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Oxford Academic
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Volume 40 Issue 4
April 2024
Original Paper
Genome analysis
ArCH: improving the performance of clonal hematopoiesis variant calling and interpretation
Irenaeus C C Chan
,
Alex Panchot
,
Evelyn Schmidt
,
Samantha McNulty
,
Brian J Wiley
...
Regional analysis to delineate intrasample heterogeneity with RegionalST
Yue Lyu
,
Chong Wu
,
Wei Sun
,
Ziyi Li
Coding genomes with gapped pattern graph convolutional network
Ruo Han Wang
,
Yen Kaow Ng
,
Xianglilan Zhang
,
Jianping Wang
,
Shuai Cheng Li
Prioritization of oligogenic variant combinations in whole exomes
Barbara Gravel
,
Alexandre Renaux
,
Sofia Papadimitriou
,
Guillaume Smits
,
Ann Nowé
...
Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation
Andrew G Duncan
,
Jennifer A Mitchell
,
Alan M Moses
Sequence analysis
CONSULT-II: accurate taxonomic identification and profiling using locality-sensitive hashing
Ali Osman Berk Şapcı
,
Eleonora Rachtman
,
Siavash Mirarab
scPathoQuant: a tool for efficient alignment and quantification of pathogen sequence reads from 10× single cell sequencing datasets
Leanne S Whitmore
,
Jennifer Tisoncik-Go
,
Michael Gale, Jr
Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra
Zhaohui Zhan
,
Lusheng Wang
MINDG: a drug'target interaction prediction method based on an integrated learning algorithm
Hailong Yang
,
Yue Chen
,
Yun Zuo
,
Zhaohong Deng
,
Xiaoyong Pan
...
TemStaPro: protein thermostability prediction using sequence representations from protein language models
Ieva Pudžiuvelyt-
,
Kliment Olechnovič
,
Egle Godliauskaite
,
Kristupas Sermokas
,
Tomas Urbaitis
...
EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery
Johanna Elena Schmitz
,
Nihit Aggarwal
,
Lukas Laufer
,
Jörn Walter
,
Abdulrahman Salhab
...
Designing efficient randstrobes for sequence similarity analyses
Moein Karami
,
Aryan Soltani Mohammadi
,
Marcel Martin
,
Barış Ekim
,
Wei Shen
...
VirusPredictor: XGBoost-based software to predict virus-related sequences in human data
Guangchen Liu
,
Xun Chen
,
Yihui Luan
,
Dawei Li
Effect of tokenization on transformers for biological sequences
Edo Dotan
,
Gal Jaschek
,
Tal Pupko
,
Yonatan Belinkov
Phylogenetics
MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction
Fang Wang
,
Yibin Wang
,
Xiaofei Zeng
,
Shengcheng Zhang
,
Jiaxin Yu
...
phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data
Divya Sharma
,
Wendy Lou
,
Wei Xu
Structural bioinformatics
Contrastive pre-training and 3D convolution neural network for RNA and small molecule binding affinity prediction
Saisai Sun
,
Lin Gao
Gene expression
HyperTMO: a trusted multi-omics integration framework based on hypergraph convolutional network for patient classification
Haohua Wang
,
Kai Lin
,
Qiang Zhang
,
Jinlong Shi
,
Xinyu Song
...
scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model
Sijing An
,
Jinhui Shi
,
Runyan Liu
,
Yaowen Chen
,
Jing Wang
...
Hi-GeoMVP: a hierarchical geometry-enhanced deep learning model for drug response prediction
Yurui Chen
,
Louxin Zhang
Systems biology
GraphPath: a graph attention model for molecular stratification with interpretability based on the pathway'pathway interaction network
Teng Ma
,
Jianxin Wang
DrugMGR: a deep bioactive molecule binding method to identify compounds targeting proteins
Xiaokun Li
,
Qiang Yang
,
Long Xu
,
Weihe Dong
,
Gongning Luo
...
Clustering single-cell multi-omics data via graph regularized multi-view ensemble learning
Fuqun Chen
,
Guanhua Zou
,
Yongxian Wu
,
Le Ou-Yang
Data and text mining
MolFeSCue: enhancing molecular property prediction in data-limited and imbalanced contexts using few-shot and contrastive learning
Ruochi Zhang
,
Chao Wu
,
Qian Yang
,
Chang Liu
,
Yan Wang
...
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis
Liang Wang
,
Chenyang Hong
,
Jiangning Song
,
Jianhua Yao
MoleMCL: a multi-level contrastive learning framework for molecular pre-training
Xinyi Zhang
,
Yanni Xu
,
Changzhi Jiang
,
Lian Shen
,
Xiangrong Liu
Advancing entity recognition in biomedicine via instruction tuning of large language models
Vipina K Keloth
,
Yan Hu
,
Qianqian Xie
,
Xueqing Peng
,
Yan Wang
...
Causal-ARG: a causality-guided framework for annotating properties of antibiotic resistance genes
Weizhong Zhao
,
Junze Wu
,
Xingpeng Jiang
,
Tingting He
,
Xiaohua Hu
Literature mining discerns latent disease'gene relationships
Priyadarshini Rai
,
Atishay Jain
,
Shivani Kumar
,
Divya Sharma
,
Neha Jha
...
