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Samantha Klasfeld, Ph.D.

@sklasfeld.bsky.social
71 followers 180 following 31 posts

Biobank genomics, Trusted Research Environments, rare variants, cloud workflows. Founder of Chrome Key Bioinformatics | Communications Co-Chair @ BWIB | Former plant epigeneticist

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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 01/06/2026
LAST DAY to submit an abstract for my fellow bioinformaticians in the Boston area!!!
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 13/05/2026
🥒🍉🧀🥑
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 08/05/2026
Is it timing? Charisma? Knowing the right people? Figuring out how to get taken seriously is its own skill. Workshops like this one are a start. 💼
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 01/05/2026
💻🧬 A wrap on the Nextflow Summit. @lopantano.bsky.social set the tone early: AI is showing us beauty we've never seen before, but not everything we receive is true. Validating outputs we have no ground truth for is genuinely hard. The consensus: guardrails aren't optional. #NextflowSummit2026
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 21/04/2026
🧬💻 The starting gun has fired. Nine posts later, you know your platforms, your phenotypes, and your genetic data. Check every box and enjoy the race that is analysis. 🔗 sklasfeld.netlify.app/blog/biobank... Cross posted with @boston-wib.bsky.social #bioinformatics #ukbiobank #allofus
sklasfeld.netlify.app
Biobank Intro Series: You Have What You Need | Samantha Klasfeld
A wrap-up of the series and a checklist before you start your analysis
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 16/04/2026
💻🧬Nobody tells you All of Us genotype data lives in 20,016 unlabeled shards. If UK Biobank gives you a filing cabinet with labeled drawers, All of Us gives you a bucket of blobs. sklasfeld.netlify.app/blog/biobank... #Bioinformatics #Genomics #AllOfUs #Biobank #WGS #CloudComputing
sklasfeld.netlify.app
Biobank Intro Series: All of Us Genetic Data | Samantha Klasfeld
Navigating All of Us genotype data for variant extraction and analysis
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 11/04/2026
After a year of leading with @boston-wib.bsky.social, building this weird little personal brand, and learning to use every tool available to keep my career moving, I start a new full-time role Monday. The bioinformatics world has been underutilizing me. That changes this week. 🧬 #womenInSTEM
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 07/04/2026
🧬💻 Have you ever opened the UK Biobank RAP and wondered where the genotype data is? If so, this one is for you. 🔗 sklasfeld.netlify.app/blog/biobank... Cross-posted with @boston-wib.bsky.social #bioinformatics #genomics #ukbiobank
sklasfeld.netlify.app
Biobank Intro Series: UK Biobank Genetic Data | Samantha Klasfeld
Traversing genetic data on the UK Biobank RAP (Research Analysis Platform) environment
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 02/04/2026
💻🧬 𝗔𝗹𝗹 𝗼𝗳 𝗨𝘀 𝗰𝗹𝗶𝗻𝗶𝗰𝗮𝗹 𝗱𝗮𝘁𝗮 𝗶𝘀 𝗽𝗼𝘄𝗲𝗿𝗳𝘂𝗹, 𝗯𝘂𝘁 𝗢𝗠𝗢𝗣 𝘄𝗶𝗹𝗹 𝗵𝘂𝗺𝗯𝗹𝗲 𝘆𝗼𝘂 𝗯𝗲𝗳𝗼𝗿𝗲 𝗶𝘁 𝗵𝗲𝗹𝗽𝘀 𝘆𝗼𝘂. new blog post on surviving All of Us clinical data 👇 sklasfeld.netlify.app/blog/biobank... Cross posted: @boston-wib.bsky.social #AllOfUs #Bioinformatics #OMOP #Biobank #EHRData #ClinicalData
sklasfeld.netlify.app
Biobank Intro Series: All of Us Observational Data (Part II) | Samantha Klasfeld
Loading observational data in the All of Us Researcher Workbench
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 01/04/2026
💻🧬 All of Us threw the tea in the harbor, metaphorically speaking. Same goal, completely different system. Post #5 is about why All of Us is organized differently than UK Biobank and where to get started. sklasfeld.netlify.app/blog/biobank... #biobank #bioinformatics #omop
sklasfeld.netlify.app
Biobank Intro Series: All of Us Observational Data (Part I) | Samantha Klasfeld
Finding concept IDs for the All of Us Researcher Workbench
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 25/03/2026
💻🧬 Field ID in paw. Data nowhere to be found. Sounds familiar? Dedicated to my feline supervisor, Post #4 of my Biobank Intro Series covers how to extract phenotype data from the UK Biobank RAP — including the gotchas nobody tells you. 🐱 sklasfeld.netlify.app/blog/biobank...
