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Frontiers in Bioinformatics, Volume 1
Volume 1, 2021
- Arne Elofsson:
Toward Characterising the Cellular 3D-Proteome. - Jonathan Hare
, David Morrison, Morten Nielsen
Sampling SARS-CoV-2 Proteomes for Predicted CD8 T-Cell Epitopes as a Tool for Understanding Immunogenic Breadth and Rational Vaccine Design. - Sébastien Tosi
AutoScanJ: A Suite of ImageJ Scripts for Intelligent Microscopy. - Maarten J. M. F. Reijnders, Robert M. Waterhouse
Summary Visualizations of Gene Ontology Terms With GO-Figure! - Heming Zhang, Yixin Chen, Fuhai Li:
Predicting Anticancer Drug Response With Deep Learning Constrained by Signaling Pathways. - Ahmed F. Roumia
OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins. - Wei Zhou, Wei Chi, Wanting Shen, Wanying Dou, Junyi Wang, Xuechen Tian
Computational Identification of Functional Centers in Complex Proteins: A Step-by-Step Guide With Examples. - Maryam Nazarieh
Identification of Biomarkers Controlling Cell Fate In Blood Cell Development. - Daniel Corcoran, Nicholas Maltbie, Shivchander Sudalairaj, Frazier N. Baker, Joseph Hirschfeld, Aleksey A. Porollo:
CoeViz 2: Protein Graphs Derived From Amino Acid Covariance. - Matthew G. Niepielko, Maria Shumskaya
Early Requirement for Bioinformatics in Undergraduate Biology Curricula. - Melvin Yin, Alexander Goncearenco, Igor N. Berezovsky:
Deriving and Using Descriptors of Elementary Functions in Rational Protein Design. - Adam Gardner, Ludovic Autin
CellPAINT: Turnkey Illustration of Molecular Cell Biology. - David W. James, Andrew Filby, M. Rowan Brown, Huw D. Summers, Lewis W. Francis
Data Driven Cell Cycle Model to Quantify the Efficacy of Cancer Therapeutics Targeting Specific Cell-Cycle Phases From Flow Cytometry Results. - Sridevi Krishnan
N-Glycosylation Network Construction and Analysis to Modify Glycans on the Spike (S) Glycoprotein of SARS-CoV-2. - Seán I. O'Donoghue:
Grand Challenges in Bioinformatics Data Visualization. - Guillaume Brysbaert
Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein-Protein Binding. - Max A. Verbiest
Beyond Microsatellite Instability: Intrinsic Disorder as a Potential Link Between Protein Short Tandem Repeats and Cancer. - Mu Gao, Jeffrey Skolnick:
A General Framework to Learn Tertiary Structure for Protein Sequence Characterization. - Mohamed Ghadie, Yu Xia
Mutation Edgotype Drives Fitness Effect in Human. - Matteo Delucchi
TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner. - Yang Liu, You Wu
COVID-19 Multi-Targeted Drug Repurposing Using Few-Shot Learning. - Ye Han, Fei He, Yongbing Chen, Wenyuan Qin, Helong Yu, Dong Xu:
Quality Assessment of Protein Docking Models Based on Graph Neural Network. - Mohamed Helmy, Rahul Agrawal, Javed Ali, Mohamed Soudy, Thuy Tien Bui, Kumar Selvarajoo
GeneCloudOmics: A Data Analytic Cloud Platform for High-Throughput Gene Expression Analysis. - Zoe Parker Cates, Antonio Facciuolo
EPIphany - A Platform for Analysis and Visualization of Peptide Immunoarray Data. - Alina-Alexandra Voicu, Michael Krützen, Tugce Bilgin Sonay:
Short Tandem Repeats as a High-Resolution Marker for Capturing Recent Orangutan Population Evolution. - Matylda Anna Izert
The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins. - Karl Gemayel, Alexandre Lomsadze, Mark Borodovsky:
StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes. - Niloofar Aghaieabiane, Ioannis Koutis:
A Novel Calibration Step in Gene Co-Expression Network Construction. - Min Zhao, Xunlei Zhang, Haizhen Chen, Wenjing Zhao, Haiyan Yu, Xiaoyun Lu, Jianyun Zhou, Xudong Chen, Aiguo Shen:
The Clinicopathologic and Prognostic Significance of c-Myc Expression in Hepatocellular Carcinoma: A Meta-Analysis. - Ron Nafshi, Timothy R. Lezon:
Predicting the Effects of Drug Combinations Using Probabilistic Matrix Factorization. - Rhiane Moody, Kirsty L. Wilson, Jennifer C. Boer, Jessica K. Holien