Bioimage informatics
A model-based hierarchical Bayesian approach to Sholl analysis
Erik VonKaenel
,
Alexis Feidler
,
Rebecca Lowery
,
Katherine Andersh
,
Tanzy Love
...
NIEND: neuronal image enhancement through noise disentanglement
Zuo-Han Zhao
,
Lijuan Liu
,
Yufeng Liu
MotGen: a closed-loop bacterial motility control framework using generative adversarial networks
BoGeum Seo
,
DoHee Lee
,
Heungjin Jeon
,
Junhyoung Ha
,
SeungBeum Suh
FPLS-DC: functional partial least squares through distance covariance for imaging genetics
Wenliang Pan
,
Yue Shan
,
Chuang Li
,
Shuai Huang
,
Tengfei Li
...
Applications Note
Genome analysis
POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy
Martin Hölzer
EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data
Sijie Li
,
Yuxi Li
,
Yu Sun
,
Yaru Li
,
Xiaoyang Chen
...
Integrative annotation scores of variants for impact on RNA binding protein activities
Jingqi Duan
,
Audrey P Gasch
,
Sündüz Keleş
GAUSS: a summary-statistics-based R package for accurate estimation of linkage disequilibrium for variants, Gaussian imputation, and TWAS analysis of cosmopolitan cohorts
Donghyung Lee
,
Silviu-Alin Bacanu
Sequence analysis
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling
Rory Munro
,
Satrio Wibowo
,
Alexander Payne
,
Matthew Loose
Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries
Jochen Weile
,
Gabrielle Ferra
,
Gabriel Boyle
,
Sriram Pendyala
,
Clara Amorosi
...
Rapid multiple protein sequence search by parallel and heterogeneous computation
Jiefu Li
,
Ziyuan Wang
,
Xuwei Fan
,
Ruijie Yao
,
Guoqing Zhang
...
Phylogenetics
AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss
Benoit Morel
,
Tom A Williams
,
Alexandros Stamatakis
,
Gergely J Szöll'si
Structural bioinformatics
CLAUDIO: automated structural analysis of cross-linking data
Alexander Röhl
,
Eugen Netz
,
Oliver Kohlbacher
,
Hadeer Elhabashy
Integrating physics in deep learning algorithms: a force field as a PyTorch module
Gabriele Orlando
,
Luis Serrano
,
Joost Schymkowitz
,
Frederic Rousseau
3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures
Victoria Ruiz-Serra
,
Samuel Valentini
,
Sergi Madroñero
,
Alfonso Valencia
,
Eduard Porta-Pardo
rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments
Jonathan L Price
,
Omer Ziv
,
Malte L Pinckert
,
Andrew Lim
,
Eric A Miska
Gene expression
ICARUS v3, a massively scalable web server for single-cell RNA-seq analysis of millions of cells
Andrew Jiang
,
Russell G Snell
,
Klaus Lehnert
shinyExprPortal: a configurable shiny' portal for sharing analysis of molecular expression data
Rafael Henkin
,
Katriona Goldmann
,
Myles Lewis
,
Michael R Barnes
Efficient cytometry analysis with FlowSOM in Python boosts interoperability with other single-cell tools
Artuur Couckuyt
,
Benjamin Rombaut
,
Yvan Saeys
,
Sofie Van Gassen
Genetics and population analysis
Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations
Kangcheng Hou
,
Stephanie Gogarten
,
Joohyun Kim
,
Xing Hua
,
Julie-Alexia Dias
...
Systems biology
PyCoMo: a python package for community metabolic model creation and analysis
Michael Predl
,
Marianne Mießkes
,
Thomas Rattei
,
Jürgen Zanghellini
pyaging
: a Python-based compendium of GPU-optimized aging clocks
Lucas Paulo de Lima Camillo
Data and text mining
GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data
Eric Odle
,
Samuel Kahng
,
Siratee Riewluang
,
Kyoko Kurihara
,
Kevin C Wakeman
longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types
Jonas Hagenberg
,
Monika Budde
,
Teodora Pandeva
,
Ivan Kondofersky
,
Sabrina K Schaupp
...
VarChat: the generative AI assistant for the interpretation of human genomic variations
Federica De Paoli
,
Silvia Berardelli
,
Ivan Limongelli
,
Ettore Rizzo
,
Susanna Zucca
DrivR-Base: a feature extraction toolkit for variant effect prediction model construction
Amy Francis
,
Colin Campbell
,
Tom R Gaunt
Databases and ontologies
PyCoM: a python library for large-scale analysis of residue'residue coevolution data
Philipp Bibik
,
Sabriyeh Alibai
,
Alessandro Pandini
,
Sarath Chandra Dantu
A machine-readable specification for genomics assays
Ali Sina Booeshaghi
,
Xi Chen
,
Lior Pachter
The IDSM mass spectrometry extension: searching mass spectra using SPARQL
Jakub Galgonek
,
Jiří Vondrášek
Bioimage informatics
ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface
Nicolas Ruffini
,
Saleh Altahini
,
Stephan Weißbach
,
Nico Weber
,
Jonas Milkovits
...
Correction
Correction to: Rapid generation of high-quality structure figures for publication with PyMOL-PUB
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