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Bioinformatics  
Volume 40 Issue 8
 
August 2024
 
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Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks border= 
 
Jiahao Gao, Mark Gerstein
 
 
 
 
 
 
 
Cellular proliferation biases clonal lineage tracing and trajectory inference border= 
 
Becca Bonham-Carter, Geoffrey Schiebinger
 
 
 
 
 
 
 
Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies border=  
 
Hanbin Lee, Buhm Han
 
 
 
 
 
 
 
ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities border=  
 
Douyue Li, Zhuochao Min, Jia Guo, Yubin Chen, Wenliang Zhang
 
 
 
Original Paper
 
 
 
 
Genome analysis
 
 
 
 
BertSNR: an interpretable deep learning framework for single-nucleotide resolution identification of transcription factor binding sites based on DNA language model border= 
 
Hanyu Luo, Li Tang, Min Zeng, Rui Yin, Pingjian Ding ...
 
 
 
 
DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts border= 
 
Shai Elkayam, Ido Tziony, Yaron Orenstein
 
 
 
Improved allele-specific single-cell copy number estimation in low-coverage DNA-sequencing border= 
 
Samson Weiner, Bingjun Li, Sheida Nabavi
 
 
 
TWAS-GKF: a novel method for causal gene identification in transcriptome-wide association studies with knockoff inference border= 
 
Anqi Wang, Peixin Tian, Yan Dora Zhang
 
 
 
Sequence analysis
 
 
 
 
TSpred: a robust prediction framework for TCR'epitope interactions using paired chain TCR sequence data border= 
 
Ha Young Kim, Sungsik Kim, Woong-Yang Park, Dongsup Kim
 
 
 
Fine-tuning protein embeddings for functional similarity evaluation border=  
 
Andrew Dickson, Mohammad R K Mofrad
 
 
 
 
Genome-wide detection of somatic mosaicism at short tandem repeats border= 
 
Aarushi Sehgal, Helyaneh Ziaei Jam, Andrew Shen, Melissa Gymrek
 
 
 
ModDotPlot'rapid and interactive visualization of tandem repeats 
 
Alexander P Sweeten, Michael C Schatz, Adam M Phillippy
 
 
 
PGAT-ABPp: harnessing protein language models and graph attention networks for antibacterial peptide identification with remarkable accuracy border= 
 
Yuelei Hao, Xuyang Liu, Haohao Fu, Xueguang Shao, Wensheng Cai
 
 
 
Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences border= 
 
Osamu Gotoh
 
 
 
Advancing mRNA subcellular localization prediction with graph neural network and RNA structure border= 
 
Fuyi Li, Yue Bi, Xudong Guo, Xiaolan Tan, Cong Wang ...
 
 
 
Phylogenetics
 
 
 
 
Estimating the mean in the space of ranked phylogenetic trees border= 
 
Lars Berling, Lena Collienne, Alex Gavryushkin
 
 
 
Structural bioinformatics
 
 
 
 
MuCoCP: a priori chemical knowledge-based multimodal contrastive learning pre-trained neural network for the prediction of cyclic peptide membrane penetration ability 
 
Yunxiang Yu, Mengyun Gu, Hai Guo, Yabo Deng, Danna Chen ...
 
 
 
Benchmarking of AlphaFold2 accuracy self-estimates as indicators of empirical model quality and ranking: a comparison with independent model quality assessment programmes border= 
 
Nicholas S Edmunds, Ahmet G Genc, Liam J McGuffin
 
 
 
Generation of a high confidence set of domain'domain interface types to guide protein complex structure predictions by AlphaFold border= 
 
Johanna Lena Geist, Chop Yan Lee, Joelle Morgan Strom, José de Jesús Naveja, Katja Luck
 
 
 
Gene expression
 
 
 
 
TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups border= 
 
Pallavi Surana, Pratik Dutta, Ramana V Davuluri
 
 
 
Genetics and population analysis
 
 
 
 
Enabling population protein dynamics through Bayesian modeling border= 
 
Sylvain Lehmann, Jérôme Vialaret, Audrey Gabelle, Luc Bauchet, Jean-Philippe Villemin ...
 
 
 
Systems biology
 
 
 
 
Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems border= 
 
Mauro Silberberg, Henning Hermjakob, Rahuman S Malik-Sheriff, Hernán E Grecco
 
 
 
New GO-based measures in multiple network alignment border=  
 
Kimia Yazdani, Reza Mousapour, Wayne B Hayes
 
 
 
An Ensemble Spectral Prediction (ESP) model for metabolite annotation border=  
 
Xinmeng Li, Yan Zhou Chen, Apurva Kalia, Hao Zhu, Li-ping Liu ...
 
 
 
Attention-based approach to predict drug'target interactions across seven target superfamilies border= 
 
Aron Schulman, Juho Rousu, Tero Aittokallio, Ziaurrehman Tanoli
 
 
 
Disease gene prioritization with quantum walks border=  
 
Harto Saarinen, Mark Goldsmith, Rui-Sheng Wang, Joseph Loscalzo, Sabrina Maniscalco
 
 
 
Data and text mining
 
 
 
 
Best practices to evaluate the impact of biomedical research software'metric collection beyond citations border= 
 
Awan Afiaz, Andrey A Ivanov, John Chamberlin, David Hanauer, Candace L Savonen ...
 