Predicted B Cell Epitopes Highlight the Potential for COVID-19 to Drive Self-Reactive Immunity. - Kiran Kadam, Noor Peerzada, Rajiv Karbhal
Antibody Class(es) Predictor for Epitopes (AbCPE): A Multi-Label Classification Algorithm. - Yongcheng Mu, Salim Sazzed
A Tool for Segmentation of Secondary Structures in 3D Cryo-EM Density Map Components Using Deep Convolutional Neural Networks. - Hande Beklen, Sema Arslan
Differential Interactome Based Drug Repositioning Unraveled Abacavir, Exemestane, Nortriptyline Hydrochloride, and Tolcapone as Potential Therapeutics for Colorectal Cancers. - Alessandra Lima da Silva
From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics. - Yier Ma, Takeyuki Tamura:
Dynamic Solution Space Division-Based Methods for Calculating Reaction Deletion Strategies for Constraint-Based Metabolic Networks for Substance Production: DynCubeProd. - Shafi Mahmud
Screening of Potent Phytochemical Inhibitors Against SARS-CoV-2 Main Protease: An Integrative Computational Approach. - Dingqian Wang, Cuicui Liu, Xiuying Wang
Automated Machine-Learning Framework Integrating Histopathological and Radiological Information for Predicting IDH1 Mutation Status in Glioma. - Erik Hartman
Peptimetric: Quantifying and Visualizing Differences in Peptidomic Data. - Hochan Cheon
Cyton2: A Model of Immune Cell Population Dynamics That Includes Familial Instructional Inheritance. - Gökçe Senger
Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer. - Saskia Kutz, Ando C. Zehrer, Roman Svetlitckii, Gülce S. Gülcüler Balta, Lucrezia Galli, Susanne Kleber, Jakob Rentsch
An Efficient GUI-Based Clustering Software for Simulation and Bayesian Cluster Analysis of Single-Molecule Localization Microscopy Data. - Kristen Feher
K-Neighbourhood Analysis: A Method for Understanding SMLM Images as Compositions of Local Neighbourhoods. - Markus Hollander, Trang Do, Thorsten Will, Volkhard Helms:
Detecting Rewiring Events in Protein-Protein Interaction Networks Based on Transcriptomic Data. - David J. Schodt, Keith A. Lidke:
Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem. - Stephan Daetwyler
U-Hack Med Gap Year - A Virtual Undergraduate Internship Program in Computer-Assisted Healthcare and Biomedical Research. - Vitor Pimentel, Diego C. B. Mariano, Letícia Xavier Silva Cantão, Luana Luiza Bastos, Pedro H. C. Fischer, Leonardo Henrique Franca de Lima, Alexandre Victor Fassio, Raquel Cardoso de Melo Minardi:
VTR: A Web Tool for Identifying Analogous Contacts on Protein Structures and Their Complexes. - Georgi I. Kapitanov, Jeffrey R. Chabot, Jatin Narula, Mahua Roy, Hendrik Neubert, Joe Palandra, Vahid Farrokhi, Jay S. Johnson, Robert Webster, Hannah M. Jones:
A Mechanistic Site-Of-Action Model: A Tool for Informing Right Target, Right Compound, And Right Dose for Therapeutic Antagonistic Antibody Programs. - Yasmmin Cortes Martins, Artur Ziviani, Marisa Fabiana Nicolás, Ana Tereza Ribeiro de Vasconcelos:
Large-Scale Protein Interactions Prediction by Multiple Evidence Analysis Associated With an In-Silico Curation Strategy. - Angel Mancebo, Dushyant Mehra
Efficient Cross-Correlation Filtering of One- and Two-Color Single Molecule Localization Microscopy Data. - Jan Christoph Thiele
Advanced Data Analysis for Fluorescence-Lifetime Single-Molecule Localization Microscopy. - Benjamin J. Blundell
3D Structure From 2D Microscopy Images Using Deep Learning. - Ziyuan Chen
NOBIAS: Analyzing Anomalous Diffusion in Single-Molecule Tracks With Nonparametric Bayesian Inference. - Vera Pancaldi
Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics. - Sankar Basu, Simon S. Assaf, Fabian Teheux, Marianne Rooman, Fabrizio Pucci:
BRANEart: Identify Stability Strength and Weakness Regions in Membrane Proteins. - Yuxing Chen, Yixin Yan, Moping Xu, Wen Chen, Jinyu Lin, Yan Zhao, Junze Wu, Xianlong Wang:
Development of a Machine Learning Classifier for Brain Tumors Diagnosis Based on DNA Methylation Profile. - Paola Lecca
