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Volume 37 Issue 22
15 November 2021
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
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
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
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
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
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 ...
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
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 ...
efam: an expanded, metaproteome-supported HMM profile database of viral protein families border= 
Ahmed A Zayed; Dominik Lücking; Mohamed Mohssen ; Dylan Cronin; Ben Bolduc ...
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
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
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 ...
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
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
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
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 ...
Tfcancer: a manually curated database of transcription factors associated with human cancers 
Qingqing Huang; Zhengtang Tan; Yanjing Li; Wenzhu Wang ; Mei Lang ...
HEAL: an automated deep learning framework for cancer histopathology image analysis 
Yanan Wang; Nicolas Coudray; Yun Zhao; Fuyi Li ; Changyuan Hu ...
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
CScape-somatic: distinguishing driver and passenger point mutations in the cancer genome border= 
Mark F Rogers; Tom R Gaunt; Colin Campbell
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