 
 
BELHD: improving biomedical entity linking with homonym disambiguation border=  
 
Samuele Garda, Ulf Leser
 
 
 
ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching border= 
 
Teer Ba, Hao Miao, Lirong Zhang, Caixia Gao, Yong Wang
 
 
 
Databases and ontologies
 
 
 
 
FAIRsoft'a practical implementation of FAIR principles for research software border= 
 
Eva Martín del Pico, Josep Lluís Gelpí, Salvador Capella-Gutierrez
 
 
 
Bioimage informatics
 
 
 
 
PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy border= 
 
Kwan-Ling Wu, Melisa J Montalvo, Prashant S Menon, Badrinath Roysam, Navin Varadarajan
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
Genome-wide analysis and visualization of copy number with CNVpytor in igv.js border= 
 
Arijit Panda, Milovan Suvakov, Helga Thorvaldsdottir, Jill P Mesirov, James T Robinson ...
 
 
 
Epigenomics coverage data extraction and aggregation in R with tidyCoverage border=  
 
Jacques Serizay, Romain Koszul
 
 
 
AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality border= 
 
Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst ...
 
 
 
Sequence analysis
 
 
 
 
RawHash2: mapping raw nanopore signals using hash-based seeding and adaptive quantization border= 
 
Can Firtina, Melina Soysal, Joël Lindegger, Onur Mutlu
 
 
 
Interactive visualization of nanopore sequencing signal data with Squigualiser border= 
 
Hiruna Samarakoon, Kisaru Liyanage, James M Ferguson, Sri Parameswaran, Hasindu Gamaarachchi ...
 
 
 
popDMS infers mutation effects from deep mutational scanning data border=  
 
Zhenchen Hong, Kai S Shimagaki, John P Barton
 
 
 
Galaxy Helm chart: a standardized method for deploying production Galaxy servers border= 
 
Nuwan Goonasekera, Alexandru Mahmoud, Keith Suderman, Enis Afgan
 
 
 
Publication-ready single nucleotide polymorphism visualization with snipit border=  
 
Áine O'Toole, Ammar Aziz, Daniel Maloney
 
 
 
Systems biology
 
 
 
 
PhysioFit: a software to quantify cell growth parameters and extracellular fluxes border= 
 
Loïc Le Grégam, Yann Guitton, Floriant Bellvert, Stéphanie Heux, Fabien Jourdan ...
 
 
 
ceas: an R package for Seahorse data analysis and visualization border=  
 
Rachel (Rae) J House, James P Eapen, Hui Shen, Carrie R Graveel, Matthew R Steensma
 
 
 
CatReNet: interactive analysis of (auto-) catalytic reaction networks border=  
 
Daniel H Huson, Joana C Xavier, Mike A Steel
 
 
 
Structural bioinformatics
 
 
 
 
HDXBoxeR: an R package for statistical analysis and visualization of multiple Hydrogen'Deuterium Exchange Mass-Spectrometry datasets of different protein states border= 
 
Maria K Janowska, Katherine Reiter, Pearl Magala, Miklos Guttman, Rachel E Klevit
 
 
 
Locuaz: an in silico platform for protein binders optimization border=  
 
German P Barletta, Rika Tandiana, Miguel Soler, Sara Fortuna, Walter Rocchia
 
 
 
WatFinder: a ProDy tool for protein'water interactions border=  
 
James M Krieger, Frane Doljanin, Anthony T Bogetti, Feng Zhang, Thiliban Manivarma ...
 
 
 
Gene expression
 
 
 
 
Accelerated dimensionality reduction of single-cell RNA sequencing data with fastglmpca border= 
 
Eric Weine, Peter Carbonetto, Matthew Stephens
 
 
 
GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization border= 
 
Julián Montoto-Louzao, Alberto Gómez-Carballa, Xabier Bello, Jacobo Pardo-Seco, Alba Camino-Mera ...
 
 
 
SpatialQC: automated quality control for spatial transcriptome data border=  
 
Guangyao Mao, Yi Yang, Zhuojuan Luo, Chengqi Lin, Peng Xie
 
 
 
R2Dtool: integration and visualization of isoform-resolved RNA features border=  
 
Aditya J Sethi, Pablo Acera Mateos, Rippei Hayashi, Nikolay E Shirokikh, Eduardo Eyras
 
 
 
cypress : an R/Bioconductor package for cell-type-specific differential expression analysis power assessment border= 
 
Shilin Yu, Guanqun Meng, Wen Tang, Wenjing Ma, Rui Wang ...
 
 
 
Genetics and population analysis
 
 
 
 
pyTWMR: transcriptome-wide Mendelian randomization in python border= 
 
Sergey Oreshkov, Kaido Lepik, Federico Santoni
 
 
 
grenedalf: population genetic statistics for the next generation of pool sequencing border= 
 
Lucas Czech, Jeffrey P Spence, Moisés Expósito-Alonso
 
 
 
Data and text mining
 
 
 
 
GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies border= 
 
James V Talwar, Adam Klie, Meghana S Pagadala, Hannah Carter
 
 
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