jing Qu ...
 
 
COVID-19: disease pathways and gene expression changes predict methylprednisolone can improve outcome in severe cases 
 
Sorin Draghici; Tuan-Minh Nguyen; Larry A. Sonna; Cordelia Ziraldo ; Radu Vanciu ...
 
 
 
DATA AND TEXT MINING
 
 
 
Knowledge enhanced LSTM for coreference resolution on biomedical texts 
 
Yufei Li; Xiaoyong Ma; Xiangyu Zhou; Pengzhen Cheng ; Kai He ...
 
 
KibioR & Kibio: a new architecture for next-generation data querying and sharing in big biology 
 
Régis Ongaro-Carcy; Marie-Pier Scott-Boyer; Adrien Dessemond; François Belleau ; Mickael Leclercq ...
 
 
Conditional canonical correlation estimation based on covariates with random forests 
 
Cansu Alaku┼č; Denis Larocque; Sébastien Jacquemont; Fanny Barlaam ; Charles-Olivier Martin ...
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
DeepViral: prediction of novel virus'host interactions from protein sequences and infectious disease phenotypes border= 
 
Wang Liu-Wei; ┼×enay Kafkas; Jun Chen ; Nicholas J. Dimonaco; Jesper Tegnér ...
 
 
 
BIOIMAGE INFORMATICS
 
 
 
Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM) 
 
Lekha Patel; David Williamson; Dylan M. Owen; Edward A. K. Cohen
 
 
 
APPLICATIONS NOTES
 
 
 
 
GENOME ANALYSIS
 
 
 
DNAModAnnot: a R toolbox for DNA modification filtering and annotation border= 
 
Alexis Hardy; Mélody Matelot; Amandine Touzeau; Christophe Klopp ; Céline Lopez-Roques ...
 
 
RAD: a web application to identify region associated differentially expressed genes 
 
Yixin Guo; Ziwei Xue; Ruihong Yuan; Jingyi Jessica Li ; William A. Pastor ...
 
 
WgLink: reconstructing whole-genome viral haplotypes using L0+L1-regularization 
 
Chen Cao; Matthew Greenberg; Quan Long
 
 
Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations 
 
Sandra Dérozier; Pierre Nicolas; Ulrike Mäder; Cyprien Guérin
 
 
BAGET 2.0: an updated web tool for the effortless retrieval of prokaryotic gene context and sequence border= 
 
Benjamin Hepp; Violette Da Cunha; Florence Lorieux ; Jacques Oberto
 
 
Crypt4GH: a file format standard enabling native access to encrypted data border= 
 
Alexander Senf; Robert Davies; Frédéric Haziza; John Marshall ; Juan Troncoso-Pastoriza ...
 
 
 
SEQUENCE ANALYSIS
 
 
 
rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output 
 
Marek Schwarz; Ji┼Öí Vohradský; Josef Pánek
 
 
MultiNanopolish: refined grouping method for reducing redundant calculations in Nanopolish 
 
Kang Hu; Neng Huang; You Zou; Xingyu Liao ; Jianxin Wang
 
 
 
STRUCTURAL BIOINFORMATICS
 
 
 
CapiPy: python-based GUI-application to assist in protein immobilization 
 
David Roura Padrosa; Valentina Marchini; Francesca Paradisi
 
 
ConPlot: web-based application for the visualization of protein contact maps integrated with other data border= 
 
Filomeno Sánchez Rodríguez; Shahram Mesdaghi; Adam J. Simpkin ; J. Javier Burgos-Mármol; David L. Murphy ...
 
 
BioCommons: a robust java library for RNA structural bioinformatics border= 
 
Tomasz Zok
 
 
 
GENE EXPRESSION
 
 
 
mzRecal: universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants 
 
Rob Marissen; Magnus Palmblad
 
 
Well Plate Maker: a user-friendly randomized block design application to limit batch effects in large-scale biomedical studies 
 
Hélène Borges; Anne-Marie Hesse; Alexandra Kraut; Yohann Couté ; Virginie Brun ...
 
 
 
GENETICS AND POPULATION ANALYSIS
 
 
 
Cox-nnet v2.0: improved neural-network-based survival prediction extended to large-scale EMR data 
 
Di Wang; Zheng Jing; Kevin He; Lana X. Garmire
 
 
 
SYSTEMS BIOLOGY
 
 
 
PrInCE: an R/Bioconductor package for protein'protein interaction network inference from co-fractionation mass spectrometry data 
 
Michael A. Skinnider; Charley Cai; R. Greg Stacey; Leonard J. Foster
 
 
CoRC: the COPASI R Connector 
 
Jonas Förster; Frank T. Bergmann; Jürgen Pahle
 
 
Mercator: a pipeline for multi-method, unsupervised visualization and distance generation border= 
 
Zachary B. Abrams; Caitlin E. Coombes; Suli Li ; Kevin R. Coombes
 
 
Compartor: a toolbox for the automatic generation of moment equations for dynamic compartment populations border= 
 
Tobias Pietzsch; Lorenzo Duso; Christoph Zechner
 
 
M2R: a Python add-on to cobrapy for modifying human genome-scale metabolic reconstruction using the gut microbiota models border= 
 
Ewelina Weglarz-Tomczak; Jakub M. Tomczak; Stanley Brul
 
 
Epidemiological modeling in StochSS Live! border= 
 
Richard Jiang; Bruno Jacob; Matthew Geiger; Sean Matthew ; Bryan Rumsey ...
 
 
 
DATA AND TEXT MINING
 
 
 
mlr3proba: an R package for machine learning in survival analysis border= 
 
Raphael Sonabend; Franz J. Király; Andreas Bender; Bernd Bischl ; Michel Lang
 
 
HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition border= 
 
Leon Weber; Mario Sänger; Jannes Münchmeyer ; Maryam Habibi; Ulf Leser ...
 
 
wiSDOM: a visual and statistical analytics for interrogating microbiome 
 
Shih-Chi Su; James E. Galvin; Shun-Fa Yang; Wen-Hung Chung ; Lun-Ching Chang
 
 
 
DATABASES AND ONTOLOGIES
 
 
 
Viral Host Range database, an online tool for recording, analyzing and disseminating virus'host interactions border= 
 
Quentin Lamy-Besnier; Bryan Brancotte; Brancotte ; Hervé Ménager; Ménager ...
 
 
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