A cloud-based learning environment for comparing RNA-seq aligners. - Elizabeth Baskin; Peter De-Ford; Allison F. Dennis; Ian Misner; Frederick J. Tan; Ben Busby (F1000Research, 2016)

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping. - Ben Busby; Matthew Lesko; Lisa Federer (F1000Research, 2016)

MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. - Eric Moyer; Megan Hastings Hagenauer; Matthew Lesko; Felix Francis; Oscar Rodriguez; Vijayaraj Nagarajan; Vojtech Huser; Ben Busby (F1000Research, 2016)

Harmonizing User-defined Phenotypic Variables using Latent Semantic Analysis (LSA) to Improve Data Discoverability in dbGaP. - Liz Amos; Satyajeet Raje; Masato Kimura; Preeti G. Kochar; Victoria Wilder; Ben Busby (AMIA, 2017)

MeSHgram: An Open Source Tool to Visually Browse Co-occurrence of MeSH Terms in PubMed. - Satyajeet Raje; Ravi Teja Bhupatiraju; Abdelrahman Hosny; Ben Busby (AMIA, 2017)

PubRunner: A light-weight framework for updating text mining results. - Kishore R. Anekalla; J. P. Courneya; Nicolas Fiorini; Jake Lever; Michael Muchow; Ben Busby (F1000Research, 2017)

DangerTrack: A scoring system to detect difficult-to-assess regions. - Igor Dolgalev; Fritz J. Sedlazeck; Ben Busby (F1000Research, 2017)

Extending TCGA queries to automatically identify analogous genomic data from dbGaP. - Erin K. Wagner; Satyajeet Raje; Liz Amos; Jessica Kurata; Abhijit Badve; Yingquan Li; Ben Busby (F1000Research, 2017)

Viewing RNA-seq data on the entire human genome. - Eric M. Weitz; Lorena Pantano; Jingzhi Zhu; Bennett Upton; Ben Busby (F1000Research, 2017)

NovoGraph: Genome graph construction from multiple long-read de novo assemblies. - Evan Biederstedt; Jeffrey C. Oliver; Nancy F. Hansen; Aarti Jajoo; Nathan A. Dunn; Andrew Olson; Ben Busby; Alexander T. Dilthey (F1000Research, 2018)

Matchmaking in Bioinformatics. - Ewy A. Mathé; Ben Busby; Helen Piontkivska; Team of Developers (F1000Research, 2018)

Reply to the paper: Misunderstood parameters of NCBI BLAST impacts the correctness of bioinformatics workflows. - Thomas L. Madden; Ben Busby; Jian Ye (Bioinform., 2019)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads. - Grzegorz M. Boratyn; Jean Thierry-Mieg; Danielle Thierry-Mieg; Ben Busby; Thomas L. Madden (BMC Bioinform., 2019)

Iron Hack - A symposium/hackathon focused on porphyrias, Friedreich's ataxia, and other rare iron-related diseases. - Gloria C. Ferreira; Jenna Oberstaller; Renée Fonseca; Thomas E. Keller; Swamy Rakesh Adapa; Justin Gibbons; Chengqi Wang; Xiaoming Liu; Chang Li; Minh Pham; Guy W. Dayhoff II; Linh M. Duong; et al. (F1000Research, 2019)

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive. - Matthew N. Bernstein; Ariella L. Gladstein; Khun Zaw Latt; Emily Clough; Ben Busby; Allissa Dillman (F1000Research, 2020)

VariantSurvival: a tool to identify genotype-treatment response. - Thomas Krannich; Marina Herrera Sarrias; Hiba Ben Aribi; Moustafa Shokrof; Alfredo Iacoangeli; Ammar Al-Chalabi; Fritz J. Sedlazeck; Ben Busby; Ahmad Al Khleifat (Frontiers Bioinform., 2023)