The African Human Microbiome Portal: a public web portal of curated metagenomic metadata - Anmol M. Kiran; Mariem Hanachi; Nihad Alsayed; Meriem Fassatoui; Ovokeraye Achinike-Oduaran; Imane Allali; Suresh Maslamoney; Ayton Meintjes; Lyndon Zass; Jorge Da Rocha; Rym Kefi; Alia Benkahla; et al. (Database J. Biol. Databases Curation, 2024)

Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit - Lyndon Zass; Lamech M. Mwapagha; Adetola F. Louis-Jacques; Imane Allali; Julius Mulindwa; Anmol M. Kiran; Mariem Hanachi; Oussama Souiai; Nicola J. Mulder; Ovokeraye Achinike-Oduaran (Database J. Biol. Databases Curation, 2024)

Consent Codes: Maintaining Consent in an Ever-expanding Open Science Ecosystem - Stephanie O. M. Dyke; Kathleen Connor; Victoria Nembaware; Nchangwi S. Munung; Kathy Reinold; Giselle Kerry; Mamana Mbiyavanga; Lyndon Zass; Mauricio Moldes; Samir Das; John Mike Davis; Jordi Rambla De Argila; et al. (Neuroinformatics, 2023)

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets - Matthys G. Potgieter; Andrew J. M. Nel; Suereta Fortuin; Shaun Garnett; Jerome M. Wendoh; David L. Tabb; Nicola J. Mulder; Jonathan M. Blackburn (PLoS Comput. Biol., 2023)

The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation - Gaston K. Mazandu; Jade Hotchkiss; Victoria Nembaware; Ambroise Wonkam; Nicola J. Mulder (Database J. Biol. Databases Curation, 2022)

Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries - Benjamin L. Moore; Patricia Carvajal López; Paballo Abel Chauke; Marco Cristancho; Victoria Dominguez Del Angel; Selene L. Fernandez-Valverde; Amel Ghouila; Piraveen Gopalasingam; Fatma Zahra Guerfali; Alice Matimba; Sarah L. Morgan; Guilherme Oliveira; et al. (PLoS Comput. Biol., 2022)

IHP-PING - generating integrated human protein-protein interaction networks on-the-fly - Gaston K. Mazandu; Christopher Hooper; Kenneth Opap; Funmilayo L. Makinde; Victoria Nembaware; Nicholas E. Thomford; Emile R. Chimusa; Ambroise Wonkam; Nicola J. Mulder (Briefings Bioinform., 2021)

Reviewing and assessing existing meta-analysis models and tools - Funmilayo L. Makinde; Milaine S. S. Tchamga; James Jafali; Segun A. Fatumo; Emile R. Chimusa; Nicola J. Mulder; Gaston K. Mazandu (Briefings Bioinform., 2021)

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings - Faisal M. Fadlelmola; Kais Ghedira; Yosr Hamdi; Mariem Hanachi; Fouzia Radouani; Imane Allali; Anmol M. Kiran; Lyndon Zass; Nihad Alsayed; Meriem Fassatoui; Chaimae Samtal; Samah Ahmed; et al. (Database J. Biol. Databases Curation, 2021)

Data Management Plans in the genomics research revolution of Africa: Challenges and recommendations - Faisal M. Fadlelmola; Lyndon Zass; Melek Chaouch; Chaimae Samtal; Verena Ras; Judit Kumuthini; Sumir Panji; Nicola J. Mulder (J. Biomed. Informatics, 2021)

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa - Verena Ras; Gerrit Botha; Shaun Aron; Katie Lennard; Imane Allali; Shantelle Claassen-Weitz; Kilaza Samson Mwaikono; Dane Kennedy; Jessica R. Holmes; Gloria Rendon; Sumir Panji; Christopher J. Fields; et al. (PLoS Comput. Biol., 2021)

Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries - Benjamin L. Moore; Patricia Carvajal López; Paballo Abel Chauke; Marco Cristancho; Victoria Dominguez Del Angel; Selene L. Fernandez-Valverde; Amel Ghouila; Piraveen Gopalasingam; Fatma Zahra Guerfali; Alice Matimba; Sarah L. Morgan; Guilherme Oliveira; et al. (PLoS Comput. Biol., 2021)

