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Volume 40 Issue 9
September 2024
AutoPeptideML: a study on how to build more trustworthy peptide bioactivity predictors
Raúl Fernández-Díaz
,
Rodrigo Cossio-Pérez
,
Clement Agoni
,
Hoang Thanh Lam
,
Vanessa Lopez
...
RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation
Xiaoyi Liu
,
Chengwei Ai
,
Hongpeng Yang
,
Ruihan Dong
,
Jijun Tang
...
Original Paper
Genome analysis
Deep5hmC: predicting genome-wide 5-hydroxymethylcytosine landscape via a multimodal deep learning model
Xin Ma
,
Sai Ritesh Thela
,
Fengdi Zhao
,
Bing Yao
,
Zhexing Wen
...
MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing
Antoine Passemiers
,
Stefania Tuveri
,
Dhanya Sudhakaran
,
Tatjana Jatsenko
,
Tina Laga
...
Sequence analysis
Are genomic language models all you need? Exploring genomic language models on protein downstream tasks
Sam Boshar
,
Evan Trop
,
Bernardo P de Almeida
,
Liviu Copoiu
,
Thomas Pierrot
SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes
William Boulton
,
Fatma Rabia Fidan
,
Hubert Denise
,
Nicola De Maio
,
Nick Goldman
SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein'protein complexes
Prawin Rimal
,
Shailesh Kumar Panday
,
Wang Xu
,
Yunhui Peng
,
Emil Alexov
CSV-Filter: a deep learning-based comprehensive structural variant filtering method for both short and long reads
Zeyu Xia
,
Weiming Xiang
,
Qingzhe Wang
,
Xingze Li
,
Yilin Li
...
Structural bioinformatics
NeoaPred: a deep-learning framework for predicting immunogenic neoantigen based on surface and structural features of peptide'human leukocyte antigen complexes
Dawei Jiang
,
Binbin Xi
,
Wenchong Tan
,
Zixi Chen
,
Jinfen Wei
...
Gene expression
scDiffusion: conditional generation of high-quality single-cell data using diffusion model
Erpai Luo
,
Minsheng Hao
,
Lei Wei
,
Xuegong Zhang
Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data
Valérie Marot-Lassauzaie
,
Sergi Beneyto-Calabuig
,
Benedikt Obermayer
,
Lars Velten
,
Dieter Beule
...
Guide assignment in single-cell CRISPR screens using crispat
Jana M Braunger
,
Britta Velten
A distribution-free and analytic method for power and sample size calculation in single-cell differential expression
Chih-Yuan Hsu
,
Qi Liu
,
Yu Shyr
SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric
Yue Lyu
,
Steven H Lin
,
Hao Wu
,
Ziyi Li
Scywalker: scalable end-to-end data analysis workflow for long-read single-cell transcriptome sequencing
Peter De Rijk
,
Tijs Watzeels
,
Fahri Küçükali
,
Jasper Van Dongen
,
Júlia Faura
...
Uncertainty quantification in high-dimensional linear models incorporating graphical structures with applications to gene set analysis
Xiangyong Tan
,
Xiao Zhang
,
Yuehua Cui
,
Xu Liu
Systems biology
FateNet: an integration of dynamical systems and deep learning for cell fate prediction
Mehrshad Sadria
,
Thomas M Bury
DTI-LM: language model powered drug'target interaction prediction
Khandakar Tanvir Ahmed
,
Md Istiaq Ansari
,
Wei Zhang
Higher-order correction of persistent batch effects in correlation networks
Soel Micheletti
,
Daniel Schlauch
,
John Quackenbush
,
Marouen Ben Guebila
Data and text mining
Multi-Omic Graph Diagnosis (MOGDx): a data integration tool to perform classification tasks for heterogeneous diseases
Barry Ryan
,
Riccardo E Marioni
,
T Ian Simpson
Triangulating evidence in health sciences with Annotated Semantic Queries
Yi Liu
,
Tom R Gaunt
ChatMol: interactive molecular discovery with natural language
Zheni Zeng
,
Bangchen Yin
,
Shipeng Wang
,
Jiarui Liu
,
Cheng Yang
...
