16S rRNA sequencing analysis: the devil is in the details by Amy M. Tsou, Scott W. Olesen, Eric J. Alm, Scott B. Snapper

“…Wet bench researchers should therefore strongly consider partnering with bioinformaticians or computational biologists when analyzing 16S data.…”
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Gene name errors: Lessons not learned. by Mandhri Abeysooriya, Megan Soria, Mary Sravya Kasu, Mark Ziemann

“…Erroneous conversion of gene names into other dates and other data types has been a frustration for computational biologists for years. We hypothesized that such errors in supplementary files might diminish after a report in 2016 highlighting the extent of the problem. …”
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A field guide to cultivating computational biology. by Gregory P Way, Casey S Greene, Piero Carninci, Benilton S Carvalho, Michiel de Hoon, Stacey D Finley, Sara J C Gosline, Kim-Anh Lȇ Cao, Jerry S H Lee, Luigi Marchionni, Nicolas Robine, Suzanne S Sindi, Fabian J Theis, Jean Y H Yang, Anne E Carpenter, Elana J Fertig

“…We believe that in order to pave the way for the next generation of discoveries, we need to improve recognition for computational biologists and better align pathways of career success with pathways of scientific progress. …”
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Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update [v1; ref status: indexed, http://f1000r.es/1w9] by Paul Pavlidis, Jesse Gillis

“…We also suggested that part of the problem is the reliance by computational biologists on gold standard annotations such as the Gene Ontology. …”
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Protein engineering in the computational age: An open source framework for exploring mutational landscapes in silico by Shirin Bamezai, Giovanni Maresca di Serracapriola, Freya Morris, Rasmus Hildebrandt, Marc Augustine Sojerido Amil, Sporadicate iGEM Team, Rodrigo Ledesma‐Amaro

“…However, much of the expertise required to engage in such projects is still concentrated in the hands of a few specialised individuals, including computational biologists and structural biochemists. The international Genetically Engineered Machine (iGEM) competition represents a platform for undergraduate students to innovate in synthetic biology. …”
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Gut microbiota: the next-gen frontier in preventive and therapeutic medicine? by Ravinder eNagpal, Hariom eYadav, Francesco eMarotta

“…Since a myriad of mysteries about the precise structures and functions of gut microbial communities in specific health situations still remains to be explicated, the emerging field of gut microbiota remains a foremost objective of research for microbiologists, computational biologists, clinicians, nutritionalists etc. …”
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Genomic impact of eukaryotic transposable elements by Arkhipova Irina R, Batzer Mark A, Brosius Juergen, Feschotte Cédric, Moran John V, Schmitz Jürgen, Jurka Jerzy

“…The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.</p>…”
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MimoDB: a New Repository for Mimotope Data Derived from Phage Display Technology by Xianlong Wang, Hui Ding, Hao Lin, Feng-Biao Guo, Shiyong Li, Zhongkui Xia, Ping Dai, Jian Huang, Beibei Ru

“…MimoDB can be browsed and searched through a user-friendly web interface. For computational biologists, MimoDB can be used to derive customized data sets and benchmarks, which are useful for new algorithm development and tool evaluation. …”
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Information-theoretic analysis of multivariate single-cell signaling responses. by Tomasz Jetka, Karol Nienałtowski, Tomasz Winarski, Sławomir Błoński, Michał Komorowski

“…Provided R-package allows the approach to be used by computational biologists with only elementary knowledge of information theory.…”
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Network-based study reveals potential infection pathways of hepatitis-C leading to various diseases. by Anirban Mukhopadhyay, Ujjwal Maulik

“…Protein-protein interaction network-based study of viral pathogenesis has been gaining popularity among computational biologists in recent days. In the present study we attempt to investigate the possible pathways of hepatitis-C virus (HCV) infection by integrating the HCV-human interaction network, human protein interactome and human genetic disease association network. …”
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A Novel Method for Alignment-free DNA Sequence Similarity Analysis Based on the Characterization of Complex Networks by Jie Zhou, Pianyu Zhong, Tinghui Zhang

“…One of the major tasks of computational biologists is to develop novel mathematical descriptors for similarity analysis. …”
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BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform by Chowdhury Saikat, Sinha Noopur, Ganguli Piyali, Bhowmick Rupa, Singh Vidhi, Nandi Sutanu, Sarkar Ram Rup

“…With its repertoire of biochemical pathway data, and computational tools for performing Topological, Logical and Dynamic analyses, BIOPYDB offers both the experimental and computational biologists to acquire a comprehensive understanding of signaling cascades in the cells. …”
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Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls by James Emmanuel San, Shakuntala Baichoo, Aquillah Kanzi, Yumna Moosa, Richard Lessells, Vagner Fonseca, Vagner Fonseca, John Mogaka, Robert Power, Tulio de Oliveira, Tulio de Oliveira

“…The development of a broadly applicable pipeline presents a real opportunity among computational biologists. Here, (i) we review the prominent and promising tools, (ii) discuss analytical pitfalls and bottlenecks in mGWAS, (iii) provide insights into the selection of appropriate tools, (iv) highlight the gaps that still need to be filled and how users and developers can work together to overcome these bottlenecks. …”
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SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments by Rovira Hector, Ramsey Stephen A, Marzolf Bruz, Lin Jake, Killcoyne Sarah, Handcock Jeremy, Cavnor Chris C, Burdick David B, Bressler Ryan, Shmulevich Ilya, Boyle John

“…Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code.…”
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COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms by Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic‐Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean‐Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban‐Medina, Maria Peña‐Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Willighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez‐Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, the COVID‐19 Disease Map Community

“…To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. …”
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Foldy: An open-source web application for interactive protein structure analysis. by Jacob B Roberts, Alberto A Nava, Allison N Pearson, Matthew R Incha, Luis E Valencia, Melody Ma, Abhay Rao, Jay D Keasling

“…Foldy is a cloud-based application that allows non-computational biologists to easily utilize advanced AI-based structural biology tools, including AlphaFold and DiffDock. …”
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Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol. by Karla Frydenvang, Marlies C A Verkade-Vreeker, Floor Dohmen, Jan N M Commandeur, Maria Rafiq, Osman Mirza, Osman Mirza, Flemming Steen Jørgensen, Daan P Geerke

“…Hence, molecular and computational biologists have in the last two decades shown strong interest in the discovery and design of novel BM3 variants with optimized activity and selectivity for substrate conversion. …”
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Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. by Paolo Fontana, Alessandro Cestaro, Riccardo Velasco, Elide Formentin, Stefano Toppo

“…The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. …”
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NETISCE: a network-based tool for cell fate reprogramming by Lauren Marazzi, Milan Shah, Shreedula Balakrishnan, Ananya Patil, Paola Vera-Licona

“…NETISCE extends cell fate reprogramming studies to larger-scale biological networks without the need for full model parameterization and can be implemented by experimental and computational biologists to identify parts of a biological system relevant to the desired reprogramming task.…”
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XRate: a fast prototyping, training and annotation tool for phylo-grammars by Kosiol Carolin, Chao Sharon, Bradley Robert K, Bendaña Yuri R, Uzilov Andrew V, Klosterman Peter S, Goldman Nick, Holmes Ian

“…Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists.</p> <p>Results</p> <p>We have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. …”
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