Ten simple rules for developing bioinformatics capacity at an academic institution - Shaun Aron; C. Victor Jongeneel; Paballo Abel Chauke; Melek Chaouch; Judit Kumuthini; Lyndon Zass; Fouzia Radouani; Samar Kamal Kassim; Faisal M. Fadlelmola; Nicola J. Mulder (PLoS Comput. Biol., 2021)

FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data - Ephifania Geza; Nicola J. Mulder; Emile R. Chimusa; Gaston K. Mazandu (Briefings Bioinform., 2020)

A comprehensive survey of models for dissecting local ancestry deconvolution in human genome - Ephifania Geza; Jacquiline W. Mugo; Nicola J. Mulder; Ambroise Wonkam; Emile R. Chimusa; Gaston K. Mazandu (Briefings Bioinform., 2019)

GenGraph: a python module for the simple generation and manipulation of genome graphs - Jon Mitchell Ambler; Shandukani Mulaudzi; Nicola J. Mulder (BMC Bioinform., 2019)

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research - Judit Kumuthini; Lyndon Zass; Sumir Panji; Samson P. Salifu; Jonathan K. Kayondo; Victoria Nembaware; Mamana Mbiyavanga; Ajayi Olabode; Ali Kishk; Gordon Wells; Nicola J. Mulder (BMC Bioinform., 2019)

Proposed Guideline for Minimum Information Stroke Research and Clinical Data Reporting - Judit Kumuthini; Lyndon Zass; Melek Chaouch; Michael Thompson; Paul Olowoyo; Mamana Mbiyavanga; Moyinoluwalogo Faniyan; Gordon Wells; Victoria Nembaware; Nicola J. Mulder; Mayowa Owolabi (Data Sci. J., 2019)

Building Infrastructure for African Human Genomic Data Management - Ziyaad Parker; Suresh Maslamoney; Ayton Meintjes; Gerrit Botha; Sumir Panji; Scott Hazelhurst; Nicola J. Mulder (Data Sci. J., 2019)

Ten simple rules for organizing a webinar series - Faisal M. Fadlelmola; Sumir Panji; Azza E. Ahmed; Amel Ghouila; Wisdom A. Akurugu; Jean-Baka Domelevo Entfellner; Oussema Souiai; Nicola J. Mulder; H3ABioNet Consortium (PLoS Comput. Biol., 2019)

Advancing the international data science workforce through shared training and education - John D. Van Horn; Sumiko Abe; José Luis Ambite; Teresa K. Attwood; Niall Beard; Louisa Bellis; Avnish Bhattrai; Alex A. T. Bui; Gully Burns; Lily Fierro; Jonathan Gordon; Jeffrey S. Grethe; et al. (F1000Research, 2019)

Large-scale data-driven integrative framework for extracting essential targets and processes from disease-associated gene data sets - Gaston K. Mazandu; Emile R. Chimusa; Kayleigh Rutherford; Elsa-Gayle Zekeng; Zoe Z. Gebremariam; Maryam Y. Onifade; Nicola J. Mulder (Briefings Bioinform., 2018)

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics - Shakuntala Baichoo; Yassine Souilmi; Sumir Panji; Gerrit Botha; Ayton Meintjes; Scott Hazelhurst; Hocine Bendou; Eugene de Beste; Phelelani T. Mpangase; Oussema Souiai; Mustafa Alghali; Long Yi; et al. (BMC Bioinform., 2018)

The development and application of bioinformatics core competencies to improve bioinformatics training and education - Nicola J. Mulder; Russell Schwartz; Michelle D. Brazas; Cath Brooksbank; Bruno A. Gaëta; Sarah L. Morgan; Mark A. Pauley; Anne G. Rosenwald; Gabriella Rustici; Michael L. Sierk; Tandy J. Warnow; Lonnie R. Welch (PLoS Comput. Biol., 2018)

Strategies and opportunities for promoting bioinformatics in Zimbabwe - Ryman Shoko; Justen Manasa; Mcebisi Maphosa; Joshua Mbanga; Reagan Mudziwapasi; Victoria Nembaware; Walter T. Sanyika; Tawanda Tinago; Zedias Chikwambi; Cephas Mawere; Alice Matimba; Grace Mugumbate; et al. (PLoS Comput. Biol., 2018)

Relating connectivity changes in brain networks to genetic information in Alzheimer patients - Samar S. M. Elsheikh; Emile R. Chimusa; Nicola J. Mulder; Alessandro Crimi (15th IEEE International Symposium on Biomedical Imaging, ISBI 2018, Washington, DC, USA, April 4-7, 2018, 2018)

