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ORCIDFrontiers in Bioinformatics, Volume 2
Volume 2, 2022
- Mark R. Winter, Andrew R. Cohen
:
LEVERSC: Cross-Platform Scriptable Multichannel 3-D Visualization for Fluorescence Microscopy Images. 740078 - Marcelo Querino Lima Afonso, Néli José da Fonseca Jr., Thainá Godinho Miranda, Lucas Bleicher:
Naview: A d3.js Based JavaScript Library for Drawing and Annotating Voltage-Gated Sodium Channels Membrane Diagrams. 774417 - Weiwei He, Anja Henning-Knechtel, Serdal Kirmizialtin:
Visualizing RNA Structures by SAXS-Driven MD Simulations. 781949 - Lina Marcela Gallego-Paez, Jan Mauer:
DJExpress: An Integrated Application for Differential Splicing Analysis and Visualization. 786898 - Daniel Weiskopf:
Uncertainty Visualization: Concepts, Methods, and Applications in Biological Data Visualization. 793819 - Magdalena C. Schneider, Gerhard J. Schütz:
Don't Be Fooled by Randomness: Valid p-Values for Single Molecule Microscopy. 811053 - Zhihua Chen, Siyuan Chen, Xiaoli Qiang:
Identification of Biomarker in Brain-specific Gene Regulatory Network Using Structural Controllability Analysis. 812314 - Corey Butler, G. Ezequiel Saraceno, Adel Kechkar, Nathan Bénac, Vincent Studer, Julien P. Dupuis, Laurent Groc, Rémi Galland, Jean-Baptiste Sibarita:
Multi-Dimensional Spectral Single Molecule Localization Microscopy. 813494 - Yubo Wang, Liguan Li, Yu Xia, Tong Zhang:
Reliable and Scalable Identification and Prioritization of Putative Cellulolytic Anaerobes With Large Genome Data. 813771 - Qiong Xu, Qiongfang Cha, Hui Qin, Bin Liu, Xueling Wu, Jiantao Shi:
Identification of Master Regulators Driving Disease Progression, Relapse, and Drug Resistance in Lung Adenocarcinoma. 813960 - Debarpan Guhathakurta, Enes Yagiz Akdas, Anna Fejtová, Eva-Maria Weiss:
Development and Application of Automatized Routines for Optical Analysis of Synaptic Activity Evoked by Chemical and Electrical Stimulation. 814081 - Ya-Ting Sabrina Chang, Ming-Ren Yen, Pao-Yang Chen:
BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity. 815289 - M. Wayne Davis, Erik M. Jorgensen:
ApE, A Plasmid Editor: A Freely Available DNA Manipulation and Visualization Program. 818619 - George Armstrong, Gibraan Rahman, Cameron Martino, Daniel McDonald, Antonio González, Gal Mishne, Rob Knight:
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. 821861 - Manuel Glöckler, Andreas Dräger, Reihaneh Mostolizadeh:
NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome. 827024 - Andreas Lardos, Ahmad Aghaebrahimian, Anna Koroleva, Julia Sidorova, Evelyn Wolfram, Maria Anisimova, Manuel Gil:
Computational Literature-based Discovery for Natural Products Research: Current State and Future Prospects. 827207 - Annelien Morlion, Eva Hulstaert, Marieke Vromman, Jasper Anckaert, Celine Everaert, Jo Vandesompele, Pieter Mestdagh:
CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin. 834034 - Yinbo Liu, Yufeng Liu, Gang-Ao Wang, Yinchu Cheng, Shoudong Bi, Xiaolei Zhu:
BERT-Kgly: A Bidirectional Encoder Representations From Transformers (BERT)-Based Model for Predicting Lysine Glycation Site for Homo sapiens. 834153 - Marieke Vromman, Jasper Anckaert, Jo Vandesompele, Pieter-Jan Volders:
CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification. 834655 - Martina Dori, Jimmy Caroli, Mattia Forcato:
Circr, a Computational Tool to Identify miRNA: circRNA Associations. 852834 - Siyou Tan, Wenyan Chen, Gaoyin Kong, Lai Wei:
ASPM May be Related to the Malignant Progression of Hepatitis B and is Associated With a Poor Prognosis of Hepatocellular Carcinoma. 871027 - Cong Gao, Karen C. Glass, Seth Frietze:
Functional networks of the human bromodomain-containing proteins. - Jacob Borgman, Karen Stark, Jeremy Carson, Loren Hauser:
Deep Learning Encoding for Rapid Sequence Identification on Microbiome Data. - Asia Gervits, Roded Sharan:
Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder. - Vittoria Cicaloni, Malancha Karmakar, Luisa Frusciante, Francesco Pettini, Anna Visibelli, Maurizio Orlandini, Federico Galvagni, Maurizio Mongiat, Michael Silk, Federica Nardi, David B. Ascher, Annalisa Santucci, Ottavia Spiga:
Bioinformatics Approaches to Predict Mutation Effects in the Binding Site of the Proangiogenic Molecule CD93. - Thomas Pengo, Siân Culley, Christian Franke:
Editorial: Single-Molecule Image Analysis. - Zhongliang Guo, Rui Yamaguchi:
Machine learning methods for protein-protein binding affinity prediction in protein design. - Shijiao Cai, Renle Du, Yuan Zhang, Zhengyi Yuan, Jie Shang, Yang Yang, Bin Han, Weilong Zhong, Hengjie Yuan, Zhengxiang Li:
Construction and Comprehensive Analysis of ceRNA Networks and Tumor-Infiltrating Immune Cells in Hepatocellular Carcinoma With Vascular Invasion. - Carlos Prieto, David Barrios, Angela Villaverde:
SingleCAnalyzer: Interactive Analysis of Single Cell RNA-Seq Data on the Cloud. - Zeying Yu, Li Cheng, Xinlian Liu, Lushun Zhang, Hui Cao:
Increased Expression of INHBA Is Correlated With Poor Prognosis and High Immune Infiltrating Level in Breast Cancer. - Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi:
Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2. - Ben Murcott, Rebecca J. Pawluk, Anna V. Protasio, Ruth Y. Akinmusola, Dominika Lastik, Vicky L. Hunt:
stepRNA: Identification of Dicer cleavage signatures and passenger strand lengths in small RNA sequences. - Rita Fioresi, P. Demurtas, G. Perini:
Deep learning for MYC binding site recognition. - Don Neumann, Soumyadip Roy, Fayyaz ul Amir Afsar Minhas, Asa Ben-Hur:
On the choice of negative examples for prediction of host-pathogen protein interactions. - Arnaud Gaudry, Florian Huber, Louis-Félix Nothias, Sylvian Cretton, Marcel Kaiser, Jean-Luc Wolfender, Pierre-Marie Allard:
MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets. - Muhammad Muneeb, Samuel F. Feng, Andreas Henschel:
Can We Convert Genotype Sequences Into Images for Cases/Controls Classification? - Yan Zhou, Xue-Chao Zhao, Lin-Qi Wang, Cheng-Wen Chen, Mei-Hua Hsu, Wan-Ting Liao, Xiao Deng, Qing Yan, Guo-Ping Zhao, Chyi-Liang Chen, Liang Zhang, Cheng-Hsun Chiu:
Detecting Genetic Variation of Colonizing Streptococcus agalactiae Genomes in Humans: A Precision Protocol. - Zichang Xu, Hendra S. Ismanto, Hao Zhou, Dianita S. Saputri, Fuminori Sugihara, Daron M. Standley:
Advances in antibody discovery from human BCR repertoires. - Carmen Saenz, Eleonora Nigro, Vithiagaran Gunalan, Manimozhiyan Arumugam:
MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration. - Robert A. Player, Angeline Aguinaldo, Brian B. Merritt, Lisa N. Maszkiewicz, Oluwaferanmi E. Adeyemo, Ellen R. Forsyth, Kathleen J. Verratti, Brant W. Chee, Sarah L. Grady, Christopher E. Bradburne:
The META tool optimizes metagenomic analyses across sequencing platforms and classifiers. - Paola Lecca:
Corrigendum: Machine Learning for Causal Inference in Biological Networks: Perspectives of This Challenge. - Ali Sepas, Ali Haider Bangash, Omar Alraoui, Khaled El Emam, Alaa El-Hussuna:
Algorithms to anonymize structured medical and healthcare data: A systematic review. - Renato R. M. Oliveira, Santelmo Vasconcelos, Guilherme Oliveira:
SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms. - Roghayyeh Alipanahi, Leila Safari, Alireza Khanteymoori:
CRISPR genome editing using computational approaches: A survey. - Erik Werner:
Strategies for the Production of Molecular Animations. - Karthik Raveendran, Nowlan H. Freese, Chaitanya Kintali, Srishti Tiwari, Pawan Bole, Chester Dias, Ann E. Loraine:
BioViz Connect: Web Application Linking CyVerse Cloud Resources to Genomic Visualization in the Integrated Genome Browser. - Christine A. Tataru, Austin Eaton, Maude M. David:
