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ORCIDFrontiers 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, Fabiola Diniz, Samir El-Dahr, Giovane G. Tortelote:
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, Trevor Bedford, John Huddleston:
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, Oliver Sedlaczek, Dirk Drasdo:
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, Abel Gil-Ley, Lívia V. Luchi, Maria G. L. da Silva, Maria L. R. Macedo, Cesar de la Fuente-Nunez, Octavio L. Franco:
Geometric deep learning as a potential tool for antimicrobial peptide prediction. - Christopher J. Soelistyo, Kristina Ulicna, Alan R. Lowe:
Machine learning enhanced cell tracking. - Samuel W. Canner, Sudhanshu Shanker, Jeffrey J. Gray:
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, Juan Carlos Ariute, Francielly Morais Rodrigues da Costa, Ana Maria Benko-Iseppon, Debmalya Barh, Vasco Ariston de Carvalho Azevedo, Flávia Figueira Aburjaile:
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, Jakob Møller-Jensen, Mikkel Girke Jørgensen:
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, Thomas Faraut, Sarah Djebali:
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, Angélica Nakagawa Lima, José Eduardo Krieger, Samantha K. Teixeira:
Before and after AlphaFold2: An overview of protein structure prediction. - Yuda Munarko, Anand K. Rampadarath, David P. Nickerson:
CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities. - Zihao Wang, Yun Zhou, Yu Zhang, Yu K. Mo, Yijie Wang:
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, Marilisa Montemurro, Livio Trusolino, Andrea Bertotti, Gianvito Urgese, Elena Grassi:
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, Coralie Grattepanche, Gwenaëlle Collod-Béroud, Estelle Ménoret, David Salgado, Christophe Béroud:
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, Sergey Ovchinnikov, Evangelos Pafilis, Nikos Kyrpides, Georgios A. Pavlopoulos:
Exploring microbial functional biodiversity at the protein family level - From metagenomic sequence reads to annotated protein clusters. - Mohammed Zidane, Ahmad Makky, Matthias Bruhns, Alexander Rochwarger, Sepideh Babaei, Manfred Claassen, Christian M. Schürch:
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, Ferran Argelaguet, Emmanuel Faure, Charles Kervrann:
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, Julie Dawn Thompson:
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, Agustín García Smith, Gustavo D. Parisi, María Silvina Fornasari, Leandro Matías Sommese:
CardIAP: calcium transients confocal image analysis tool. - Enes Fahri Tezcan, Yigit Demirtas, Zeynep Petek Cakar, Kutlu Ö. Ülgen:
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, Marc Baaden, Matthieu Chavent:
A brief history of visualizing membrane systems in molecular dynamics simulations. - Jessica Xin Hjaltelin, Hannah Currant, Isabella Friis Jørgensen, Søren Brunak:
Visualising disease trajectories from population-wide data. - Andreas Bueckle, Catherine Qing, Shefali Luley, Yash Kumar, Naval Pandey, Katy Börner:
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, D. J. Cuthbertson, J. P. Despres, Michael Brady:
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, Irina Balaur, Adrien Rougny, Danielle Welter, Anna Niarakis, Diana Ramirez Ardila, Ugur Dogrusoz, Piotr Gawron, Venkata P. Satagopam, Wei Gu, Andreas Kremer, Reinhard Schneider, Marek Ostaszewski:
A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. - Ryan S. McClure, Yvonne Rericha, Katrina M. Waters, Robyn L. Tanguay:
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, Amalendu Si, Tapas Bhadra, Zhongming Zhao:
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, Khanh Dao Duc:
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, Benjamin Mimee, Elroy Cober, James R. Green, Bahram Samanfar:
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, Minghui Li:
Editorial: Protein recognition and associated diseases. - Sangeetha Muthamilselvan, Ashok Palaniappan:
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, Hui Guo:
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, Elizabeth McDonough, Chrystal Chadwick, Soumya Ghose, Jonathan Owens, Kyeong Joo Jung, Raghu Machiraju, Robert West, James D. Brooks, Parag Mallick, Fiona Ginty:
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, Nikolaos Pechlivanis, Fotis E. Psomopoulos:
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, Giorgio Valle, Anna Bernasconi:
Editorial: Identification of phenotypically important genomic variants. - Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, Andreas Dräger:
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, Yana Rose, Chunxiao Bi, Jose M. Duarte, Stephen K. Burley, Sebastian Bittrich:
RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins. - Jack M. Craig, Sudhir Kumar, S. Blair Hedges:
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, Michiaki Hamada:
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, Nisha Pillai, Inimary T. Toby:
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, Mauno Vihinen:
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, Alessia Candeo, Petra Paiè, Francesca Bragheri, Andrea Bassi:
Artificial intelligence in imaging flow cytometry. - Jan Rothörl, Maarten A. Brems, Tim J. Stevens, Peter Virnau:
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, Steven L. Foley, Hailin Tang, Shaohua Zhao, Dereje D. Gudeta, Bijay K. Khajanchi, Steven C. Ricke, Jing Han:
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, Leonardo Pestana Legori, Louis Kraft, Peter Wad Sackett, Gabriel Renaud:
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, Perugu Shyam:
A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches. - Rahul Kumar, Kumardeep Chaudhary, Sandeep Kumar Dhanda:
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, John H. Miller:
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, Fuyuan Pang, Can Cui, Hongyu Zhao:
Genomic risk prediction of cardiovascular diseases among type 2 diabetes patients in the UK Biobank. - Bela T. L. Vogler, Francesco Reina, Christian Eggeling:
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, Marina Herrera Sarrias, Hiba Ben Aribi, Moustafa Shokrof, Alfredo Iacoangeli, Ammar Al-Chalabi, Fritz J. Sedlazeck, Ben Busby, Ahmad Al Khleifat:
VariantSurvival: a tool to identify genotype-treatment response. - Paul Klemm, Peter F. Stadler, Marcus Lechner:
Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs. - Giorgio Valentini, Dario Malchiodi, Jessica Gliozzo, Marco Mesiti, Mauricio Soto Gomez, Alberto Cabri, Justin T. Reese, Elena Casiraghi, Peter N. Robinson:
The promises of large language models for protein design and modeling.
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