Welcome to the Pluto Resources & Blog page, where we share the latest insights and breakthroughs in computational biology. Explore articles on the cutting-edge developments in single cell RNA-seq analysis, keep up on product updates, and explore significant research findings and industry news. Welcome to the community shaping the future of scientific discovery and collaboration, we're glad you're here!
Funding led by new investor Kickstart, with continued support from Silverton Partners and other investors
Read more 
Accelerate cancer research with the Cancer Cell Line Encyclopedia (CCLE) and Pluto Bio’s no-code platform. Discover biomarkers, test therapies, and unlock insights from extensive cancer cell line data.
Read more
Accelerate cancer research with TCGA data—uncover biomarkers and targets effortlessly using Pluto Bio’s intuitive, no-code bioinformatics platform.
Read more
Discover how proteomics empowers translational scientists to uncover disease biomarkers, identify novel drug targets, and optimize clinical decisions.
Read more
Explore the differences between GSEA and ORA for pathway analysis of next-gen sequencing data. Learn how these two key approaches help interpret gene expression results and reveal underlying biological processes.
Read more
Explore NIH's updated genomic data security best practices and learn how researchers can ensure compliance and protect sensitive data using platforms like Pluto Bio.
Read more
Compare top bioinformatics platforms—Pluto Bio, Partek Flow, Basepair, and Rosalind—to find the best fit for your NGS data analysis needs. Assess supported assays, analyses, visualizations, and collaboration features.
Read more
Discover the differences between RNA-seq and scRNA-seq, their applications in target discovery, and how pseudobulking bridges bulk and single-cell analysis. Unlock insights into gene expression for drug development and personalized medicine.
Read more
Explore how multi-omics integrates diverse datasets like RNA-seq, ATAC-seq, and ChIP-seq to unlock biological insights, accelerate drug discovery, and drive personalized therapies. Learn more about its impact on cancer research and target identification.
Read more
Discover how Pluto’s multi-omics pipelines accelerate target validation in drug discovery. Learn how integrated platforms streamline the path from omics data to validated therapeutic targets.
Read more
Discover top alternatives to Rosalind for bioinformatics and computational biology. Explore platforms like Pluto Bio, BaseSpace, GenePattern, and more to find the right solution for your research needs.
Read more
Discover how multi-omics revolutionizes drug discovery by integrating genomics, proteomics, and more to reveal complex disease networks, enabling precise target validation and accelerated breakthroughs.
Read more
Learn how Nimbus Therapeutics is simplifying Multi-Omics Data Analysis: Nimbus Therapeutics' Success with Pluto Bio
Read more
Announcing 3 new visualizations available in Pluto for analyzing single cell data! Investigate marker gene expression and signatures with ridge plots, violin plots, and UMAPs. Customize colors and layouts to make your plots truly presentation-ready 😍
Read more
Discover how the Al Diri Lab improved efficiency and productivity in retinal research using Pluto Bio.
Read more
The Wyss Brain Targeting Program announced it will use Pluto’s target discovery software platform to analyze and visualize -omics data, curate evidence from various published literature sources, and integrate these findings with expert insight from Wyss Institute scientists to efficiently identify and prioritize genes and proteins with transport capacity that can significantly increase drug transport into the brain.
Read more
Multi-omics has emerged as a transformative technology in drug discovery. Layering genomics, transcriptomics, proteomics and other molecular analyses in a single experiment can provide deep biological insight and identify new therapeutic targets. However, developers face challenging data integration and analysis to get the most out of multi-omics data. Here, we explore how bioinformatics is key to unlocking the full potential of multi-omics and transforming drug discovery.
Read more
Learn how Nimbus Therapeutics is simplifying multi-omics data analysis and accelerating small molecule drug discovery with Pluto’s bioinformatics platform
Read more
Even for clinicians and lab members without coding experience, Pluto makes it easy for any of us to look at our own data and make publication- ready plots.
Read more
Pluto Bio partners with Wyss Institute Brain Targeting Program on novel target discovery. Leading institute to use Pluto’s target discovery platform to integrate -omics data, literature, and other evidence in their discovery of brain-targeting shuttles for drug delivery that can help revolutionize the treatment of brain diseases.
Read more
Learn the basics of RNA-seq, including its methodology, applications, experimental design, and data analysis techniques. This 101 overview is perfect for biologists and bioinformaticists investigating transcriptomics for the first time.
Read more
Products that Count is a 501(c)3 nonprofit that helps everyone build great products. It celebrates product excellence through coveted Awards that inspire 500,000+ product managers and honor great products and the professionals responsible for their success.
Read more
ColoradoBiz profiles Pluto, a Denver start-up that helps accelerate drug development
Read more
We're thrilled to announce that Pluto has been selected as one of 20 companies in the 2024 cohort of the BioTools Innovator Accelerator, the first accelerator dedicated to supporting life science tools.
Read more
We've released some exciting updates in Pluto recently to help your team gain even more insight from your data. Read on for the latest
Read more
We're excited to unveil an updated brand for Pluto Bio! The new brand elevates our mission to empower every scientist to run analyses & create beautiful visualizations with modern, collaborative software.
