Powering insights
across the life sciences
If it involves biology and big data, Watershed is the solution. With 100+ unique data analysis templates, customizable workflows, and a dedicated team of bioinformaticians, no analysis is too complex.
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Whole Genome Sequencing (WGS) & Whole Exome Sequencing (WES)
Robustly identify indels, copy-number alterations, structural variants, and more.
Variant Calling
Compare WGS and WES data to reference genomes to identify and quantify variations.
Long-read sequencing
Perform phase-aware analyses of long-read data from PacBio or Oxford Nanopore.
Gene editing
Analyze data from BLISS, GUIDE-Seq, CRISPResso, Digenome-Seq, and other techniques to characterize on-target efficacy and off-target profiles.
Public datasets
Effectively utilize data from public sources like Open Targets, Genebass, gnomAD, CCLE, and dbSNP.
Whole Genome Sequencing (WGS) & Whole Exome Sequencing (WES)
Variant Calling
Long-Read Sequencing
Gene Editing
Public Datasets
Genome-Wide Association Studies (GWAS)
Identify SNPs correlated with a phenotype of interest at scale using your own or public datasets such as CCLE and ClinVar.
Mendelian Randomization
Perform phase-aware analyses of long-read data from PacBio or Oxford Nanopore.
ATAC-Seq
Determine chromatin accessibility at whole-genome or single-cell resolution and pair with RNA-Seq to understand chromatin's impact on gene expression.
ChIP-Seq
Map DNA-binding proteins and histone modifications to understand epigenetics' role in health and disease.
RNA-Seq
Perform alignment, differential expression, isoform analysis, pathwayenrichment and more. Plus, leverage long-read sequencing data to fully characterize isoform-specific expression across the transcriptome.
Single Cell RNA-Seq
Access comprehensive interpretation of scRNAseq data, including robust QC, multi-sample comparison, cell annotation, RNA velocity analysis, and more.
Public Datasets
Effectively utilize data from public sources like recount3.
Geneformer
Make tissue-specific predictions of the effects of gene perturbation.
Spatial Sequencing
Analyze spatially-resolved data from platforms like 10X’s Visium and NanoString's GeoMx or CosMx.
Immune Repertoire Sequencing
Analyze spaStudy the full set of T and B cell clonotypes to understand the immune system's role in health and disease.tially-resolved data from platforms like 10X’s Visium and NanoString's GeoMx or CosMx.
Whole Genome Sequencing (WGS) & Whole Exome Sequencing (WES)
Variant Calling
Long-Read Sequencing
Gene Editing
Public Datasets
Mass Spectrometry
Easily identify and quantify proteins and post-translational modifications (PTMs) from any mass spectrometry instrument.
Olink
Analyze multiplexed protein expression from Olink® assay kits.
AlphaFold2
Predict the 3D structures of proteins from their amino acid sequences.
Custom Integrations
Uncover important relationships across diverse datasets and data types.
Public Datasets
Effectively leverage data from public sources like gnomAD, CCLE, ClinVar, recount3, and many more.
Cellranger
Profile combined transcript- or probe-based gene expression, immune repertoire characterization, and/or surface protein tags.
Metagenomics
Characterize bacterial diversity across environments and microbiomes using 16s rRNA sequencing data.
de novo Assembly
Assemble and annotate completely novel genomes with tools like SPAdes, Trinity, and other state-of-the-art assemblers.
Metagenomics
Characterize bacterial diversity across environments and microbiomes using 16s rRNA sequencing data.
de novo Assembly
Assemble and annotate completely novel genomes with tools like SPAdes, Trinity, and other state-of-the-art assemblers.
Metatranscriptomics
Understand a microbial community's complete expression profile.
Read the latest insights
Learn about new research, best data practices, and more.
Blog
Accelerating Biology with GPUs
Graphical processing units (GPUs) are powerful computing components that are increasingly being used by biology researchers to run foundation models and accelerate analyses.
Read More
Blog
Science Chat with Tom Backus
Tom Backus is an Associate and the Commercial Lead at Amplify, an early-stage translational investment fund of Mass General Brigham Innovation. We spoke to Tom about bridging the gap from lab to commercial product, and fostering curiosity through community.