sklasfeld.netlify.app
Biobank Intro Series: UK Biobank Observational Data (Part II) | Samantha Klasfeld
Loading phenotype data in the UK Biobank RAP (Research Analysis Platform) environment
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Reposted by Samantha Klasfeld, Ph.D.
Boston Women in Bioinformatics @boston-wib.bsky.social · 14/03/2026
In case you missed it 📬 Issue 5 of the BWIB newsletter is live! New board, new committees, new podcast, and data on the gender gap in leadership worth reading. 🧬 🔗 boston-wib.org/newsletter/i... #bioinformatics #womeninstem
media.tenor.com
a yellow minion sits at a desk with a computer
Alt: a yellow minion sits at a desk with a computer
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 11/03/2026
💻🧬 𝗧𝗵𝗲 𝗨𝗞 𝗕𝗶𝗼𝗯𝗮𝗻𝗸 𝗦𝗵𝗼𝘄𝗰𝗮𝘀𝗲 𝗶𝘀 𝗯𝗲𝗮𝘂𝘁𝗶𝗳𝘂𝗹𝗹𝘆 𝗼𝗿𝗴𝗮𝗻𝗶𝘇𝗲𝗱, 𝗯𝘂𝘁 𝗶𝘁'𝘀 𝗻𝗼𝘁 𝘀𝗲𝗹𝗳-𝗲𝘅𝗽𝗹𝗮𝗻𝗮𝘁𝗼𝗿𝘆. I walk through how to actually read a showcase entry: what to check and look out for in Part 3 of my Biobank Intro Series 🔗 sklasfeld.netlify.app/blog/biobank...
sklasfeld.netlify.app
Biobank Intro Series: UK Biobank Observational Data (Part I) | Samantha Klasfeld
An ode to the UK Biobank Showcase
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 03/03/2026
💻🧬 𝗖𝗼𝗺𝗽𝘂𝘁𝗲 𝗮𝗻𝗱 𝘀𝘁𝗼𝗿𝗮𝗴𝗲 𝗮𝗿𝗲𝗻'𝘁 𝘆𝗼𝘂𝗿 𝘀𝗰𝗮𝗿𝗰𝗲𝘀𝘁 𝗿𝗲𝘀𝗼𝘂𝗿𝗰𝗲, 𝘆𝗼𝘂𝗿 𝘁𝗶𝗺𝗲 𝗶𝘀. 𝗔 𝗹𝗶𝘁𝘁𝗹𝗲 𝗽𝗿𝗲𝗽 𝗯𝗲𝗳𝗼𝗿𝗲 𝘆𝗼𝘂 𝘀𝘁𝗮𝗿𝘁 𝗴𝗼𝗲𝘀 𝗮 𝗹𝗼𝗻𝗴 𝘄𝗮𝘆. Part 2 of my Biobank Intro Series covers the hardware setup lessons, so you're not learning them mid-analysis. 🔗 sklasfeld.netlify.app/blog/biobank... #ukb #aou #tre #bioinformatics
sklasfeld.netlify.app
Biobank Intro Series: Hardware Settings | Samantha Klasfeld
Hardware setup lessons for UK Biobank Research Analysis Platform and All of Us Workbench
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 28/02/2026
Rare genetic diseases are rare due to survivorship bias. The variants that cause them are often lethal. Survivors show us where biology is most fundamental, providing a foundation for the rest of medicine. #RareDiseaseDay 🦓
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Reposted by Samantha Klasfeld, Ph.D.