Read more
Ready to experience the most intuitive scRNA-seq experience yet?
Read more
We’re proud to highlight a new paper citing Pluto, published in Cardiovascular Research by Dr. Priyatansh Gurha at The University of Texas Health Science Center.
Read more
Increase collaboration with third-party apps in Pluto
Read more
Pluto is excited to attend the 42nd annual JPM Healthcare Conference.
Read more
We’re excited to share a look at some of the latest product updates we’ve been working on, and give you a sneak peek into new features. Here’s the latest: Comments and Notes, Covariates, Export to Microsoft Word and Powerpoint, and more.
Read more
To draw accurate and meaningful conclusions from RNA-seq data, it is essential to consider covariates, which are additional, potentially “hidden” variables that may impact gene expression in your experiment
Read more
We’re proud to highlight a new paper citing Pluto, published in Nature Communications by Dr. Queeny Dasgupta at the Wyss Institute at Harvard University.
Read more
Comments and research notes allow team collaboration within Pluto
Read more
New in Pluto: Graphpad Prism support, SDKs, and expanded experiments ✨
Read more
The results are in for G2's Best of Pharma & Biotech software - Fall 2023
Read more
Check out the latest summer feature releases from Pluto! Sync your interactive analyses, visualizations and results to Benchling, create private and public share links, plus build multi-panel figures with Storyboards
Read more
Accelerate workflows by syncing interactive Pluto visualizations to the Benchling R&D Cloud
Read more
Dive into the world of Precision Run-On sequencing (PRO-seq) in this comprehensive blog post. Discover the origins of PRO-seq, how it compares with traditional RNA-seq, and explore a step-by-step guide on conducting a PRO-seq experiment. Uncover how this innovative technology is advancing our understanding of transcriptional dynamics and revolutionizing genomic research.
Read more
Pluto was named one of the 2023 Top Vertical SaaS Companies to Watch by Headline VC and Bain Capital Ventures.
Read more
The company born from a Harvard research institute is ramping up its sales strategy.
Read more
The Wyss Institute article on advice from Wyss lumineers to life science entrepreneurs
Read more
The Company’s web-based, computational biology platform empowers researchers to analyze and visualize high-dimensional biological data, and intuitively interpret and present novel findings
Read more
RNA sequencing (RNA-Seq) has revolutionized the way we study gene expression. The data deluge it produces, however, presents a critical question: how can we make valid comparisons between different samples or conditions?
Read more
Learn about key file formats in high-throughput research, including FASTQ, FASTA, BAM/SAM, BAI, SAM, VCF, GFF/GTF, BED, BedGraph, BigWig, and PDB. Discover how each format is used, what information it contains, and its significance in analyzing ChIP-seq and ATAC-seq data. Understanding these formats is crucial for efficiently handling and analyzing high-throughput data, enabling valuable biological insights and discoveries.
Read more
Check out the latest features from Pluto for 2023! Upgrade your presentation game with interactive slides and live data, get early access to the new Scientific Storyboards feature, auto-detect RNA-seq strandedness, and access over 14,000 published experiments. Plus, learn about differential expression analysis in the latest Pluto Learning Series. Join the Pluto community today!
Read more
In the field of genomics and bioinformatics, research discovery can be slowed down by the time and resources required to analyze and interpret large datasets. Bioinformatics platforms, which are specialized software or online tools that provide a range of analysis functions, can help to streamline the process and accelerate research discovery.
Read more
See your end-of-year wrap-up with real-time metrics
Read more
Pluto will be participating in the upcoming 41st annual JPM Healthcare Conference.
Read more
We’re proud to highlight a new paper citing Pluto, published today in Cells by Dr. Holger Russ’ lab at the Barbara Davis Center for Diabetes, University of Colorado School of Medicine.
Read more
Curious about CUT&RUN and when you would use it? Learn more in this Pluto blog post about getting started with CUT&RUN.
Read more
This blog post explains the differences between computational biology and bioinformatics. Bioinformatics is concerned with the development and application of computational methods for analyzing and interpreting large biological datasets, while computational biology involves mathematical models and computer simulations to study complex biological systems and processes. The post also describes the different tools and platforms used in each field and how modern SaaS platforms are bringing the two fields together. Finally, a top 10 list summarizes the main differences between computational biology and bioinformatics.
Read more
The Wyss Institute article on advice from Wyss lumineers to life science entrepreneurs
Read more
Kaplan-Meier curves are an essential tool in computational biology research, allowing analysis of survival data and identification of important genes and pathways associated with specific traits or diseases. Learn more about their importance in this blog post. #computationalbiology #KaplanMeier #survivalanalysis
Read more
A mini intro to RSEM, a workhorse in RNA-seq data quantification.
Read more
Pluto is revolutionizing how R&D teams think about their results and figures.