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News
Watershed's 2024 Year in Review
As 2024 comes to a close, we take a moment to reflect on the incredible journey we've had this year. From hosting engaging webinars to showcasing our innovations at global conferences, it has been a year full of opportunities, learning, and meaningful connections. Here's a recap of our standout events from the past year.
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Blog
Foundation Models for Biomedical Research
Foundation models use advanced machine learning algorithms and massive training datasets to infer patterns and make predictions from a variety of data types. These models are enabling biomedical scientists to probe increasingly complex research questions.
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Blog
Transposons: Jumping from the Lab to the Clinic
Transposons are genetic elements that can move locations in the genome. As relatively straightforward systems for gene editing, transposons have enabled the development of many new research and clinical tools.
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Webinar
IRGQ: A novel protein target for cancer therapeutics
Watch our webinar with protein and cancer biology expert Dr. Vinay Eapen to learn about IRGQ, a novel protein target for cancer therapeutics.
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Blog
Spatial Transcriptomics: Applications, Methods, & Challenges
Spatial transcriptomics approaches are used to measure gene expression in the spatial context of a tissue sample. While these techniques hold tremendous promise for many research fields, there are still analysis and interpretation challenges to resolve.
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Blog
Lipid Rafts in Disease & Therapeutics
Lipid rafts are components of the cell membrane formed by tightly-packed lipids, cholesterol, and proteins. They play an integral role in many cellular processes, making them a topic of interest for drug development and disease research.
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Blog
Science Chat with Dr. Daria Shlyueva
Dr. Daria Shlyueva is a Senior Scientist at Novo Nordisk. We spoke to Dr. Shlyueva about the fundamentals of a scientific education, the importance of metadata in research, and much more.
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Webinar
Bugs and Junk: Transforming data from emerging -omics fields into novel therapeutics
Watch our webinar with computational biologist Dr. Liyang Diao to learn how novel bioinformatics approaches are unlocking the therapeutic potential of emerging research areas.
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Blog
Science Chat with Dr. Andrew Spencley
Dr. Andrew Spencley is a Genome Editing Scientist at Novo Nordisk. We spoke to Dr. Spencley about navigating the scientific process from bench to analysis, the importance of mentorship, and more.
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Webinar
The limits of dimensionality reduction tools for single-cell analysis
Learn how to visualize single-cell data and interrogate the outputs of dimensionality reduction tools like t-SNE and uMAP.
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Webinar
Cytometry in the -Omics Era for All
Learn how to overcome computational and technical barriers in flow cytometry data analysis and access cytomics insights with Dr. Andrew Wight.
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Blog
Science Chat with Dr. Alisa Vershinina
Dr. Alisa Vershinina is a Senior Scientist in Bioinformatics at SalioGen Therapeutics. We spoke to Dr. Vershinina about her fascinating background in paleogenomics and her journey from entomology in Russia to biotech in the U.S.
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Blog
Science Chat with Dr. Paola Moreno-Roman
In our new Science Chat, we speak to professor and STEM outreach expert Dr. Paola Moreno-Roman about how her communities in both her native Peru and the U.S. shaped her research career & advocacy work.
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Blog
CPTAC and the Impact of Proteogenomics on Cancer Research
By applying novel proteogenomic data analysis tools to datasets like the Clinical Proteomic Tumor Analysis Consortium (CPTAC), researchers are rapidly advancing our understanding of cancer.
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Blog
Science Chat with Dr. Mallori Upshaw
Dr. Mallori Upshaw is the Director of Business Insights and Strategy at AstraZeneca, focusing on COVID-19 vaccines and immunotherapies. We spoke with Dr. Upshaw about her unique scientific journey and her experiences as a Black woman in STEM.
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Blog
Large Language Models in Biology
Popularly used in chat interfaces like ChatGPT, Large Language Models (LLMs) are also being used to decode the various languages of biology.
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News
Dr. Stefanie Morgan's SciMed Podcast
Hear our own Stefanie Morgan's discussion with Adam Stasio and SciMed on Streamlining Bioinformatics.
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Blog
Science Chat with Dr. Miranda Stratton
Check out our new series, “Science Chats”, with our first guest - Dr. Miranda Stratton!
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Case Study
Developing a Next-Generation Gene Editing Platform with Watershed
A privately-held biotechnology company is developing a new category of gene therapies.
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Webinar
The Future of Human Gene Editing
Coming on 3/7, Watershed has the honor of hosting a webinar by groundbreaking genetics researcher Nancy L. Craig.