Boston Women in Bioinformatics @boston-wib.bsky.social · 26/02/2026
We're on Bluesky! 🎉To kick things off, tune into Season 2, Ep. 2 of the BWiB podcast — we're talking hackathons! Whether you're a first-timer or a seasoned hacker, this one's for you. 🧬🎧 🎙️Listen here: boston-wib.org/blog/coffeew...
boston-wib.org
A Coffee with CompBio: New Year Resolutions
12 New Year Resolutions For Computational Biologists
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 24/02/2026
🧬💻 Before you touch any code in a biobank analysis, you need to answer two questions: what's your research question, and who's your audience? My new blog series on the BWIB blog starts there. 🔗 boston-wib.org/blog/biobank...
Iceberg diagram illustrating hidden complexities in biobank data: visible raw data above the waterline, and three categories of hidden challenges below: batch effects, population stratification, and inaccurate phenotype data.
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 30/12/2025
💻🧬 Kick off 2026 with Boston Women in Bioinformatics! Join us Jan 15 for informal networking. Women, gender-diverse folks, & allies welcome. CambridgeSide Mall, 5:30pm. luma.com/6lpamkjb Please share with your Boston bioinformatics community! #boston #bioinformatics #event #cambridge
luma.com
BWIB: New Year, New Connections Social · Luma
Who Should Attend: This event is open to the bioinformatics community, with a focus on supporting women and gender-diverse individuals. Allies at any career…
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 20/12/2025
Read to the tune of "I Have a Little Dreidel" 🕎 : I have a great event planned In Cambridge it will be For bioinformatics friends On January fifteen! Oh network, network, network With friends old and new Oh network, network, network We're saving space for you! boston-wib.org/events/event...
boston-wib.org
New Year, New Connections Social
The online presence of Women in Bioinformatics in the Boston Area
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Reposted by Samantha Klasfeld, Ph.D.
Jonathan Frazer @jonnyfrazer.bsky.social · 24/11/2025
popEVE is out in Nature Genetics! 🎉 We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders. rdcu.be/eRu7K
rdcu.be
Proteome-wide model for human disease genetics
Nature Genetics - popEVE is a proteome-wide deep generative model to identify and predict pathogenicity of missense mutations causing genetic disorders.
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 24/11/2025
✨What Your Favorite Biobank Says About You✨ We spend so much time talking about pipelines, QC, and variant harmonization, but sometimes it’s nice to laugh at ourselves and the quirks of our field. 👉 boston-wib.org/blog/quickta... #human-genetics #science-humour #biobanks
lnkd.in
What Your Favorite Biobank Says About You
We asked 500,000 researchers which biobank they stan, and the results were… scientifically significant.
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 04/09/2025
🧬 💻 In my first blog post with Boston Women in Bioinformatics, I unpack how meaningful inclusion in genetics research not only addresses ethical imperatives but also unlocks more robust scientific insights. 🔗 boston-wib.org/blog/deepdiv... #InclusiveResearch #EquityInScience #DiversityInSTEM
boston-wib.org
The Genomics Diversity Crisis: Why DEI Isn't Just About Workplace Culture
When 86% of genomic data comes from European ancestry, treatments built on this data will inevitably fail marginalized communities.
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 22/08/2025
💻 🧬 New survey for job seekers AND hiring teams in biotech/bioinformatics/data science. ~10 min, anonymous, results shared with community. Please take it AND share with your network! tinyurl.com/biotechjobma...
tinyurl.com
State of the Biotech Job Market: A Survey on Employment Experiences in Biotechnology, Bioinformatics, and Data Science
This survey aims to understand the current employment landscape and job search experiences of professionals in biotechnology, bioinformatics, and data science fields. We're collecting data on various ...
