Transform Your Data into Breakthrough Discoveries
Bridging advanced genomics, computational methods, and innovative software solutions to accelerate scientific innovation and drug discovery. We also have experience creating insightful, reproducible data visualizations across non-scientific domains.
Our Specialized Services
Software Development
Custom bioinformatics solutions using cutting-edge technologies: R, Python, Nextflow, and modern web frameworks.
Database Development
Custom database architecture and pipelines using cutting-edge technologies. We have experience creating standard and novel SQL and NoSQL solutions with SQLite, Postgres, Neo4j, and more.
Data Visualization
10+ years of experience creating insightful, reproducible data visualizations across complex scientific domains. See our gallery for some public examples.
Genomic Analysis
Advanced genomic and metagenomic data processing with state-of-the-art computational techniques.
Drug Discovery
End-to-end natural product drug discovery consults. From bioinformatics to lab technique and chemistry.
CI/CD
Experienced in developing robust continuous integration and deployment environments for complex scientific workflows.
Tutorials and Documentation
We cofounded and contribute to a technical blog at https://code4np.github.io and have experience with writing technical documentation with mkdocs, sphinx, quarto, rmarkdown, etc.
Workshops and Demonstrations
We have experience in advanced technical education and are available for workshops across a variety of dry and wet lab domains.
Our Open Source Projects
Besides contributions to other open source and client projects, we are the primary developers and maintainers of the following open-source projects:
SocialGene
Extensive Nextflow workflow and Python library for creating and analyzing repository scale genomic and multi-omics graph databases.
IDBac
One of the earliest large bioinformatics Shiny apps, pioneering interactive scientific data analysis.
Publications we have led or been involved with
Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene
Journal not available
2024
Chase M. Clark, Jason C Kwan
Artificial intelligence for natural product drug discovery
Nature Reviews Drug Discovery
2023
Michael W. Mullowney, Katherine R. Duncan, Somayah S. Elsayed, Neha Garg, Justin J. J. van der Hooft, Nathaniel I. Martin, David Meijer, Barbara R. Terlouw, Friederike Biermann, Kai Blin, Janani Durairaj, Marina Gorostiola González, Eric J. N. Helfrich, Florian Huber, Stefan Leopold-Messer, Kohulan Rajan, Tristan de Rond, Jeffrey A. van Santen, Maria Sorokina, Marcy J. Balunas, Mehdi A. Beniddir, Doris A. van Bergeijk, Laura M. Carroll, Chase M. Clark, Djork-Arné Clevert, Chris A. Dejong, Chao Du, Scarlet Ferrinho, Francesca Grisoni, Albert Hofstetter, Willem Jespers, Olga V. Kalinina, Satria A. Kautsar, Hyunwoo Kim, Tiago F. Leao, Joleen Masschelein, Evan R. Rees, Raphael Reher, Daniel Reker, Philippe Schwaller, Marwin Segler, Michael A. Skinnider, Allison S. Walker, Egon L. Willighagen, Barbara Zdrazil, Nadine Ziemert, Rebecca J. M. Goss, Pierre Guyomard, Andrea Volkamer, William H. Gerwick, Hyun Uk Kim, Rolf Müller, Gilles P. van Wezel, Gerard J. P. van Westen, Anna K. H. Hirsch, Roger G. Linington, Serina L. Robinson, Marnix H. Medema
Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities
Journal not available
2023
Evan R. Rees, Siddharth Uppal, Chase M. Clark, Andrew J. Lail, Samantha C. Waterworth, Shane D. Roesemann, Kyle A. Wolf, Jason C. Kwan
Relationship between bacterial phylotype and specialized metabolite production in the culturable microbiome of two freshwater sponges
ISME Communications
2022
Chase M Clark, Antonio Hernandez, Michael W Mullowney, Jhewelle Fitz-Henley, Emma Li, Sean B Romanowski, Roberto Pronzato, Renata Manconi, Laura M Sanchez, Brian T Murphy
Automated Microbial Library Generation Using the Bioinformatics Platform IDBac
Molecules
2022
Chase M. Clark, Linh Nguyen, Van Cuong Pham, Laura M. Sanchez, Brian T. Murphy
Quick-start infrastructure for untargeted metabolomics analysis in GNPS
Nature Metabolism
2021
Tiago F. Leao, Chase M. Clark, Anelize Bauermeister, Emmanuel O. Elijah, Emily C. Gentry, Makhai Husband, Michelli F. Oliveira, Nuno Bandeira, Mingxun Wang, Pieter C. Dorrestein
Evaluating the Distribution of Bacterial Natural Product Biosynthetic Genes across Lake Huron Sediment
ACS Chemical Biology
2021
Maryam Elfeki, Shrikant Mantri, Chase M. Clark, Stefan J. Green, Nadine Ziemert, Brian T. Murphy
A Call to Action: the Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination
mSystems
2020
Chase M. Clark, Brian T. Murphy, Laura M. Sanchez
Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data
Journal of Visualized Experiments
2019
Chase M. Clark, Maria S. Costa, Erin Conley, Emma Li, Laura M. Sanchez, Brian T. Murphy
Minimizing Taxonomic and Natural Product Redundancy in Microbial Libraries Using MALDI-TOF MS and the Bioinformatics Pipeline IDBac
Journal of Natural Products
2019
Maria S. Costa, Chase M. Clark, Sesselja Ómarsdóttir, Laura M. Sanchez, Brian T. Murphy
Selected Presentations
Information-rich Platforms for Natural Product Antibiotic Discovery
Northeastern University Seminar, exploring innovative approaches to natural product research.
Multi-Repository Genomic Search Engine
GRC Conference presentation on a comprehensive genomic and chemical search engine for discovery.
Programming in R for Metabolomics
May Institute presentation on advanced programming techniques for mass spectrometry data analysis.
Ready to Accelerate Your Work?
Connect with us and discover how we can transform your scientific data into breakthrough discoveries.