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Case Study
How Violet Therapeutics Scaled Their Target Discovery Platform with Watershed
Violet Therapeutics is a pre-clinical stage company leveraging their first-in-class platform, based on RABID-seq technology, to map and mine the cellular connectome at scale.
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Blog
Geneformer: Powering Drug Target Discovery with Network Biology
Geneformer is a tool developed by Theodoris et al. (Nature 2023) to predict tissue-specific gene network dynamics from single-cell transcriptomic data.
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News
New Automation Features for Streamlined Data Processing and Analysis
Our new workflow automation features help you accelerate high-volume data processing from upload to output.
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Blog
AlphaFold: Applications for Biomedical Research
AlphaFold2 predictions have been used to probe questions at the heart of biomedical research, like how to design superior drugs, and how protein structure impacts disease.
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News
Watershed's 2023 Year In Review
From closing Series A to processing over a petabyte of data, 2023 was a pivotal year in Watershed's growth. Check out this collection of some of our top highlights from this year.
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Blog
Nobel Prize Day 2023: The Road to mRNA Vaccines
Drs. Karikó and Weissman’s research into mRNA and the immune system enabled the rapid development of vaccines against the SARS-CoV-2 virus.
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Webinar
Advances in Big Data for Immuno-Oncology
Watch our webinar with cancer researcher Dr. Michelle Atallah to learn about the latest challenges and opportunities towards realizing the potential of big data in immunology and proteomics.
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White Paper
Accelerating Multi-omics Analysis
Download our white paper to learn how Watershed is revolutionizing the use of big data in biology.
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News
Watershed Secures $14.5M Series A to Help Scientists Unlock Multi-Omic Insights for Drug Discovery
Financing will accelerate commercial roll-out of the company's cloud-based platform that provides a unified workspace for data-intensive biomedical research accessible by both biologists and bioinformaticians
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Blog
Cell Painting with Watershed
The JUMP-Cell Painting Consortium combines images from nearly 120,000 chemical and 18,000 genetic perturbations with high-dimensional data analytics to streamline the drug discovery process.
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Blog
Leveraging Public Datasets for Drug Discovery
The amount of public biological data available to researchers has exploded – but garnering insights requires appropriate infrastructure, expertise, and resources.
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Blog
Variant Calling for Disease-Causing Mutations: The state-of-art process
Explore important considerations for effective and accurate variant calling in WGS/WES data.
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Blog
Unlock the Power of Genomics Data Analysis: Watershed's Seamless Cloud Computing Solution
Dr. Tommy Tang reviews the challenges with cloud computing in biotech, with an emphasis on concerns facing startups.
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Blog
Watershed Informatics: The First Omics Bench for Modern Researchers
Watershed was founded to empower the world’s scientists to transform today’s big data into tomorrow’s precision medicines.
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Case Study
Building an Innovative Drug Discovery Platform with Watershed
Learn how a pre-clinical stage company is using Watershed to develop a novel approach to small molecule drug discovery.
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Blog
Using gnomAD to Drive Insights in Precision Medicine
The Genome Aggregation Database (gnomAD) is a collaborative effort to make data from large-scale sequencing projects publicly available for scientific use. Learn how to leverage the latest updates to the database, including new data from more than 700k individuals.
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Blog
Science Chat with Tom Backus
Tom Backus is an Associate and the Commercial Lead at Amplify, an early-stage translational investment fund of Mass General Brigham Innovation. We spoke to Tom about bridging the gap from lab to commercial product, and fostering curiosity through community.
Read More
Blog
Accelerating Biology with GPUs
Graphical processing units (GPUs) are powerful computing components that are increasingly being used by biology researchers to run foundation models and accelerate analyses.
Read More
News
Watershed's 2024 Year in Review
As 2024 comes to a close, we take a moment to reflect on the incredible journey we've had this year. From hosting engaging webinars to showcasing our innovations at global conferences, it has been a year full of opportunities, learning, and meaningful connections. Here's a recap of our standout events from the past year.
Read More
Blog
Foundation Models for Biomedical Research
Foundation models use advanced machine learning algorithms and massive training datasets to infer patterns and make predictions from a variety of data types. These models are enabling biomedical scientists to probe increasingly complex research questions.
Read More
Public datasets
