Frontiers Bioinform.

Keyphrases

Publications

volume 3, 2023

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. Frontiers Bioinform. 3 (2023)
T. Waddell, Ana I. L. Namburete, P. Duckworth, N. Eichert, H. Thomaides-Brears, D. J. Cuthbertson, J. P. Despres, M. Brady
Bayesian networks and imaging-derived phenotypes highlight the role of fat deposition in COVID-19 hospitalisation risk. Frontiers Bioinform. 3 (2023)
Juan G. Díaz Ochoa, André Marquardt
Editorial: Transparent machine learning in bio-medicine. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
John P. Santa Maria, Yuan Wang, Luiz Miguel Camargo
Perspective on the challenges and opportunities of accelerating drug discovery with artificial intelligence. Frontiers Bioinform. 3 (2023)
Juan G. Díaz Ochoa, Lukas Maier, Orsolya Csiszár
Bayesian logical neural networks for human-centered applications in medicine. Frontiers Bioinform. 3 (2023)
Zihao Wang, Yun Zhou, Yu Zhang, Yu K. Mo, Yijie Wang
XMR: an explainable multimodal neural network for drug response prediction. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Aziz Fouché, Andrei Yu. Zinovyev
Omics data integration in computational biology viewed through the prism of machine learning paradigms. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Carla Mölbert, Laleh Haghverdi
Adjustments to the reference dataset design improve cell type label transfer. Frontiers Bioinform. 3 (2023)
Marija Cvijovic, Annikka Polster
Network medicine: facilitating a new view on complex diseases. Frontiers Bioinform. 3 (2023)
Teng Ann Ng, Shamima Rashid, Chee Keong Kwoh
Virulence network of interacting domains of influenza a and mouse proteins. Frontiers Bioinform. 3 (2023)
Haruki Yamane, Takashi Ishida
Helix encoder: a compound-protein interaction prediction model specifically designed for class A GPCRs. Frontiers Bioinform. 3 (2023)
Letícia M. F. Bertoline, Angélica Nakagawa Lima, José Eduardo Krieger, Samantha K. Teixeira
Before and after AlphaFold2: An overview of protein structure prediction. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Daniel H. Huson, Banu Cetinkaya
Visualizing incompatibilities in phylogenetic trees using consensus outlines. Frontiers Bioinform. 3 (2023)
Michael John Fanous, Nir Pillar, Aydogan Ozcan
Digital staining facilitates biomedical microscopy. Frontiers Bioinform. 3 (2023)
Yusuke Azuma, Hatsumi Okada, Shuichi Onami
Systematic analysis of cell morphodynamics in C. elegans early embryogenesis. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Ahmed Abdelmonem Hemedan, Reinhard Schneider, Marek Ostaszewski
Applications of Boolean modeling to study the dynamics of a complex disease and therapeutics responses. Frontiers Bioinform. 3 (2023)
Samuel W. Canner, Sudhanshu Shanker, Jeffrey J. Gray
Structure-based neural network protein-carbohydrate interaction predictions at the residue level. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Dexter Pratt, Rudolf T. Pillich, John H. Morris
Translating desktop success to the web in the cytoscape project. Frontiers Bioinform. 3 (2023)
Hamid Younesy, Joseph Pober, Torsten Möller, Mohammad M. Karimi
ModEx: a general purpose computer model exploration system. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
M. Michael Gromiha, Petras Kundrotas, Marcelo Adrian Marti, Ceslovas Venclovas, Minghui Li
Editorial: Protein recognition and associated diseases. Frontiers Bioinform. 3 (2023)
Pierre Tufféry, Philippe Derreumaux
A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Yuda Munarko, Anand K. Rampadarath, David P. Nickerson
CASBERT: BERT-based retrieval for compositely annotated biosimulation model entities. Frontiers Bioinform. 3 (2023)
Jared Huzar, Madelyn Shenoy, Maxwell D. Sanderford, Sudhir Kumar, Sayaka Miura
Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Jessica Xin Hjaltelin, Hannah Currant, Isabella Friis Jørgensen, Søren Brunak
Visualising disease trajectories from population-wide data. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Adriano Lucieri, Andreas Dengel, Sheraz Ahmed
Translating theory into practice: assessing the privacy implications of concept-based explanations for biomedical AI. Frontiers Bioinform. 3 (2023)
Sangeetha Muthamilselvan, Ashok Palaniappan
BrcaDx: precise identification of breast cancer from expression data using a minimal set of features. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Yi Liu, Xiaoyan Liu, Hantao Zhang, Junlin Liu, Chaofan Shan, Yinglu Guo, Xun Gong, Min Tang
Editorial: Artificial intelligence in digital pathology image analysis. Frontiers Bioinform. 3 (2023)
Jose Barba-Montoya, Sudip Sharma, Sudhir Kumar
Molecular timetrees using relaxed clocks and uncertain phylogenies. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)
Xinling Li, Greg Gibson, Peng Qiu
Gene representation in scRNA-seq is correlated with common motifs at the 3′ end of transcripts. Frontiers Bioinform. 3 (2023)
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. Frontiers Bioinform. 3 (2023)