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Oxford Academic
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Volume 40 Issue 3
March 2024
Review
Genetics and population analysis
Tutorial on survival modeling with applications to omics data
Zhi Zhao
,
John Zobolas
,
Manuela Zucknick
,
Tero Aittokallio
Original Papers
Genome analysis
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment
Zuher Jahshan
,
Leonid Yavits
ARGprofiler'a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
Hannah-Marie Martiny
,
Nikiforos Pyrounakis
,
Thomas N Petersen
,
Oksana Lukjančenko
,
Frank M Aarestrup
...
Ribotin: automated assembly and phasing of rDNA morphs
Mikko Rautiainen
A compressive seeding algorithm in conjunction with reordering-based compression
Fahu Ji
,
Qian Zhou
,
Jue Ruan
,
Zexuan Zhu
,
Xianming Liu
Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection
Erhu Liu
,
Hongqiang Lyu
,
Yuan Liu
,
Laiyi Fu
,
Xiaoliang Cheng
...
Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network
Jakob Woerner
,
Vivek Sriram
,
Yonghyun Nam
,
Anurag Verma
,
Dokyoon Kim
EpiVar Browser: advanced exploration of epigenomics data under controlled access
David R Lougheed
,
Hanshi Liu
,
Katherine A Aracena
,
Romain Grégoire
,
Alain Pacis
...
Sequence analysis
Flexiplex: a versatile demultiplexer and search tool for omics data
Oliver Cheng
,
Min Hao Ling
,
Changqing Wang
,
Shuyi Wu
,
Matthew E Ritchie
...
Exact global alignment using A* with chaining seed heuristic and match pruning
Ragnar Groot Koerkamp
,
Pesho Ivanov
A dual-rule encoding DNA storage system using chaotic mapping to control GC content
Xuncai Zhang
,
Baonan Qi
,
Ying Niu
PySNV for complex intra-host variation detection
Liandong Li
,
Haoyi Fu
,
Wentai Ma
,
Mingkun Li
Insights into the inner workings of transformer models for protein function prediction
Markus Wenzel
,
Erik Grüner
,
Nils Strodthoff
NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data
Michael D Linderman
,
Jacob Wallace
,
Alderik van der Heyde
,
Eliza Wieman
,
Daniel Brey
...
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life
Jose L Figueroa III
,
Eliza Dhungel
,
Madeline Bellanger
,
Cory R Brouwer
,
Richard Allen White III
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences
Hannes Hauswedell
,
Sara Hetzel
,
Simon G Gottlieb
,
Helene Kretzmer
,
Alexander Meissner
...
AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides
Shengli Zhang
,
Ya Zhao
,
Yunyun Liang
Phylogenetics
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation
David Ferreiro
,
Catarina Branco
,
Miguel Arenas
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS
Emese I Végh
,
Katerina Douka
Structural bioinformatics
RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification
Jun Xue
,
Bingyi Wang
,
Hongchao Ji
,
WeiHua Li
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space
Hamza Biyuzan
,
Mohamed-Akram Masrour
,
Lucas Grandmougin
,
Frédéric Payan
,
Dominique Douguet
Optimizing representations for integrative structural modeling using Bayesian model selection
Shreyas Arvindekar
,
Aditi S Pathak
,
Kartik Majila
,
Shruthi Viswanath
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison
Zhengyang Guo
,
Yang Wang
,
Guangshuo Ou
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs
Ashwin Dhakal
,
Rajan Gyawali
,
Liguo Wang
,
Jianlin Cheng
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes
Florian J Gisdon
,
Mariella Zunker
,
Jan Niclas Wolf
,
Kai Prüfer
,
Jörg Ackermann
...
iNGNN-DTI: prediction of drug'target interaction with interpretable nested graph neural network and pretrained molecule models
Yan Sun
,
Yan Yi Li
,
Carson K Leung
,
Pingzhao Hu
AbFlex: designing antibody complementarity determining regions with flexible CDR definition
Woosung Jeon
,
Dongsup Kim
Gene expression
Information-incorporated gene network construction with FDR control
Hao Wang
,
Yumou Qiu
,
Hongqing Guo
,
Yanhai Yin
,
Peng Liu
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework
Xiangxin Zhan
,
Yanbin Yin
,
Han Zhang
Uncertainty-aware single-cell annotation with a hierarchical reject option
Lauren Theunissen
,
Thomas Mortier
,
Yvan Saeys
,
Willem Waegeman
Systems biology
Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence
Jason Y Cain
,
Jacob I Evarts
,
Jessica S Yu
,
Neda Bagheri
Data and text mining
LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies
Melpomeni Kasapi
,
Kexin Xu
,
Timothy M D Ebbels
,
Declan P O'Regan
,
James S Ware
...