Multi-stage Association Analysis of Glioblastoma Gene Expressions with Texture and Spatial Patterns - Samar S. M. Elsheikh; Spyridon Bakas; Nicola J. Mulder; Emile R. Chimusa; Christos Davatzikos; Alessandro Crimi (Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 4th International Workshop, BrainLes 2018, Held in Conjunction with MICCAI 2018, Granada, Spain, September 16, 2018, Revised Selected Papers, Part I, 2018)

Gene Ontology semantic similarity tools: survey on features and challenges for biological knowledge discovery - Gaston K. Mazandu; Emile R. Chimusa; Nicola J. Mulder (Briefings Bioinform., 2017)

A multi-scenario genome-wide medical population genetics simulation framework - Jacquiline W. Mugo; Ephifania Geza; Joel Defo; Samar S. M. Elsheikh; Gaston K. Mazandu; Nicola J. Mulder; Emile R. Chimusa (Bioinform., 2017)

Genomic Research Data Generation, Analysis and Sharing - Challenges in the African Setting - Nicola J. Mulder; Clement A. Adebamowo; Sally N. Adebamowo; Oladimeji Adebayo; Osimhiarherhuo Adeleye; Mohamed Alibi; Shakuntala Baichoo; Alia Benkahla; Faisal M. Fadlelmola; Hassan Ghazal; Kais Ghedira; Alice Matimba; et al. (Data Sci. J., 2017)

Ten simple rules for forming a scientific professional society - Bruno A. Gaëta; Javier De Las Rivas; Paul Horton; Pieter Meysman; Nicola J. Mulder; Paolo Romano; Lonnie R. Welch (PLoS Comput. Biol., 2017)

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network - C. Victor Jongeneel; Ovokeraye Achinike-Oduaran; Ezekiel F. Adebiyi; Marion O. Adebiyi; Seun Adeyemi; Bola Akanle; Shaun Aron; Efejiro Ashano; Hocine Bendou; Gerrit Botha; Emile R. Chimusa; Ananyo Choudhury; et al. (PLoS Comput. Biol., 2017)

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience - Kim T. Gurwitz; Shaun Aron; Sumir Panji; Suresh Maslamoney; Pedro L. Fernandes; David P. Judge; Amel Ghouila; Jean-Baka Domelevo Entfellner; Fatma Z. Guerfali; Colleen Saunders; Ahmed Mansour Alzohairy; Samson P. Salifu; et al. (PLoS Comput. Biol., 2017)

Four simple recommendations to encourage best practices in research software - Rafael C. Jiménez; Mateusz Kuzak; Monther Alhamdoosh; Michelle Barker; Bérénice Batut; Mikael Borg; Salvador Capella-Gutiérrez; Neil P. Chue Hong; Martin Cook; Manuel Corpas; Madison Flannery; Leyla J. García; et al. (F1000Research, 2017)

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool - Gaston K. Mazandu; Emile R. Chimusa; Mamana Mbiyavanga; Nicola J. Mulder (Bioinform., 2016)

ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations - Emile R. Chimusa; Mamana Mbiyavanga; Gaston K. Mazandu; Nicola J. Mulder (Bioinform., 2016)

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt - Nicola J. Mulder; Alan Christoffels; Tulio de Oliveira; Junaid Gamieldien; Scott Hazelhurst; Fourie Joubert; Judit Kumuthini; Ché S. Pillay; Jacky L. Snoep; Özlem Tastan Bishop; Nicki Tiffin (PLoS Comput. Biol., 2016)

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee) - Lonnie R. Welch; Cath Brooksbank; Russell Schwartz; Sarah L. Morgan; Bruno A. Gaëta; Alastair M. Kilpatrick; Daniel Mietchen; Benjamin L. Moore; Nicola J. Mulder; Mark A. Pauley; William R. Pearson; Predrag Radivojac; et al. (PLoS Comput. Biol., 2016)

Bioinformatics Education - Perspectives and Challenges out of Africa - Özlem Tastan Bishop; Ezekiel F. Adebiyi; Ahmed M. Alzohairy; Dean Everett; Kais Ghedira; Amel Ghouila; Judit Kumuthini; Nicola J. Mulder; Sumir Panji; Hugh-George Patterton (Briefings Bioinform., 2015)

