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Oxford Academic
New issue alert
Volume 40 Issue 2
February 2024
Bioframe: operations on genomic intervals in
Pandas
dataframes
Nezar Abdennur
,
Geoffrey Fudenberg
,
Ilya M Flyamer
,
Aleksandra A Galitsyna
,
Anton Goloborodko
...
Original Papers
Genome analysis
BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies
Giulio Genovese
,
Nicole B Rockweiler
,
Bryan R Gorman
,
Tim B Bigdeli
,
Michelle T Pato
...
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice
Bjarne Daenekas
,
Eilís Pérez
,
Fabio Boniolo
,
Sabina Stefan
,
Salvatore Benfatto
...
Zero is not absence: censoring-based differential abundance analysis for microbiome data
Lap Sum Chan
,
Gen Li
Sequence analysis
A simple refined DNA minimizer operator enables 2-fold faster computation
Chenxu Pan
,
Knut Reinert
cloudrna
SP
Ades
: isoform assembly using bulk barcoded RNA sequencing data
Dmitry Meleshko
,
Andrey D Prjbelski
,
Mikhail Raiko
,
Alexandru I Tomescu
,
Hagen Tilgner
...
Using explainable machine learning to uncover the kinase'substrate interaction landscape
Zhongliang Zhou
,
Wayland Yeung
,
Saber Soleymani
,
Nathan Gravel
,
Mariah Salcedo
...
YACHT
: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample
David Koslicki
,
Stephen White
,
Chunyu Ma
,
Alexei Novikov
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction
Kexin Shi
,
Yuanpeng Xiong
,
Yu Wang
,
Yifan Deng
,
Wenjia Wang
...
Protein language models meet reduced amino acid alphabets
Ioan Ieremie
,
Rob M Ewing
,
Mahesan Niranjan
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection
Chenglin Yin
,
Ruheng Wang
,
Jianbo Qiao
,
Hua Shi
,
Hongliang Duan
...
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning
Jun Wang
,
Marc Horlacher
,
Lixin Cheng
,
Ole Winther
Highly efficient clustering of long-read transcriptomic data with GeLuster
Junchi Ma
,
Xiaoyu Zhao
,
Enfeng Qi
,
Renmin Han
,
Ting Yu
...
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
Anna Sintsova
,
Hans-Joachim Ruscheweyh
,
Christopher M Field
,
Lilith Feer
,
Bidong D Nguyen
...
T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition
Xiaoyu Guan
,
Wei Shao
,
Daoqiang Zhang
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides
Ding Wang
,
Junru Jin
,
Zhongshen Li
,
Yu Wang
,
Mushuang Fan
...
Phylogenetics
Many-core algorithms for high-dimensional gradients on phylogenetic trees
Karthik Gangavarapu
,
Xiang Ji
,
Guy Baele
,
Mathieu Fourment
,
Philippe Lemey
...
Statistical framework to determine indel-length distribution
Elya Wygoda
,
Gil Loewenthal
,
Asher Moshe
,
Michael Alburquerque
,
Itay Mayrose
...
Structural bioinformatics
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework
Gabriel Loyer
,
Vladimir Reinharz
Multi-indicator comparative evaluation for deep learning-based protein sequence design methods
Jinyu Yu
,
Junxi Mu
,
Ting Wei
,
Hai-Feng Chen
PERFUMES: pipeline to extract RNA functional motifs and exposed structures
Arnaud Chol
,
Roman Sarrazin-Gendron
,
Éric Lécuyer
,
Mathieu Blanchette
,
Jérôme Waldispühl
PMIpred: a physics-informed web server for quantitative protein'membrane interaction prediction
Niek van Hilten
,
Nino Verwei
,
Jeroen Methorst
,
Carsten Nase
,
Andrius Bernatavicius
...
RNA threading with secondary structure and sequence profile
Zongyang Du
,
Zhenling Peng
,
Jianyi Yang
Dynamic correlations: exact and approximate methods for mutual information
Kemal DemirtaÅŸ
,
Burak Erman
,
Türkan HaliloÄŸlu
Geometry-complete perceptron networks for 3D molecular graphs
Alex Morehead
,
Jianlin Cheng
Gene expression
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data
Mikaela Koutrouli
,
Katerina Nastou
,
Pau Piera Líndez
,
Robbin Bouwmeester
,
Simon Rasmussen
...
DESpace
: spatially variable gene detection via differential expression testing of spatial clusters
Peiying Cai
,
Mark D Robinson
,
Simone Tiberi
scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution
Zeyu Chen
,
Yuxin Miao
,
Zhiyuan Tan
,
Qifan Hu
,
Yanhong Wu
...