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning
J Harry Caufield
,
Harshad Hegde
,
Vincent Emonet
,
Nomi L Harris
,
Marcin P Joachimiak
...
MARS: a motif-based autoregressive model for retrosynthesis prediction
Jiahan Liu
,
Chaochao Yan
,
Yang Yu
,
Chan Lu
,
Junzhou Huang
...
Databases and ontologies
HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies
Milind Misra
,
Jeffy Jeffy
,
Charis Liao
,
Stephanie Pickthorn
,
Kshitij Wagh
...
Applications Note
Genome analysis
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization
Guillermo Dufort y Álvarez
,
Martí Xargay-Ferrer
,
Alba Pagès-Zamora
,
Idoia Ochoa
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification
Jung Kim
,
Ammar S Naqvi
,
Ryan J Corbett
,
Rebecca S Kaufman
,
Zalman Vaksman
...
Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies
William D Lees
,
Swati Saha
,
Gur Yaari
,
Corey T Watson
Sequence analysis
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow
Yiyang Yu
,
Shivani Muthukumar
,
Peter K Koo
Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification
Kristofer Sandås
,
Jacob Lewerentz
,
Edvin Karlsson
,
Linda Karlsson
,
David Sundell
...
Fast and scalable querying of eukaryotic linear motifs with
gget elm
Laura Luebbert
,
Chi Hoang
,
Manjeet Kumar
,
Lior Pachter
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements
Orit Adato
,
Anna Sloutskin
,
Hodaya Komemi
,
Ian Brabb
,
Sascha Duttke
...
Structural bioinformatics
Rapid generation of high-quality structure figures for publication with PyMOL-PUB
Yuting Chen
,
Haoling Zhang
,
Wen Wang
,
Yue Shen
,
Zhi Ping
Gene expression
GPro: generative AI-empowered toolkit for promoter design
Haochen Wang
,
Qixiu Du
,
Ye Wang
,
Hanwen Xu
,
Zheng Wei
...
KaMRaT
: a C++ toolkit for
k
-mer count matrix dimension reduction
Haoliang Xue
,
Mélina Gallopin
,
Camille Marchet
,
Ha N Nguyen
,
Yunfeng Wang
...
vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data
Xingyu Bi
,
Wenbin Ye
,
Xin Cheng
,
Ning Yang
,
Xiaohui Wu
ICELLNET v2: a versatile method for cell'cell communication analysis from human transcriptomic data
Lucile Massenet-Regad
,
Vassili Soumelis
SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments
Chitrasen Mohanty
,
Aman Prasad
,
Lingxin Cheng
,
Lisa M Arkin
,
Bridget E Shields
...
Systems biology
Shu: visualization of high-dimensional biological pathways
Jorge Carrasco Muriel
,
Nicholas Cowie
,
Shannara Taylor Parkins
,
Marjan Mansouvar
,
Teddy Groves
...
Data and text mining
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology
Arik Ermshaus
,
Michael Piechotta
,
Gina Rüter
,
Ulrich Keilholz
,
Ulf Leser
...
imputomics: web server and R package for missing values imputation in metabolomics data
Jarosław Chilimoniuk
,
Krystyna Grzesiak
,
Jakub Kała
,
Dominik Nowakowski
,
Adam Krętowski
...
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution
Chiung-Ting Wu
,
Dongping Du
,
Lulu Chen
,
Rujia Dai
,
Chunyu Liu
...
Bioimage informatics
SST-editing:
in silico
spatial transcriptomic editing at single-cell resolution
Jiqing Wu
,
Viktor H Koelzer
pyM
2
aia: Python interface for mass spectrometry imaging with focus on deep learning
Jonas Cordes
,
Thomas Enzlein
,
Carsten Hopf
,
Ivo Wolf
Correction
Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data
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