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Oxford Academic
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Volume 40 Issue 1
January 2024
Original Paper
Genome analysis
MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification
Huang Xu
,
Tian Wang
,
Yuqi Miao
,
Min Qian
,
Yaning Yang
...
Multiomics-integrated deep language model enables
in silico
genome-wide detection of transcription factor binding site in unexplored biosamples
Zikun Yang
,
Xin Li
,
Lele Sheng
,
Ming Zhu
,
Xun Lan
...
Sequence analysis
HAT:
de novo
variant calling for highly accurate short-read and long-read sequencing data
Jeffrey K Ng
,
Tychele N Turner
MHCSeqNet2'improved peptide-class I MHC binding prediction for alleles with low data
Patiphan Wongklaew
,
Sira Sriswasdi
,
Ekapol Chuangsuwanich
CircSI-SSL: circRNA-binding site identification based on self-supervised learning
Chao Cao
,
Chunyu Wang
,
Shuhong Yang
,
Quan Zou
Seq-InSite: sequence supersedes structure for protein interaction site prediction
SeyedMohsen Hosseini
,
G Brian Golding
,
Lucian Ilie
RPEMHC: improved prediction of MHC'peptide binding affinity by a deep learning approach based on residue'residue pair encoding
Xuejiao Wang
,
Tingfang Wu
,
Yelu Jiang
,
Taoning Chen
,
Deng Pan
...
FMAlign2: a novel fast multiple nucleotide sequence alignment method for ultralong datasets
Pinglu Zhang
,
Huan Liu
,
Yanming Wei
,
Yixiao Zhai
,
Qinzhong Tian
...
Structural bioinformatics
Guiding discovery of protein sequence-structure-function modeling
Azam Hussain
,
Charles L Brooks III
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings
Aditi Shenoy
,
Yogesh Kalakoti
,
Durai Sundar
,
Arne Elofsson
Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone
Lorenzo Pantolini
,
Gabriel Studer
,
Joana Pereira
,
Janani Durairaj
,
Gerardo Tauriello
...
Gene expression
scDMV: a zero'one inflated beta mixture model for DNA methylation variability with scBS-seq data
Yan Zhou
,
Ying Zhang
,
Minjiao Peng
,
Yaru Zhang
,
Chenghao Li
...
MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data
Jackson Barth
,
Yuqiu Yang
,
Guanghua Xiao
,
Xinlei Wang
scMAE: a masked autoencoder for single-cell RNA-seq clustering
Zhaoyu Fang
,
Ruiqing Zheng
,
Min Li
Assembling spatial clustering framework for heterogeneous spatial transcriptomics data with GRAPHDeep
Teng Liu
,
Zhaoyu Fang
,
Xin Li
,
Lining Zhang
,
Dong-Sheng Cao
...
Systems biology
ELISL: early'late integrated synthetic lethality prediction in cancer
Yasin I Tepeli
,
Colm Seale
,
Joana P Gonçalves
Pathway analysis through mutual information
Gustavo S Jeuken
,
Lukas Käll
Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution
Parsa Ghadermazi
,
Siu Hung Joshua Chan
Genetics and population analysis
Clumppling
: cluster matching and permutation program with integer linear programming
Xiran Liu
,
Naama M Kopelman
,
Noah A Rosenberg
selscan 2.0: scanning for sweeps in unphased data
Zachary A Szpiech
Subset scanning for multi-trait analysis using GWAS summary statistics
Rui Cao
,
Evan Olawsky
,
Edward McFowland, III
,
Erin Marcotte
,
Logan Spector
...
Data and text mining
Drug repositioning with adaptive graph convolutional networks
Xinliang Sun
,
Xiao Jia
,
Zhangli Lu
,
Jing Tang
,
Min Li
Mining literature and pathway data to explore the relations of ketamine with neurotransmitters and gut microbiota using a knowledge-graph
Ting Liu
,
K Anton Feenstra
,
Zhisheng Huang
,
Jaap Heringa
Ge
N
Nius
: an ultrafast drug'target interaction inference method based on graph neural networks
Uxía Veleiro
,
Jesús de la Fuente
,
Guillermo Serrano
,
Marija Pizurica
,
Mikel Casals
...