GTAM: a molecular pretraining model with geometric triangle awareness
Xiaoyang Hou
,
Tian Zhu
,
Milong Ren
,
Bo Duan
,
Chunming Zhang
...
Feature selection by replicate reproducibility and non-redundancy
Tümay Capraz
,
Wolfgang Huber
STRING-ing together protein complexes: corpus and methods for extracting physical protein interactions from the biomedical literature
Farrokh Mehryary
,
Katerina Nastou
,
Tomoko Ohta
,
Lars Juhl Jensen
,
Sampo Pyysalo
Dynamic category-sensitive hypergraph inferring and homo-heterogeneous neighbor feature learning for drug-related microbe prediction
Ping Xuan
,
Zelong Xu
,
Hui Cui
,
Jing Gu
,
Cheng Liu
...
Databases and ontologies
Biomedical knowledge graph-optimized prompt generation for large language models
Karthik Soman
,
Peter W Rose
,
John H Morris
,
Rabia E Akbas
,
Brett Smith
...
Bioimage informatics
KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs
Dhruv Khatri
,
Shivani A Yadav
,
Chaitanya A Athale
Applications Note
Genome analysis
MEHunter: transformer-based mobile element variant detection from long reads
Tao Jiang
,
Zuji Zhou
,
Zhendong Zhang
,
Shuqi Cao
,
Yadong Wang
...
Sequence analysis
mgikit: demultiplexing toolkit for MGI fastq files
Ziad Al Bkhetan
,
Sen Wang
Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications
Steven B Cannon
,
Hyun-Oh Lee
,
Nathan T Weeks
,
Joel Berendzen
Accurate and efficient protein embedding using multi-teacher distillation learning
Jiayu Shang
,
Cheng Peng
,
Yongxin Ji
,
Jiaojiao Guan
,
Dehan Cai
...
Gene expression
Signature Search Polestar: a comprehensive drug repurposing method evaluation assistant for customized oncogenic signature
Jinbo Zhang
,
Shunling Yuan
,
Wen Cao
,
Xianrui Jiang
,
Cheng Yang
...
Bin2cell reconstructs cells from high resolution Visium HD data
Krzysztof PolaÅ"ski
,
Raquel Bartolomé-Casado
,
Ioannis Sarropoulos
,
Chuan Xu
,
Nick England
...
Genetics and population analysis
CELEBRIMBOR: core and accessory genes from metagenomes
Joel Hellewell
,
Samuel T Horsfield
,
Johanna von Wachsmann
,
Tatiana A Gurbich
,
Robert D Finn
...
Systems biology
sparsesurv
: a Python package for fitting sparse survival models via knowledge distillation
David Wissel
,
Nikita Janakarajan
,
Julius Schulte
,
Daniel Rowson
,
Xintian Yuan
...
SCMeTA: a pipeline for single-cell metabolic analysis data processing
Xingyu Pan
,
Siyuan Pan
,
Murong Du
,
Jinlei Yang
,
Huan Yao
...
Eliater
: a Python package for estimating outcomes of perturbations in biomolecular networks
Sara Mohammad-Taheri
,
Pruthvi Prakash Navada
,
Charles Tapley Hoyt
,
Jeremy Zucker
,
Karen Sachs
...
Structural bioinformatics
bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties
Jose Gavalda-Garcia
,
Adrián Díaz
,
Wim Vranken
Data and text mining
BenchStab: a tool for automated querying of web-based stability predictors
Jan Velecký
,
Matej Berezný
,
Milos Musil
,
Jiri Damborsky
,
David Bednar
...
Databases and ontologies
RCPedia: a global resource for studying and exploring retrocopies in diverse species
Helena B Conceição
,
Rafael L V Mercuri
,
Matheus P M de Castro
,
Daniel T Ohara
,
Gabriela D A Guardia
...
Bioimage informatics
SpatialOne: end-to-end analysis of visium data at scale
Mena Kamel
,
Amrut Sarangi
,
Pavel Senin
,
Sergio Villordo
,
Mathew Sunaal
...
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