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Frontiers in Bioinformatics, Volume 3
Volume 3, May 2023
- Jared Huzar, Madelyn Shenoy, Maxwell D. Sanderford, Sudhir Kumar
, Sayaka Miura:
Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. - Constance J. Jeffery:
Current successes and remaining challenges in protein function prediction. - Pierre Tufféry, Philippe Derreumaux:
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. - Ricardo R. Pavan
Gene length is a pivotal feature to explain disparities in transcript capture between single transcriptome techniques. - Jover Lee, James Hadfield, Allison Black, Thomas R. Sibley, Richard A. Neher
Joint visualization of seasonal influenza serology and phylogeny to inform vaccine composition. - Camilo Valdes, Vitalii Stebliankin, Daniel Ruiz-Perez, Ji In Park, Hajeong Lee, Giri Narasimhan
Microbiome maps: Hilbert curve visualizations of metagenomic profiles. - Dexter Pratt, Rudolf T. Pillich, John H. Morris:
Translating desktop success to the web in the cytoscape project. - Carla Mölbert, Laleh Haghverdi:
Adjustments to the reference dataset design improve cell type label transfer. - Irene E. Vignon-Clementel, Nick Jagiella, Jules Dichamp, Jérôme Kowalski, Wiltrud Lederle, Hendrik Laue, Fabian Kiessling
A proof-of-concept pipeline to guide evaluation of tumor tissue perfusion by dynamic contrast-agent imaging: Direct simulation and inverse tracer-kinetic procedures. - Diego C. B. Mariano, Néli José da Fonseca Jr., Lucianna Helene Santos, Raquel Cardoso de Melo Minardi:
Editorial: Bioinformatics in the age of data science: algorithms, methods, and tools applied from Omics to structural data. - Fabiano C. Fernandes, Marlon H. Cardoso
Geometric deep learning as a potential tool for antimicrobial peptide prediction. - Christopher J. Soelistyo
Machine learning enhanced cell tracking. - Samuel W. Canner, Sudhanshu Shanker
Structure-based neural network protein-carbohydrate interaction predictions at the residue level. - Xinling Li, Greg Gibson, Peng Qiu:
Gene representation in scRNA-seq is correlated with common motifs at the 3′ end of transcripts. - Haruki Yamane, Takashi Ishida:
Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs. - Yi Liu, Xiaoyan Liu, Hantao Zhang, Junlin Liu, Chaofan Shan, Yinglu Guo, Xun Gong, Min Tang
Editorial: Artificial intelligence in digital pathology image analysis. - Paola Lecca
Editorial: Expert Opinions in Network bioinformatics: 2022. - Isaac Olatunji, Feng Cui:
Multimodal AI for prediction of distant metastasis in carcinoma patients. - Diego Lucas Neres Rodrigues
PanViTa: Pan Virulence and resisTance analysis. - Chang Li, Ian Hou, Mingjia Ma, Grace Wang, Yongsheng Bai, Xiaoming Liu
Orthogonal analysis of variants in APOE gene using in-silico approaches reveals novel disrupting variants. - Flemming Damgaard Nielsen
Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae. - Yuexing Liu, Yixue Li, Tao Zeng:
Multi-omics of extracellular vesicles: An integrative representation of functional mediators and perspectives on lung disease study. - Tristan Hoellinger, Camille Mestre, Hugues Aschard, Wilfried Le Goff, Sylvain Foissac
Enhancer/gene relationships: Need for more reliable genome-wide reference sets. - Marcos Vinicius Ferreira, Tatiane Nogueira Rios, Ricardo Araújo Rios, Tiago J. S. Lopes:
A graph-based machine learning framework identifies critical properties of FVIII that lead to hemophilia A. - Marija Cvijovic, Annikka Polster:
Network medicine: facilitating a new view on complex diseases. - Letícia M. F. Bertoline
Before and after AlphaFold2: An overview of protein structure prediction. - Yuda Munarko
CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities. - Zihao Wang, Yun Zhou
XMR: an explainable multimodal neural network for drug response prediction. - Emilia Ståhlbom, Jesper Molin, Anders Ynnerman, Claes Lundström:
The thorny complexities of visualization research for clinical settings: A case study from genomics. - Marco Viviani
EGAsubmitter: A software to automate submission of nucleic acid sequencing data to the European Genome-phenome Archive. - Mélanie Corcuff, Marc Garibal, Jean-Pierre Desvignes, Céline Guien