Read more
Unlocking the power of big data in biology with dimensionality reduction techniques. Explore how PCA, t-SNE, and other methods are driving insights in computational biology. #DimensionalityReduction #ComputationalBiology #BigDataInsights
Read more
Discover the power of Integrative Genomics Viewer (IGV) plots - a highly customizable and interactive tool for visualizing and exploring genomic data. Learn how IGV plots can be used in genomic research and the methods for creating data used in these plots. #genomics #bioinformatics.
Read more
Differential expression analysis is a powerful tool used to identify genes or transcripts that are differentially expressed between two or more conditions or sample types. This technique is commonly used in the field of genomics, transcriptomics, and proteomics to study the molecular mechanisms underlying different biological processes, such as disease development, response to treatment, or adaptation to different environments.
Read more
In this blog post we will explain what Z-scores are how they are calculated and how they can be used in RNA-seq analysis.
Read more
The Best of Show Awards offers exhibitors at the Bio-IT World Conference & Expo an opportunity to showcase their new products.
Read more
We’re excited to share a look at some of the latest product updates we’ve been working on, and give you a sneak peek into new features. Here’s the latest: Flexible plot layouts, New analysis type: Time-to-event or survival analysis, Normalization for count data, and more.
Read more
The Pluto team is attending our first Bio-IT World Conference & Expo in Boston May 3-5, 2022! We’re looking forward to learning about all of the impactful research the attendees are doing, and sharing how Pluto is accelerating R&D for life sciences organizations of all sizes.
Read more
Read the Data Magazine news post which features Pluto in their article showcasing their top picks for the best Denver, Colorado based Machine Learning companies.
Read more
qPCR has transformed molecular biology by providing unparalleled accuracy and sensitivity in the detection and quantification of nucleic acid sequences. Despite its potential drawbacks, such as cost and optimization requirements, qPCR has proven invaluable in research, clinical diagnostics, and food safety testing. Recent advancements in qPCR technology, such as Digital PCR and CRISPR-based qPCR, have further expanded its applications. Learn more about the origins and potential of qPCR in our latest blog post.
Read more
ChIP-seq, or chromatin immunoprecipitation sequencing, is a powerful tool used to study protein-DNA interactions in the genome.
Read more
We will explain what these factors are and how they are used to analyze ChIP-seq and ATAC-seq data
Read more
November is Epilepsy Awareness Month and organizations, researchers, journals and foundations around the world are taking this time to come together as a community and address how to best use our resources towards improving outcomes for epilepsy patients. There have been exciting advances recently in new target identification, animal research models, biomarker discoveries and stem cell therapies.
Read more
ATAC-seq, or assay for transposase-accessible chromatin sequencing, is a powerful tool used to study the accessibility of the genome.
Read more
Next-generation sequencing (NGS) is a powerful tool used to generate high-throughput DNA sequencing data.
Read more
DESeq2 is a popular and widely used package in the field of bioinformatics for the analysis of RNA-Seq data. It provides a more comprehensive view of gene expression compared to traditional microarray technology.
Read more
Announcing Pluto's first round of funding to fuel an industry-first collaborative platform for biological data analysis
Read more
Read more about how Pluto Biosciences spun out of the Wyss Institute for its collaborative bioinformatics platform
Read more
Cytokines are small proteins that play a crucial role in regulating the immune system, inflammation, and cell growth.
Read more
For decades, scientists have been trying to find cures for all the various cancers that plague humanity and have made incredible strides towards this goal. We currently have various treatments that are able to significantly prolong survival and in some cases completely treat the cancerous tumor. One of the major roadblocks in our ability to cure this disease is related to the incredible heterogeneity that exists within each tumor and each patient. Additionally, the way each organism responds to the tumor cells is also extremely varied placing a lot of pressure on clinicians and scientists to constantly adapt.
Read more
Press release on Pluto launching the cloud-based data management and analysis platform.
Read more
Pluto, a biological data management platform stattup, was lauched from the Wyss Insitute at Harvard.
Read more
SAMtools is a software package for interacting with and processing next-generation sequencing data
Read more
A great article by Lindsay Browne on how Pluto launched from teh Harvard's Wyss Institute to speed scientific discovery.
Read more
Motor neurons are important cells in our body that send signals to our skeletal muscle that allow us to do activities like walk, speak, swallow, and even breathe. Motor neuron diseases like amyotrophic lateral sclerosis (ALS) destroy motor neurons. When muscles don’t receive normal signals from our motor neurons, the muscles atrophy (weaken and shrink) and we lose the ability to do those activities over time.
Read more
Hello world! After six foundational months of work, we are humbled and proud to announce the launch of our company: Pluto Biosciences, Inc.
Read more
How effectively do the Moderna and Pfizer mRNA vaccines mount a response against the SARS-CoV-2 variants causing new waves of infections? This study measured antibody levels in serum and found that both provided strong protection against new variants.
Read more
In this blog post, we will walk through the steps of trimming RNA-seq data using popular software tools such as Trimmomatic and Cutadapt.
Read more
Mastering Key Skills and Coding Languages for Effective Analysis of Biological Data: A Guide to Bioinformatics Engineering
Read more
