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.

Nextflow Python Neo4j Metagenomics Genomics Proteomics Metabolomics

IDBac

One of the earliest large bioinformatics Shiny apps, pioneering interactive scientific data analysis.

R Shiny MS Chemistry Microbiology Proteomics Metabolomics

electricShine

Software to create installable R Shiny apps (archived)

R Shiny Electron Javascript™

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

Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function

Proceedings of the National Academy of Sciences

2018

Chase M. Clark, Maria S. Costa, 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?

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EVOQUANT LLC

Transforming Scientific Data into Breakthrough Discoveries

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