Protein domains provide a new layer of information for classifying human variations in rare diseases. - Fotis A. Baltoumas, Evangelos Karatzas, David Páez-Espino, Nefeli K. Venetsianou, Eleni Aplakidou, Anastasis Oulas, Robert D. Finn
Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. - Mohammed Zidane, Ahmad Makky
A review on deep learning applications in highly multiplexed tissue imaging data analysis. - Juan G. Díaz Ochoa, Lukas Maier, Orsolya Csiszár:
Bayesian logical neural networks for human-centered applications in medicine. - Gwendal Fouché
Immersive and interactive visualization of 3D spatio-temporal data using a space time hypercube: Application to cell division and morphogenesis analysis. - Arnaud Kress, Olivier Poch, Odile Lecompte
Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events. - John P. Santa Maria, Yuan Wang, Luiz Miguel Camargo:
Perspective on the challenges and opportunities of accelerating drug discovery with artificial intelligence. - Toluwase Hezekiah Fatoki:
Human adenovirus DNA polymerase is evolutionarily and functionally associated with human telomerase reverse transcriptase based on in silico molecular characterization that implicate abacavir and zidovudine. - Aziz Fouché, Andrei Yu. Zinovyev:
Omics data integration in computational biology viewed through the prism of machine learning paradigms. - Ana Julia Velez Rueda, Luis Alberto Gonano
CardIAP: calcium transients confocal image analysis tool. - Enes Fahri Tezcan
Comprehensive genome-scale metabolic model of the human pathogen Cryptococcus neoformans: A platform for understanding pathogen metabolism and identifying new drug targets. - Robin A. Corey
A brief history of visualizing membrane systems in molecular dynamics simulations. - Jessica Xin Hjaltelin, Hannah Currant
Visualising disease trajectories from population-wide data. - Andreas Bueckle
The HRA Organ Gallery affords immersive superpowers for building and exploring the Human Reference Atlas with virtual reality. - Hamid Younesy, Joseph Pober, Torsten Möller, Mohammad M. Karimi
ModEx: a general purpose computer model exploration system. - T. Waddell, Ana I. L. Namburete, Paul Duckworth, N. Eichert, H. Thomaides-Brears
Bayesian networks and imaging-derived phenotypes highlight the role of fat deposition in COVID-19 hospitalisation risk. - Florian Levet:
Optimizing Voronoi-based quantifications for reaching interactive analysis of 3D localizations in the million range. - Joran Deschamps, Damian Dalle Nogare, Florian Jug:
Better research software tools to elevate the rate of scientific discovery or why we need to invest in research software engineering. - Swarup Roy, Pietro Hiram Guzzi, Jugal Kalita:
Editorial: Graph representation learning in biological network. - Alexander Mazein, Marcio Luis Acencio
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. - Ryan S. McClure, Yvonne Rericha, Katrina M. Waters
3′ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior at identifying toxicity pathways in a model organism. - Saurav Mallik, Soumita Seth
Optimal ranking and directional signature classification using the integral strategy of multi-objective optimization-based association rule mining of multi-omics data. - Wanxin Li, Jules Mirone, Ashok Prasad, Nina Miolane, Carine Legrand
Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets. - Xueguang Li, Mingyue Du, Shanru Zuo, Mingqing Zhou, Qiyao Peng, Ziyao Chen, Junhua Zhou, Quan-Yuan He:
Deep convolutional neural networks using an active learning strategy for cervical cancer screening and diagnosis. - Piotr Gawron, David Hoksza, Janet Piñero, María Peña-Chilet, Marina Esteban-Medina, Jose Luis Fernandez-Rueda, Vincenza Colonna, Ewa Smula, Laurent Heirendt, François Ancien, Valentin Grouès, Venkata P. Satagopam, Reinhard Schneider, Joaquín Dopazo, Laura I. Furlong, Marek Ostaszewski:
Visualization of automatically combined disease maps and pathway diagrams for rare diseases. - Daniele M. Papetti, Simone Spolaor, Iman Nazari, Andrea Tirelli, Tommaso Leonardi, Chiara Caprioli, Daniela Besozzi, Thalia Vlachou, Pier Giuseppe Pelicci, Paolo Cazzaniga, Marco S. Nobile:
Barcode demultiplexing of nanopore sequencing raw signals by unsupervised machine learning. - Wei Ouyang, Kevin W. Eliceiri, Beth A. Cimini
Moving beyond the desktop: prospects for practical bioimage analysis via the web. - Michael John Fanous, Nir Pillar, Aydogan Ozcan:
Digital staining facilitates biomedical microscopy. - Teng Ann Ng, Shamima Rashid, Chee Keong Kwoh:
Virulence network of interacting domains of influenza a and mouse proteins. - Nour Nissan, Julia Hooker, Eric Arezza, Kevin Dick, Ashkan Golshani
Large-scale data mining pipeline for identifying novel soybean genes involved in resistance against the soybean cyst nematode. - M. Michael Gromiha, Petras Kundrotas, Marcelo Adrian Marti, Ceslovas Venclovas
Editorial: Protein recognition and associated diseases. - Sangeetha Muthamilselvan
BrcaDx: precise identification of breast cancer from expression data using a minimal set of features. - Tao Zeng, Chuanchao Zhang:
Editorial: Expert opinions in integrative bioinformatics: 2022. - Juan G. Díaz Ochoa, André Marquardt:
Editorial: Transparent machine learning in bio-medicine. - Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar
Molecular timetrees using relaxed clocks and uncertain phylogenies. - Linghao Hu, Blanche Ter Hofstede, Dhavan Sharma, Feng Zhao, Alex J. Walsh:
Comparison of phasor analysis and biexponential decay curve fitting of autofluorescence lifetime imaging data for machine learning prediction of cellular phenotypes. - Pedro Martins, Diego C. B. Mariano, Frederico Chaves Carvalho, Luana Luiza Bastos, Lucas Moraes, Vivian Morais Paixão, Raquel Cardoso de Melo Minardi:
Propedia v2.3: A novel representation approach for the peptide-protein interaction database using graph-based structural signatures. - Gabriel Wajnberg, Eric P. Allain, Jeremy W. Roy, Shruti Srivastava, Daniel Saucier, Pier Morin, Alier Marrero, Colleen O'connell, Anirban Ghosh, Stephen M. Lewis, Rodney J. Ouellette, Nicolas Crapoulet:
Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy. - Wenhua Wei
Leveraging primate-specific genomic information for genetic studies of complex diseases. - Tyler N. Thompson, Anna Vickrey, Michael D. Shapiro, Edward Hsu:
A computer vision framework for quantification of feather growth patterns. - Yusuke Azuma, Hatsumi Okada, Shuichi Onami:
Systematic analysis of cell morphodynamics in C. elegans early embryogenesis. - Ahmed Abdelmonem Hemedan, Reinhard Schneider, Marek Ostaszewski:
Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses. - Daniel H. Huson, Banu Cetinkaya:
Visualizing incompatibilities in phylogenetic trees using consensus outlines. - Adriano Lucieri, Andreas Dengel, Sheraz Ahmed:
Translating theory into practice: assessing the privacy implications of concept-based explanations for biomedical AI. - Sumita Choudhary, Anup Kumar Kesavan, Vijay Juneja, Sheetal Thakur:
Molecular modeling, simulation and docking of Rv1250 protein from Mycobacterium tuberculosis. - Kyohei Koyama, Kosuke Hashimoto, Chioko Nagao, Kenji Mizuguchi:
Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties. - Grigorios M. Karageorgos, Sanghee Cho
Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images. - Archana Machireddy, Guillaume Thibault, Kevin G. Loftis, Kevin Stoltz, Cecilia E. Bueno, Hannah R. Smith, Jessica L. Riesterer, Joe W. Gray, Xubo Song:
Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning. - Helena Klara Jambor
Insights on poster preparation practices in life sciences. - Yanlin Zhang, Christopher J. F. Cameron, Mathieu Blanchette:
Posterior inference of Hi-C contact frequency through sampling. - Konstantinos A Kyritsis
Software pipelines for RNA-Seq, ChIP-Seq and germline variant calling analyses in common workflow language (CWL). - Xu Yang, Langwen Lai, Xiaoli Qiang, Ming Deng, Yuhao Xie, Xiaolong Shi, Zheng Kou
Towards Chinese text and DNA shift encoding scheme based on biomass plasmid storage. - Elizabeth A. Heron
Editorial: Identification of phenotypically important genomic variants. - Famke Bäuerle
Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. - Dmitrii K. Chebanov, Vsevolod A. Misyurin, Irina Zh. Shubina:
An algorithm for drug discovery based on deep learning with an example of developing a drug for the treatment of lung cancer. - Joan Segura
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins. - Jack M. Craig, Sudhir Kumar
The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. - Daisuke Kihara:
Editorial: Expert opinions in protein bioinformatics: 2022. - Zhi-Ping Liu:
Editorial: Insights in integrative bioinformatics-2021. - Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga
DeepRaccess: high-speed RNA accessibility prediction using deep learning. - Claudia Caudai, Emanuele Salerno
Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct. - Jack M. Craig, Grace L. Bamba, Jose Barba-Montoya, S. Blair Hedges, Sudhir Kumar
Completing a molecular timetree of apes and monkeys. - Varun Mannam, Jacob Brandt, Cody J. Smith, Xiaotong Yuan, Scott S. Howard:
Improving fluorescence lifetime imaging microscopy phasor accuracy using convolutional neural networks. - David Bryant, Daniel H. Huson:
NeighborNet: improved algorithms and implementation. - Mohammed Zidane, Ahmad Makky, Matthias Bruhns, Alexander Rochwarger, Sepideh Babaei, Manfred Claassen, Christian M. Schürch:
Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis. - Prajay Patel
No-boundary thinking for artificial intelligence in bioinformatics and education. - Benedetta Frida Baldi, Jenny Vuong, Seán I. O'Donoghue:
Assessing 2D visual encoding of 3D spatial connectivity. - Erik A. Burlingame, Luke Ternes, Jia-Ren Lin, Yu-An Chen, Eun Na Kim, Joe W. Gray, Young Hwan Chang:
3D multiplexed tissue imaging reconstruction and optimized region of interest (ROI) selection through deep learning model of channels embedding. - Niloofar Shirvanizadeh
VariBench, new variation benchmark categories and data sets. - Szabolcs Elias, Clemens Wrzodek, Charlotte M. Deane, Alain C. Tissot, Stefan Klostermann, Francesca Ros:
Prediction of polyspecificity from antibody sequence data by machine learning. - Paolo Pozzi
Artificial intelligence in imaging flow cytometry. - Jan Rothörl
Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach. - Luca Panconi, Dylan M. Owen, Juliette Griffié:
Cluster analysis for localisation-based data sets: dos and don'ts when quantifying protein aggregates. - Suad Algarni
Development of an antimicrobial resistance plasmid transfer gene database for enteric bacteria. - Soumyadip Roy, Asa Ben-Hur:
Protein quality assessment with a loss function designed for high-quality decoys. - Kevin K. D. Tan, Mark A. Tsuchida, Jenu Varghese Chacko, Niklas A. Gahm, Kevin W. Eliceiri:
Real-time open-source FLIM analysis. - Huyen Le, Ru Chen, Stephen C. Harris, Hong Fang, Beverly Lyn-Cook, Huixiao Hong, Weigong Ge, Paul Rogers, Weida Tong, Wen Zou:
RxNorm for drug name normalization: a case study of prescription opioids in the FDA adverse events reporting system. - Annette Lien
Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA. - Lucas Pagano, Guillaume Thibault, Walid Bousselham, Jessica L. Riesterer, Xubo Song, Joe W. Gray:
Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations. - Anush Karampuri
A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches. - Rahul Kumar, Kumardeep Chaudhary
Editorial: Recent advances in peptide informatics: challenges and opportunities. - Colin Farrell, Chanyue Hu, Kalsuda Lapborisuth, Kyle Pu, Sagi Snir, Matteo Pellegrini:
Identifying epigenetic aging moderators using the epigenetic pacemaker. - Patricia Soto, Davis T. Thalhuber, Frank Luceri, Jamie Janos, Mason R. Borgman, Noah M. Greenwood, Sofia Acosta, Hunter Stoffel:
Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches. - Suraiya Akhter
BPAGS: a web application for bacteriocin prediction via feature evaluation using alternating decision tree, genetic algorithm, and linear support vector classifier. - Nasser Hashemi, Boran Hao, Mikhail Ignatov, Ioannis Ch. Paschalidis, Pirooz Vakili, Sandor Vajda, Dima Kozakov
Improved prediction of MHC-peptide binding using protein language models. - Yixuan Ye, Jiaqi Hu
Genomic risk prediction of cardiovascular diseases among type 2 diabetes patients in the UK Biobank. - Bela T. L. Vogler
Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data. - Kejue Jia, Mesih Kilinc, Robert L. Jernigan
New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions. - Thomas Krannich
VariantSurvival: a tool to identify genotype-treatment response. - Paul Klemm
Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. - Giorgio Valentini
The promises of large language models for protein design and modeling.
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