TEFDTA: a transformer encoder and fingerprint representation combined prediction method for bonded and non-bonded drug'target affinities
Zongquan Li
,
Pengxuan Ren
,
Hao Yang
,
Jie Zheng
,
Fang Bai
Text mining for contexts and relationships in cancer genomics literature
Charlotte Collins
,
Simon Baker
,
Jason Brown
,
Huiyuan Zheng
,
Adelyne Chan
...
Bioimage informatics
Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging
Hu Cang
,
Yang Liu
,
Jianhua Xing
ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images
Eric Lee
,
Dongkyu Lee
,
Wayne Fan
,
Andrew Lytle
,
Yuxiang Fu
...
Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis
Chunyue Feng
,
Kokhaur Ong
,
David M Young
,
Bingxian Chen
,
Longjie Li
...
Applications Note
Genome analysis
nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis
Alexander Peltzer
,
Christopher Mohr
,
Kai B Stadermann
,
Matthias Zwick
,
Ramona Schmid
SOHPIE: statistical approach via pseudo-value information and estimation for differential network analysis of microbiome data
Seungjun Ahn
,
Somnath Datta
ViralWasm: a client-side user-friendly web application suite for viral genomics
Daniel Ji
,
Robert Aboukhalil
,
Niema Moshiri
Sequence analysis
A fast machine learning dataloader for epigenetic tracks from BigWig files
Joren Sebastian Retel
,
Andreas Poehlmann
,
Josh Chiou
,
Andreas Steffen
,
Djork-Arné Clevert
Phylogenetics
ReMASTER:
improved phylodynamic simulation for BEAST 2.7
Timothy G Vaughan
Structural bioinformatics
pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells
Colin Brown
,
Anuradha Agarwal
,
Antoni Luque
Gene expression
SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments
Tareian Cazares
,
Richard E Higgs
,
Jibo Wang
,
Hatice Gulcin Ozer
Systems biology
CellularPotts.jl: simulating multiscale cellular models in Julia
Robert W Gregg
,
Panayiotis V Benos
GatekeepR: an R Shiny application for the identification of nodes with high dynamic impact in Boolean networks
Felix M Weidner
,
Nensi Ikonomi
,
Silke D Werle
,
Julian D Schwab
,
Hans A Kestler
SimService: a lightweight library for building simulation services in Python
T J Sego
Data and text mining
Coracle'a machine learning framework to identify bacteria associated with continuous variables
Sebastian Staab
,
Anny Cardénas
,
Raquel S Peixoto
,
Falk Schreiber
,
Christian R Voolstra
FLAMS: Find Lysine Acylations and other Modification Sites
Hannelore Longin
,
Nand Broeckaert
,
Maarten Langen
,
Roshan Hari
,
Anna Kramarska
...
SciDataFlow: a tool for improving the flow of data through science
Vince Buffalo
Fragmentstein'facilitating data reuse for cell-free DNA fragment analysis
Zsolt Balázs
,
Todor Gitchev
,
Ivna Ivanković
,
Michael Krauthammer
ExEmPLAR (Extracting, Exploring, and Embedding Pathways Leading to Actionable Research): a user-friendly interface for knowledge graph mining
Jon-Michael T Beasley
,
Daniel R Korn
,
Nyssa N Tucker
,
Erick T M Alves
,
Eugene N Muratov
...
methyLImp2: faster missing value estimation for DNA methylation data
Anna Plaksienko
,
Pietro Di Lena
,
Christine Nardini
,
Claudia Angelini
Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes
Louise Ryan
,
Colleen Lawless
,
Graham M Hughes
Bioimage informatics
QATS: an ImageJ plugin for the quantification of toroidal nuclei in biological images
Carles Pons
,
Caroline Mauvezin
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