Genetics, Bioinformatics, and Biomedical Research

Characterization of heterogeneous bioinformatics training needs in the AI era

The paper introduces a network-based clustering method to identify distinct learner profiles from training-needs surveys, revealing heterogeneous bioinformatics training needs in the AI era.

The yEvo Mutation Browser: Enhancing student understanding of experimental evolution and genomics through interactive data visualization

The yEvo Mutation Browser helps students and researchers visualize and interpret genome sequencing data from experimental evolution studies of yeast.

A Course-Undergraduate Research Experience (CURE) to explore the effect of structural variants on gene expression in C. elegans balancers

Students investigated structural variants' effects on gene expression in C. elegans balancers using bioinformatics tools and reported molecular mechanisms and unexpected gene expression effects.

Bridging the Python Training Gap for Bioscientists in Brazil: Improvements and Challenges

This paper describes improvements and challenges in a Brazilian Python workshop for bioscientists, focusing on structural changes, new teaching strategies, and enhanced outreach.

Student-Driven Microbiome Exploration: A Low-Cost 16S rRNA Sequencing Curriculum for Undergraduate Biology Education

This paper presents a low-cost 16S rRNA sequencing curriculum for undergraduates, enabling hands-on microbiome research through open-source tools and simplified workflows.

Using user-centered design to better understand challengesfaced during genetic analyses by novice genomicresearchers

This paper identifies challenges faced by novice genomic researchers with bioinformatics tools and proposes an evaluation rubric to improve software usability.

Assessing the Efficacy of Computational Workshops and Participatory Live Coding in Evolutionary Biology

The paper evaluates the effectiveness of computational workshops in evolutionary biology by assessing participant motivation and perceptions of instructional techniques.

Chromatin profiling for everyone: FFPE-CUTAC for the theory and practice of modern molecular biology

The paper describes a summer research program where students learned chromatin profiling using FFPE-CUTAC, focusing on practical lab techniques and bioinformatics analysis.

Leveraging a hybrid cross-disciplinary training model to accelerate global bioinformatics capacity

This paper introduces a hybrid training model to enhance bioinformatics capacity globally, demonstrating its effectiveness through an Eastern European workshop series.

Eduomics: a Nextflow pipeline to simulate -omics data for education

Eduomics is a Nextflow pipeline that simulates genomic and transcriptomic data for educational purposes, providing realistic clinical scenarios to enhance bioinformatics learning.

Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024

This study surveys the AnVIL community to understand user needs, training preferences, and platform adoption opportunities.

Utilisation of genomic services among physicians in Kenya

This study assesses genomic service utilization among Kenyan physicians, finding low involvement in genetic testing and pharmacogenomics due to lack of training, limited specialists, and high costs.

Evaluating peer-to-peer bioinformatics education: a case study of student learning outcomes and community impact in an undergraduate multi-omic data analysis course

This paper evaluates a peer-to-peer bioinformatics course, finding it improves student confidence and skills through collaborative learning.

Catalyzing computational biology research at an academic institute through an interest network

The paper describes how a volunteer-led affinity group enhances computational biology skills and networking among researchers at an academic institute.

Artificial Intelligence for Genomics and Bioinformatics: Is Africa Lagging Behind?

The paper surveys AI usage in African genomics research and finds low familiarity with AI applications among researchers.

ERSAtool: A User-Friendly R/Shiny Comprehensive Transcriptomic Analysis Interface Suitable for Education

ERSAtool provides an intuitive R/Shiny interface for RNA-seq analysis, reducing technical barriers and supporting educational use with comprehensive reporting.

Enhancing student comprehension of paternity assignment in molecular primatology: a pilot study using a Shiny web application in Kenya

This paper evaluates a Shiny web app for teaching paternity inference in primatology, showing improved student understanding and engagement in a Kenyan setting.

"The Metagenomics Days": a simplified workshop on amplicon sequencing analysis with open cloud bioinformatics for eDNA and Microbiomes

This paper evaluates the impact of a metagenomics workshop through pre- and post-event surveys, showing significant improvements in participants' confidence and knowledge in bioinformatics pipelines, diversity metrics, and cloud computing.

Data Hunters: bridging bioinformatics education and microbiome research

The paper describes a workshop that trains students to curate metagenomics metadata from human skin microbiome sequencing projects, enhancing data standardization and accessibility.

Design and implementation of an asynchronous online course-based undergraduate research experience (CURE) in computational genomics

This paper describes the design and implementation of an online CURE in computational genomics that improved student learning and engagement through asynchronous communication and tailored resources.

A workflow for practical training in ecological genomics using Oxford Nanopore long-read sequencing

The paper presents a long-read sequencing workflow for ecological genomics education, enabling students to assemble and identify plant genomes within two weeks.

Who Grows There? A Course-based Undergraduate Research Experience to explore the human microbiome through 16S DNA metabarcoding

This paper describes a CURE that teaches undergraduates DNA sequencing, molecular biology, and bioinformatics through analyzing the human microbiome using 16S metabarcoding.

UNIGEMS: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli

The paper introduces Unigems, a set of plasmids for teaching synthetic biology concepts like gene expression control and logic gates in E. coli.

Empowering Beginners in Bioinformatics with ChatGPT

This study explores using ChatGPT to assist beginners in bioinformatics by fine-tuning it to generate code for data analysis tasks and discusses its educational applications and limitations.

Galaxy Training: A Powerful Framework for Teaching!

The paper introduces Galaxy Training Network (GTN) as a framework for creating and sharing FAIR training materials for data analysis, with recent improvements to support educators and expand its use in various learning environments.

Training Infrastructure as a Service

TIaaS provides scalable infrastructure for efficient bioinformatics training, enabling remote and in-person classes with minimal delays and administrative overhead.

Manual Annotation of Genes within Drosophila Species: the Genomics Education Partnership protocol

The paper describes a manual gene annotation protocol for Drosophila species used by undergraduate students to improve gene annotations in genomic databases.

Understanding changes in genetic literacy over time and in genetic research participants

The paper assesses changes in genetic literacy over time and between genetic research participants and the general population, finding improvements in familiarity, knowledge, and skills in 2021 compared to 2013.

A repository of web-based bioinformatics resources developed in India

IndiaBioDb is a curated repository of bioinformatics resources developed in India, providing access to 258 databases and 543 resources with search and browsing tools.

Molecular Biology Information Service: An innovative medical library-based bioinformatics support service for biomedical researchers

The paper describes a bioinformatics support service model for biomedical researchers, detailing its four facets and outcomes from a survey of University of Pittsburgh researchers.