GMEmbeddings: An R Package to Apply Embedding Techniques to Microbiome Data. - Jay Burkhardt, Aaryaman Sharma, Jack Tan, Loraine Franke, Jahnavi Leburu, Jay Jeschke, Sasha Devore, Daniel Friedman, Jingyun Chen, Daniel Haehn:
N-Tools-Browser: Web-Based Visualization of Electrocorticography Data for Epilepsy Surgery. - Evangelia Intze, Ilias Lagkouvardos:
DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons. - Larry Chen, Patricia A. Ganz, Mary E. Sehl:
DNA Methylation, Aging, and Cancer Risk: A Mini-Review. - Davide Chicco, Giuseppe Jurman:
A brief survey of tools for genomic regions enrichment analysis. - Catherine M. Mageeney, Gareth Trubl, Kelly P. Williams:
Improved Mobilome Delineation in Fragmented Genomes. - Michael P. Mariani, Jennifer A. Chen, Ze Zhang, Steven C. Pike, Lucas A. Salas:
MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions. - Ru Zhang, Cuiping Zhang, Chengyu Yu, Jungang Dong, Jihong Hu:
Integration of multi-omics technologies for crop improvement: Status and prospects. - Grigorii Sukhorukov, Maryam Khalili, Olivier Gascuel, Thierry Candresse, Armelle Marais-Colombel, Macha Nikolski:
VirHunter: A Deep Learning-Based Method for Detection of Novel RNA Viruses in Plant Sequencing Data. - Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker:
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. - Elizabeth V. Castro, John W. Shepherd, Ryan S. Guggenheim, Manimone Sengvoravong, Bailey C. Hall, McKenzie K. Chappell, Jessica A. Hearn, Olivia N. Caraccio, Cora Bissman, Sydney Lantow, Damian Buehner, Harry R. Costlow, David M. Prather, Abigail M. Zonza, Mallory Witt, Jeffrey A. Zahratka:
ChanFAD: A Functional Annotation Database for Ion Channels. - Antonios Kioukis, Mohsen Pourjam, Klaus Neuhaus, Ilias Lagkouvardos:
Taxonomy Informed Clustering, an Optimized Method for Purer and More Informative Clusters in Diversity Analysis and Microbiome Profiling. - Shihao Zheng, Tianyu Xue, Bin Wang, Haolin Guo, Qiquan Liu:
Application of network pharmacology in the study of mechanism of Chinese medicine in the treatment of ulcerative colitis: A review. - Alison Tarke, Alba Grifoni, Alessandro Sette:
Bioinformatic and Experimental Analysis of T Cell Immune Reactivity to SARS-CoV-2 and its Variants. - J. C. Phillips:
Darwinian Evolution of Intelligence. - Shabnam Ataee, Xavier Brochet, Carlos Andrés Peña-Reyes:
Bacteriophage Genetic Edition Using LSTM. - Muhammed Khawatmi, Yoann Steux, Saddam Zourob, Heba Sailem:
ShapoGraphy: A User-Friendly Web Application for Creating Bespoke and Intuitive Visualisation of Biomedical Data. - Tiago J. S. Lopes, Tatiane M. Nogueira, Ricardo Araújo Rios:
A Machine Learning Framework Predicts the Clinical Severity of Hemophilia B Caused by Point-Mutations. - Peter D. Karp, Suzanne M. Paley, Markus Krummenacker, Anamika Kothari, Michael J. Wannemuehler, Gregory J. Phillips:
Pathway Tools Management of Pathway/Genome Data for Microbial Communities. - Vishalkumar Vekariya, Kalpdrum Passi, Chakresh Kumar Jain:
Predicting liver cancer on epigenomics data using machine learning. - Cesar Augusto Valades-Cruz, Ludovic Leconte, Gwendal Fouché, Thomas Blanc, Nathan Van Hille, Kevin Fournier, Tao Laurent, Benjamin Gallean, Francois Deslandes, Bassam Hajj, Emmanuel Faure, Ferran Argelaguet, Alain Trubuil, Tobias Isenberg, Jean-Baptiste Masson, Jean Salamero, Charles Kervrann:
Challenges of intracellular visualization using virtual and augmented reality. - Geert Cremers, Mike S. M. Jetten, Huub J. M. Op den Camp, Sebastian Lücker:
Metascan: METabolic Analysis, SCreening and ANnotation of Metagenomes. - Dagmar Ilzhöfer, Michael Heinzinger, Burkhard Rost:
SETH predicts nuances of residue disorder from protein embeddings. - Stephen Taylor, Shamit Soneji:
Bioinformatics and the Metaverse: Are We Ready? - Harry Bowles, Renata Kabiljo, Ahmad Al Khleifat, Ashley Jones, John P. Quinn, Richard J. B. Dobson, Chad M. Swanson, Ammar Al-Chalabi, Alfredo Iacoangeli:
An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data. - Berk Turhan, Zeynep H. Gümüs:
A Brave New World: Virtual Reality and Augmented Reality in Systems Biology. - Zachary S. Wallace, James J. Davis, Anna Maria Niewiadomska, Robert D. Olson, Maulik Shukla, Rick Stevens, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann:
Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation. - Junjie Chen, Ashley J. Zhu, René R. Sevag Packard, Thomas M. Vondriska, Douglas J. Chapski:
genomeSidekick: A user-friendly epigenomics data analysis tool. - Chris J. Radoux, Francesca V. Vianello, Jake E. McGreig, Nikita Desai, Anthony R. Bradley:
The druggable genome: Twenty years later. - Aristeidis Litos, Evangelia Intze, Pavlos Pavlidis, Ilias Lagkouvardos:
Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time. - Maryam Ayat, Mike Domaratzki:
Sparse bayesian learning for genomic selection in yeast. - Huiqiong Zeng, Shuai Chen, Xiaoping Lu, Zhenbo Yan:
Investigating the molecular mechanism of iguratimod act on SLE using network pharmacology and molecular docking analysis. - Lisa Neums, Devin C. Koestler, Qing Xia, Jinxiang Hu, Shachi Patel, Shelby Bell-Glenn, Dong Pei, Bo Zhang, Samuel Boyd, Prabhakar Chalise, Jeffrey A. Thompson:
Assessing equivalent and inverse change in genes between diverse experiments. - Moshe Eliasof, Tue Boesen, Eldad Haber, Chen Keasar, Eran Treister:
Mimetic Neural Networks: A Unified Framework for Protein Design and Folding. - Daniel V. Olivença, Jacob D. Davis, Eberhard O. Voit:
Inference of dynamic interaction networks: A comparison between Lotka-Volterra and multivariate autoregressive models. - Ali Al-Fatlawi, Nazia Afrin, Cigdem Ozen, Negin Malekian, Michael Schroeder:
NetRank Recovers Known Cancer Hallmark Genes as Universal Biomarker Signature for Cancer Outcome Prediction. - Xiao Wang, Mizuho Kittaka, Yilin He, Yiwei Zhang, Yasuyoshi Ueki, Daisuke Kihara:
OC_Finder: Osteoclast Segmentation, Counting, and Classification Using Watershed and Deep Learning. - Priscila S. F. C. Gomes, Diego Enry Barreto Gomes, Rafael C. Bernardi:
Protein structure prediction in the era of AI: Challenges and limitations when applying to in silico force spectroscopy. - David W. Baggett, Anna Medyukhina, Swarnendu Tripathi, Hazheen K. Shirnekhi, Huiyun Wu, Stanley B. Pounds, Khaled Khairy, Richard W. Kriwacki:
An Image Analysis Pipeline for Quantifying the Features of Fluorescently-Labeled Biomolecular Condensates in Cells. - Brook E. Santangelo, Lucas A. Gillenwater, Nourah M. Salem, Lawrence E. Hunter:
Molecular cartooning with knowledge graphs. - Timothy Ongaba, Christian Ndekezi, Nana Nakiddu:
A Molecular Docking Study of Human STEAP2 for the Discovery of New Potential Anti-Prostate Cancer Chemotherapeutic Candidates. - Shahinur Alam, Tae-Yeon Eom, Jeffrey Steinberg, David Ackerman, J. Eric Schmitt, Walter J. Akers, Stanislav S. Zakharenko, Khaled Khairy:
An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery. - Anjalie Schlaeppi, Wilson Adams, Robert Haase, Jan Huisken, Ryan B. Macdonald, Kevin W. Eliceiri, Elisabeth Kugler:
Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration. - Konstantin Schütze, Michael Heinzinger, Martin Steinegger, Burkhard Rost:
Nearest neighbor search on embeddings rapidly identifies distant protein relations. - Zeying Yu, Li Cheng, Xinlian Liu, Lushun Zhang, Hui Cao:
Corrigendum: Increased Expression of INHBA Is Correlated With Poor Prognosis and High Immune Infiltrating Level in Breast Cancer. - Corinna Lorenz, Xinyu Hao, Tomas Tomka, Linus Rüttimann, Richard H. R. Hahnloser:
Interactive extraction of diverse vocal units from a planar embedding without the need for prior sound segmentation. - Vivek Ruhela, Anubha Gupta, K. Sriram, Gaurav Ahuja, Gurvinder Kaur, Ritu Gupta:
A Unified Computational Framework for a Robust, Reliable, and Reproducible Identification of Novel miRNAs From the RNA Sequencing Data. - Edgar Lefevre, Emmanuel Bouilhol, Antoine Chauvière, Wilfried Souleyreau, Marie-Alix Derieppe, Aurélien J. Trotier, Sylvain Miraux, Andreas Bikfalvi, Emeline J. Ribot, Macha Nikolski:
Deep learning model for automatic segmentation of lungs and pulmonary metastasis in small animal MR images. - Luís Cláudio Lima De Jesus, Flávia Figueira Aburjaile, Thiago De Jesus Sousa, Andrei Giacchetto Felice, Siomar de Castro Soares, Luiz Carlos Júnior Alcântara, Vasco Ariston de Carvalho Azevedo:
Genomic Characterization of Lactobacillus delbrueckii Strains with Probiotics Properties. - Rocco Meli, Garrett M. Morris, Philip C. Biggin:
Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review. - Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera:
Metagenomic Analysis Using Phylogenetic Placement - A Review of the First Decade. - Isak Johansson-Åkhe, Björn Wallner:
Improving peptide-protein docking with AlphaFold-Multimer using forced sampling. - Yu-Peng Hsieh, Yuan-Mao Hung, Mong-Hsun Tsai, Liang-Chuan Lai, Eric Y. Chuang:
16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences. - Kenny da Costa Pinheiro, Bruna Verônica Azevedo Gois, Wylerson Guimarães Nogueira, Fabrício Almeida Araújo, Ana Lídia Cavalcante Queiroz, Oscar Cardenas-Alegria, Artur Luiz da Costa da Silva, Antônio Márcio Gomes Martins Júnior, Rommel Thiago Juca Ramos:
In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes. - Olalekan Olanrewaju Bakare, Arun Gokul, Muhali Olaide Jimoh, Ashwil Klein, Marshall Keyster:
In silico discovery of biomarkers for the accurate and sensitive detection of Fusarium solani. - Yuki Kagaya, Sean Flannery, Aashish Jain, Daisuke Kihara:
ContactPFP: Protein Function Prediction Using Predicted Contact Information. - Pietro Di Lena, Christine Nardini, Matteo Pellegrini:
Editorial: Computational Methods for Analysis of DNA Methylation Data. - Cristiano Galletti, Joaquim Aguirre-Plans, Baldo Oliva, Narcis Fernandez-Fuentes:
Prediction of Adverse Drug Reaction Linked to Protein Targets Using Network-Based Information and Machine Learning. - Daniele Raimondi, Gabriele Orlando, Nora Verplaetse, Piero Fariselli, Yves Moreau:
Editorial: Towards genome interpretation: Computational methods to model the genotype-phenotype relationship. - Sidharth Mohan, Hatice Gulcin Ozer, William C. Ray:
The Importance of Weakly Co-Evolving Residue Networks in Proteins is Revealed by Visual Analytics. - Bikash Ranjan Samal, Jens Uwe Loers, Vanessa Vermeirssen, Katleen De Preter:
Opportunities and challenges in interpretable deep learning for drug sensitivity prediction of cancer cells. - Byron J. Smith, Xiangpeng Li, Zhou Jason Shi, Adam R. Abate, Katherine S. Pollard:
Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts. - Rui Li, Vaibhav Sharma, Subasini Thangamani, Artur Yakimovich:
Open-Source Biomedical Image Analysis Models: A Meta-Analysis and Continuous Survey. - Francesco Petrizzelli, Tommaso Biagini, Salvatore Daniele Bianco, Niccolò Liorni, Alessandro Napoli, Stefano Castellana, Tommaso Mazza:
Connecting the dots: A practical evaluation of web-tools for describing protein dynamics as networks. - Kenta Nakai, Leyi Wei:
Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. - Ulas Karaoz, Eoin L. Brodie:
microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes. - Shelby Bell-Glenn, Jeffrey A. Thompson, Lucas A. Salas, Devin C. Koestler:
A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures. - Liwei Chang, Arup Mondal, Alberto Perez:
Towards rational computational peptide design. - Nicholas Pudjihartono, Tayaza Fadason, Andreas W. Kempa-Liehr, Justin M. O'Sullivan:
A Review of Feature Selection Methods for Machine Learning-Based Disease Risk Prediction.
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