Machine Learning for Causal Inference in Biological Networks: Perspectives of This Challenge. - Ulf W. Liebal, Sebastian Köbbing, Linus Netze, Artur M. Schweidtmann
Insight to Gene Expression From Promoter Libraries With the Machine Learning Workflow Exp2Ipynb. - Jin Tao, Kelly A. Brayton, Shira L. Broschat:
PASS: Protein Annotation Surveillance Site for Protein Annotation Using Homologous Clusters, NLP, and Sequence Similarity Networks. - Andreas Berberich, Andreas Kurz, Sebastian Reinhard
Fourier Ring Correlation and Anisotropic Kernel Density Estimation Improve Deep Learning Based SMLM Reconstruction of Microtubules. - Shilpita Mitra-Behura, Reto Paul Fiolka, Stephan Daetwyler
Singularity Containers Improve Reproducibility and Ease of Use in Computational Image Analysis Workflows. - Georgii Vasiukov, Tatiana Novitskaya, Maria-Fernanda Senosain, Alex Camai, Anna Menshikh, Pierre Massion, Andries Zijlstra
Integrated Cells and Collagen Fibers Spatial Image Analysis. - Isak Johansson-Åkhe, Claudio Mirabello, Björn Wallner:
InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network. - Wenhui Yu
Integrative In Silico Investigation Reveals the Host-Virus Interactions in Repurposed Drugs Against SARS-CoV-2. - Jianhu Zhang, Xiuli Zhang, Yuan Sh
Diagnostic AI Modeling and Pseudo Time Series Profiling of AD and PD Based on Individualized Serum Proteome Data. - Yumi L. Briones
Visualizing Phytochemical-Protein Interaction Networks: Momordica charantia and Cancer. - Viktor Zenkov, James O'Connor
A New Method Based on the von Mises-Fisher Distribution Shows that a Minority of Liver-Localized CD8 T Cells Display Hard-To-Detect Attraction to Plasmodium-Infected Hepatocytes. - Kerstin Schmid, Andreas Knote, Alexander Mück, Keram Pfeiffer, Sebastian von Mammen, Sabine C. Fischer:
Interactive, Visual Simulation of a Spatio-Temporal Model of Gas Exchange in the Human Alveolus. - Jannes Peeters
Exploring the Microbiome Analysis and Visualization Landscape. - Thomas Blanc, Hippolyte Verdier, Louise Regnier
Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication Features in Virtual Reality. - Corentin Guérinot, Valentin Marcon, Charlotte Godard, Thomas Blanc, Hippolyte Verdier, Guillaume Planchon, Francesca Raimondi, Nathalie Boddaert, Mariana Alonso, Kurt Sailor
New Approach to Accelerated Image Annotation by Leveraging Virtual Reality and Cloud Computing. - Makoto Kashima, Yuki Shida, Takashi Yamashiro, Hiromi Hirata, Hiroshi Kurosaka:
Intracellular and Intercellular Gene Regulatory Network Inference From Time-Course Individual RNA-Seq. - Wei-Hau Chang
Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules. - Elior Rahmani, Brandon Jew, Eran Halperin:
The Effect of Model Directionality on Cell-Type-Specific Differential DNA Methylation Analysis. - Giulia Agostinetto, Anna Sandionigi, Antonia Bruno, Dario Pescini, Maurizio Casiraghi:
Extending Association Rule Mining to Microbiome Pattern Analysis: Tools and Guidelines to Support Real Applications. - Marek Cebecauer:
A Tribute to Professor Katharina Gaus. - Xi Zhang, Yining Hu, David Roy Smith
HSDFinder: A BLAST-Based Strategy for Identifying Highly Similar Duplicated Genes in Eukaryotic Genomes. - Steven L. Salzberg, Derrick E. Wood:
Releasing the Kraken. - Zhi-Hao Guo, Li Yuan, Ya-Lan Tan, Ben-gong Zhang
RNAStat: An Integrated Tool for Statistical Analysis of RNA 3D Structures. - Koen J. A. Martens
Raw Data to Results: A Hands-On Introduction and Overview of Computational Analysis for Single-Molecule Localization Microscopy. - Tatsuya Akutsu, Hongmin Cai:
Editorial: Inference of Biological Networks. - Bin Hu
Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. - Kenji Gerhardt, Carlos A. Ruiz-Perez, Luis M. Rodriguez-R, Roth E. Conrad, Konstantinos T. Konstantinidis:
RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity. - David J. Schodt, Keith A. Lidke:
Corrigendum: Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem.
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