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 20/08/2025
💻🧬 Are you a computational biologist? Working in an adjacent field? Please respond to this survey to support community-driven research and programming. Conducted by Boston Women in Bioinformatics (BWIB), all responses are anonymous. [~5 min] Google Form: tinyurl.com/mm424zdw
media.tenor.com
a cat wearing a pair of glasses with the words talk data to me above it
ALT: a cat wearing a pair of glasses with the words talk data to me above it
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 24/06/2025
🧬💻 "It was the best of times, it was the worst of times" - Eric Green, Former Director of the National Human Genome Research Institute, quoting Mark Twain #FoG #FoGBoston #FoG2025 #FestivalOfGenomics #FesivalOfGenomicsBoston
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Reposted by Samantha Klasfeld, Ph.D.
American Society of Human Genetics (ASHG) @geneticssociety.bsky.social · 29/05/2025
Exploring the interplay of rare pathogenic variants and common genetic modifiers of cardiomyopathy, @hggadvances.bsky.social's latest study carefully assesses the benefits provided by variant effect predictions: www.cell.com/hgg-advances... @sklasfeld.bsky.social #ASHG #HumanGenetics
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 29/05/2025
Excited to share my work is published in HGG Advances! 🧬🖥️ Thankful to my mentors at Pfizer for the incredible opportunity. TL;DR We explore the interplay between rare pathogenic variants and common genetic modifiers of cardiomyopathy and provide an assessment of variant effect predictions.
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 28/05/2025
🧬🖥️ Super cool work! This blog post introduces the idea that our sociopolitical ecosystem can cause inherit biases in statistical methods, and the paper reviews existing and future approaches to improve our practices.
datascienceforhealthequity.com
Can Stats be Fair? The Importance of Statistical Methods for Equity in Genomic Data Analysis
by Leandra Bräuninger and Brieuc LehmannHave you ever wondered whether the statistical methods we use actually help—or hurt—health equity? It's a big question, especially in fields like genomics, wher...
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Reposted by Samantha Klasfeld, Ph.D.
E. Rosalie @erosalie.infoepi.com · 13/03/2025
A French University is funding a Safe Place For Science program meant to recruit scientists who cannot continue their work in the US. www.univ-amu.fr/fr/public/a...
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 07/03/2025
Taylor swift or Tailor Swiftiles? emze.csail.mit.edu/tailors #wids2025 #widscambridge #womenindatascience #efficientcomputing
emze.csail.mit.edu
Tailors
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 07/01/2025
🧬 I'm delighted to share the preprint to my postdoc project where we used predicted rare pathogenic variants to improve our understanding of the interplay between common genetic modifiers and rare pathogenic mutations in cardiomyopathy risk. www.medrxiv.org/content/10.1... #Genetics #Bioinformatics
medrxiv.org
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 03/01/2025
🧬 New DNA language model using evolutionary conservation provides exciting results and an intriguing discussion on where specific models may outperform due to certain conditions.
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Reposted by Samantha Klasfeld, Ph.D.
Kexin Huang @kexinhuang.bsky.social · 09/12/2024
🧬 Thrilled to share Knowledge Graph GWAS (KGWAS), the largest AI model that integrates >10 millions of multi-modal and multi-scale functional genomics data to improve GWAS power by 100% while discovering novel disease-critical variants, genes, cells, and networks! 1/15🧵
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Samantha Klasfeld, Ph.D. @sklasfeld.bsky.social · 12/12/2024
For many quantitative phenotypes with selective pressure at their high and low ends (the "tails"), the association between PRS and the trait is diminished at these extremes due to high-impact rare variant alleles not included in the PRS. www.biorxiv.org/content/10.1...
biorxiv.org
Striking Departures from Polygenic Architecture in the Tails of Complex Traits
Understanding the genetic architecture of human traits is of key biological, medical and evolutionary importance[[1][1]]. Despite much progress, little is known about how genetic architecture varies a...
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