A Quick Guide for Building a Successful Bioinformatics Community - Aidan Budd; Manuel Corpas; Michelle D. Brazas; Jonathan C. Fuller; Jeremy Goecks; Nicola J. Mulder; Magali Michaut; B. F. Francis Ouellette; Aleksandra Pawlik; Niklas Blomberg (PLoS Comput. Biol., 2015)

GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training - Teresa K. Attwood; Erik Bongcam-Rudloff; Michelle D. Brazas; Manuel Corpas; Pascale Gaudet; Fran Lewitter; Nicola J. Mulder; Patricia M. Palagi; Maria Victoria Schneider; Celia W. G. van Gelder (PLoS Comput. Biol., 2015)

A web-based protein interaction network visualizer - Gustavo A. Salazar; Ayton Meintjes; Gaston K. Mazandu; Holifidy A. Rapanoël; Richard O. Akinola; Nicola J. Mulder (BMC Bioinform., 2014)

PPI layouts: BioJS components for the display of Protein-Protein Interactions - Gustavo A. Salazar; Ayton Meintjes; Nicola J. Mulder (F1000Research, 2014)

Best practices in bioinformatics training for life scientists - Allegra Via; Thomas Blicher; Erik Bongcam-Rudloff; Michelle D. Brazas; Catherine Brooksbank; Aidan Budd; Javier De Las Rivas; Jacqueline Dreyer; Pedro L. Fernandes; Celia W. G. van Gelder; Joachim Jacob; Rafael C. Jiménez; et al. (Briefings Bioinform., 2013)

iAnn: an event sharing platform for the life sciences - Rafael C. Jiménez; Juan P. Albar; Jong Bhak; Marie-Claude Blatter; Thomas Blicher; Michelle D. Brazas; Catherine Brooksbank; Aidan Budd; Javier De Las Rivas; Jacqueline Dreyer; Marc A. van Driel; Michael J. Dunn; et al. (Bioinform., 2013)

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures - Gaston K. Mazandu; Nicola J. Mulder (BMC Bioinform., 2013)

Identification of All Exact and Approximate Inverted Repeats in Regular and Weighted Sequences - Carl Barton; Costas S. Iliopoulos; Nicola J. Mulder; Bruce W. Watson (Engineering Applications of Neural Networks - 14th International Conference, EANN 2013, Halkidiki, Greece, September 13-16, 2013 Proceedings, Part II, 2013)

A Topology-Based Metric for Measuring Term Similarity in the Gene Ontology - Gaston K. Mazandu; Nicola J. Mulder (Adv. Bioinformatics, 2012)

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation - Sarah W. Burge; Elizabeth Kelly; David Lonsdale; Prudence Mutowo-Meullenet; Craig McAnulla; Alex L. Mitchell; Amaia Sangrador-Vegas; Siew-Yit Yong; Nicola J. Mulder; Sarah Hunter (Database J. Biol. Databases Curation, 2012)

InterPro in 2011: new developments in the family and domain prediction database - Sarah Hunter; Philip Jones; Alex L. Mitchell; Rolf Apweiler; Teresa K. Attwood; Alex Bateman; Thomas Bernard; David Binns; Peer Bork; Sarah W. Burge; Edouard De Castro; Penny C. Coggill; et al. (Nucleic Acids Res., 2012)

Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification - Gaston K. Mazandu; Nicola J. Mulder (Adv. Bioinformatics, 2011)

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems - Ludwig Geistlinger; Gergely Csaba; Robert Küffner; Nicola J. Mulder; Ralf Zimmer (Bioinform., 2011)

Dasty3, a WEB framework for DAS - Jose M. Villaveces; Rafael C. Jiménez; Leyla J. García; Gustavo A. Salazar; Bernat Gel; Nicola J. Mulder; Maria Jesus Martin; Alexander García Castro; Henning Hermjakob (Bioinform., 2011)

Investigating the effect of paralogs on microarray gene-set analysis - Andre J. Faure; Cathal Seoighe; Nicola J. Mulder (BMC Bioinform., 2011)

DAS Writeback: A Collaborative Annotation System - Gustavo A. Salazar; Rafael C. Jiménez; Alexander García Castro; Henning Hermjakob; Nicola J. Mulder; Edwin H. Blake (BMC Bioinform., 2011)