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data
Chih-Yuan Hsu
,
Chia-Jung Chang
,
Qi Liu
,
Yu Shyr
Deep centroid: a general deep cascade classifier for biomedical omics data classification
Kuan Xie
,
Yuying Hou
,
Xionghui Zhou
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data
Xiao Wang
,
Ziyi Chai
,
Shaohua Li
,
Yan Liu
,
Chen Li
...
AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification
Xiaoshu Zhu
,
Shuang Meng
,
Gaoshi Li
,
Jianxin Wang
,
Xiaoqing Peng
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data
Juanru Guo
,
Wenjin Zhang
,
Xuhua Chen
,
Allen Yen
,
Lucy Chen
...
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks
Yuzhen Mao
,
Yen-Yi Lin
,
Nelson K Y Wong
,
Stanislav Volik
,
Funda Sar
...
scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision
Jue Yang
,
Weiwen Wang
,
Xiwen Zhang
Genetics and population analysis
MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems
Yue Zhuo
,
Heng Du
,
ChenGuang Diao
,
WeiNing Li
,
Lei Zhou
...
The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population
Hagai Levi
,
Ran Elkon
,
Ron Shamir
2dGBH: Two-dimensional group Benjamini'Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data
Lu Yang
,
Pei Wang
,
Jun Chen
High-dimensional quantile mediation analysis with application to a birth cohort study of mother'newborn pairs
Haixiang Zhang
,
Xiumei Hong
,
Yinan Zheng
,
Lifang Hou
,
Cheng Zheng
...
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states
Yongtao Guan
,
Daniel Levy
Systems biology
DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion
Momoko Hamano
,
Toru Nakamura
,
Ryoku Ito
,
Yuki Shimada
,
Michio Iwata
...
Pitfalls of machine learning models for protein'protein interaction networks
Loïc Lannelongue
,
Michael Inouye
Expanding the coverage of spatial proteomics: a machine learning approach
Huangqingbo Sun
,
Jiayi Li
,
Robert F Murphy
Data and text mining
Multi-scale topology and position feature learning and relationship-aware graph reasoning for prediction of drug-related microbes
Ping Xuan
,
Jing Gu
,
Hui Cui
,
Shuai Wang
,
Nakaguchi Toshiya
...
Interpreting protein abundance in
Saccharomyces cerevisiae
through relational learning
Daniel Brunnsåker
,
Filip Kronström
,
Ievgeniia A Tiukova
,
Ross D King
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information
Qiao Jin
,
Yifan Yang
,
Qingyu Chen
,
Zhiyong Lu
Bioimage informatics
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties
Diogo A C Narciso
,
Ana Pereira
,
Nuno O Dias
,
Manuel Monteiro
,
Luis F Melo
...
BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images
Xinyuan Huang
,
Xiujuan Gao
,
Ling Fu
Applications Note
Genome analysis
vcfpp: a C++ API for rapid processing of the variant call format
Zilong Li
PanEffect: a pan-genome visualization tool for variant effects in maize
Carson M Andorf
,
Olivia C Haley
,
Rita K Hayford
,
John L Portwood, II
,
Stephen Harding
...
NFTest: automated testing of Nextflow pipelines
Yash Patel
,
Chenghao Zhu
,
Takafumi N Yamaguchi
,
Yuan Zhe Bugh
,
Mao Tian
...
PipeVal: light-weight extensible tool for file validation
Yash Patel
,
Arpi Beshlikyan
,
Madison Jordan
,
Gina Kim
,
Aaron Holmes
...
Sequence analysis
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
Fatih KaraoÄŸlanoÄŸlu
,
Baraa Orabi
,
Ryan Flannigan
,
Cedric Chauve
,
Faraz Hach
GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function
Danielle Miller
,
Ofir Arias
,
David Burstein
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing
James M Holt
,
Christopher T Saunders
,
William J Rowell
,
Zev Kronenberg
,
Aaron M Wenger
...
pycofitness'Evaluating the fitness landscape of RNA and protein sequences
Fabrizio Pucci
,
Mehari B Zerihun
,
Marianne Rooman
,
Alexander Schug
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs
Philippe Charron
,
Mingsong Kang
Gene expression
Scbean: a python library for single-cell multi-omics data analysis
Haohui Zhang
,
Yuwei Wang
,
Bin Lian
,
Yiran Wang
,
Xingyi Li
...
SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks
Diego Mañanes
,
Inés Rivero-García
,
Carlos Relaño
,
Miguel Torres
,
David Sancho
...
Systems biology
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality
Xin Liu
,
Jieni Hu
,
Jie Zheng
Databases and ontologies
PERSEUS:
an interactive and intuitive web-based tool for pedigree visualization
Nicole Pradas
,
Federico Jurado-Ruiz
,
Carles Onielfa
,
Pere Arús
,
Maria José Aranzana
Correction
Correction to: GTExVisualizer: a web platform for supporting ageing studies
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