InterPro: the integrative protein signature database - Sarah Hunter; Rolf Apweiler; Teresa K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Peer Bork; Ujjwal Das; Louise C. Daugherty; Lauranne Duquenne; Robert D. Finn; Julian Gough; et al. (Nucleic Acids Res., 2009)

New developments in the InterPro database - Nicola J. Mulder; Rolf Apweiler; Teresa K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Peer Bork; Virginie Buillard; Lorenzo Cerutti; Richard R. Copley; Emmanuel Courcelle; Ujjwal Das; et al. (Nucleic Acids Res., 2007)

InterPro, progress and status in 2005 - Nicola J. Mulder; Rolf Apweiler; Teresa K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Paul Bradley; Peer Bork; Phillip Bucher; Lorenzo Cerutti; Richard R. Copley; Emmanuel Courcelle; et al. (Nucleic Acids Res., 2005)

InterProScan: protein domains identifier - Emmanuel Quevillon; Ville Silventoinen; Sharmila Pillai; Nicola Harte; Nicola J. Mulder; Rolf Apweiler; Rodrigo Lopez (Nucleic Acids Res., 2005)

The European Bioinformatics Institute's data resources - Catherine Brooksbank; Evelyn Camon; Midori A. Harris; Michele Magrane; Maria Jesus Martin; Nicola J. Mulder; Claire O'Donovan; Helen E. Parkinson; Mary Ann Tuli; Rolf Apweiler; Ewan Birney; Alvis Brazma; et al. (Nucleic Acids Res., 2003)

The InterPro Database, 2003 brings increased coverage and new features - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Daniel Barrell; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; et al. (Nucleic Acids Res., 2003)

The Proteome Analysis database: a tool for the in silico analysis of whole proteomes - Manuela Pruess; Wolfgang Fleischmann; Alexander Kanapin; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Isabelle Phan; Florence Servant; Rolf Apweiler (Nucleic Acids Res., 2003)

InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites - Nicola J. Mulder; Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Margaret Biswas; Paul Bradley; Peer Bork; Philipp Bucher; Richard R. Copley; Emmanuel Courcelle; et al. (Briefings Bioinform., 2002)

Applications of InterPro in Protein Annotation and Genome Analysis - Margaret Biswas; Joseph F. O'Rourke; Evelyn Camon; Gillian Fraser; Alexander Kanapin; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Isabelle Phan; Florence Servant; et al. (Briefings Bioinform., 2002)

Interactive InterPro-based comparisons of proteins in whole genomes - Alexander Kanapin; Rolf Apweiler; Margaret Biswas; Wolfgang Fleischmann; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Thomas M. Oinn; Isabelle Phan; Florence Servant; et al. (Bioinform., 2002)

Automation of Protein Sequence Characterization and Its Application in Whole Proteome Analysis - Rolf Apweiler; Margaret Biswas; Wolfgang Fleischmann; Evgenia V. Kriventseva; Nicola J. Mulder (Gene Regulations and Metabolism - Postgenomic Computational Approaches, 2002)

The InterPro database, an integrated documentation resource for protein families, domains and functional sites - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Nucleic Acids Res., 2001)

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes - Rolf Apweiler; Margaret Biswas; Wolfgang Fleischmann; Alexander Kanapin; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Isabelle Phan; Evgeni M. Zdobnov (Nucleic Acids Res., 2001)

InterPro-an integrated documentation resource for protein families, domains and functional sites - Rolf Apweiler; Terri K. Attwood; Amos Bairoch; Alex Bateman; Ewan Birney; Margaret Biswas; Philipp Bucher; Lorenzo Cerutti; Florence Corpet; Michael D. R. Croning; Richard Durbin; Laurent Falquet; et al. (Bioinform., 2000)

Proteome Analysis: Application of InterPro and CluSTr for the Functional Classification of Proteins in Whole Genomes - Margaret Biswas; Rolf Apweiler; Wolfgang Fleischmann; Alexander Kanapin; Youla Karavidopoulou; Paul J. Kersey; Evgenia V. Kriventseva; Virginie Mittard; Nicola J. Mulder; Thomas M. Oinn; Isabelle Phan; Evgeni M. Zdobnov (Proceedings of the German Conference on Bioinformatics (GCB 2000), Heidelberg, October 5-7, 2000, 2000)