Lappalainen Lab @tuuliel_lab Twitter profile

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Lappalainen Lab

@tuuliel_lab

4 years

Very happy and proud to present: The GTEx papers. This set of 15 papers published today describes the final phase of this 10-year effort, providing the genomics community an atlas of genetic regulatory variants and a deep dive into the biology behind it.

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Lappalainen Lab

@tuuliel_lab

3 years

Excited to share the news: I will be moving to Sweden in May to start as a Professor of Genomics at Royal Institute of Technology, and as the Director of National Genomics Institute at @scilifelab . I'll continue to run a lab at @nygenome as an Associate Faculty Member.

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Lappalainen Lab

@tuuliel_lab

2 years

Excited to share our paper, out today in @Nature , where we characterize transcriptome variation in human tissues by long-read sequencing. Huge thanks to @g_dafni @beryl_bbc Garrett Garborcauskas @dgmacarthur and other collaborators. 🧵

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Lappalainen Lab

@tuuliel_lab

10 months

Interested in doing a PhD with me in Sweden? Experimental+computational genomics skills or interests? We have an open position! Great environment at KTH on @SciLifeLab campus, staff benefits, well-funded project, close interactions with our New York team. Link in the replies 👇

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Lappalainen Lab

@tuuliel_lab

5 months

We know the importance of subtle gene dosage variation, and yet the main tool of molbio is gene KO/KD. In our new preprint, @JuliaDiumenge introduced subtle modulations of transcription factor dosage by CRISPRi/a, and quantified responses by scRNA-seq. 1/

Non-linear transcriptional responses to gradual modulation of transcription factor dosage

Genomic loci associated with common traits and diseases are typically non-coding and likely impact gene expression, sometimes coinciding with rare loss-of-function variants in the target gene....

www.biorxiv.org

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Lappalainen Lab

@tuuliel_lab

9 months

This is an appalling decision with a chilling effect on free speech.

Michael Eisen

@mbeisen

9 months

I have been informed that I am being replaced as the Editor in Chief of @eLife for retweeting a @TheOnion piece that calls out indifference to the lives of Palestinian civilians.

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Lappalainen Lab

@tuuliel_lab

5 months

Excited to share our review paper in Cell! With @SashaGusevPosts @s_ramach @yang_i_li we discuss the genetic and molecular architecture of human traits, future opportunities and challenges and ways forward.

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Lappalainen Lab

@tuuliel_lab

3 months

We’re recruiting for multiple positions in my lab in New York and Stockholm, at MSc and PhD levels. If you’re interested in pursuing creative systems genetics questions with tools/data like Developmental GTEx, CRISPR and single-cell, please read further / share. 1/

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Lappalainen Lab

@tuuliel_lab

2 months

The Leena Peltonen Prize of 2024 goes to @SashaGusevPosts 🎉! I was honored to announce this and introduce Sasha just minutes ago at #ESHG24 . Huge congrats!

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Lappalainen Lab

@tuuliel_lab

2 years

As scientists, we all try create new knowledge & methods. Many of us approach this with a positive attitude of "happy to present our contribution, hoping you find it useful". For some, the focus is on berating other people's work and lifting their own by pushing others down. #sad

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Lappalainen Lab

@tuuliel_lab

2 years

Proud to present our molecular QTL primer! All you've ever wanted to know about mapping genetic associations to molecular traits. We discuss data, methods, interpretation, and opportunities and challenges in the field.

Nature Reviews Methods Primers

@MethodsPrimers

2 years

New this week! Our authors discuss the study design and implementation of molecular quantitative trait loci mapping, focusing on technical developments for functional characterization @alexisjbattle @JHUMCEH @tuuliel_lab @scilifelab @nygenome

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Lappalainen Lab

@tuuliel_lab

8 months

A real moonshot project in biomedical research would be a decisive legal, regulatory and IT effort to really make data access work for researchers across the world. Less sexy, but better bang for the buck & more transformative than e.g. AI, CRISPR, ginormous sequencing projects.

Scientists Who Lift

@ScientistsLift

9 months

What unpopular academia opinion would get you in this situation?

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Lappalainen Lab

@tuuliel_lab

1 year

Biology of Genome 2023 is on! The meeting was launched with words in memoriam of Casey Brown @casey6r0wn #BoG23

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Lappalainen Lab

@tuuliel_lab

3 years

This is huge. And while TOPMed was the first project with massive-scale WGS - and should be praised for the higher diversity of ancestries - the impact of UKBB is likely to be way higher due to less red tape in accessing the data.

UK Biobank

@uk_biobank

3 years

#UKBiobank has made the #WholeGenomeSequencing data of 200k participants available to approved researchers. These data will help researchers understand the genetic determinants of disease and may accelerate innovative drug discovery work. More info here:

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Lappalainen Lab

@tuuliel_lab

1 year

Excited to share our latest paper, using CRISPR and single cell sequencing to characterize GWAS locus effects on gene expression in cis and trans. Huge thanks to @johnomix , @nevillesanjana and other collaborators!

John Morris

@johnomix

1 year

🚨Our work on multi-modal, single-cell pooled CRISPR screens to study GWAS variant-to-function, STING-seq, is now out in @ScienceMagazine ! Read on for 6⃣ of the main findings from our study, led by myself and co-advised by @nevillesanjana and @tuuliel ! 🎉

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Lappalainen Lab

@tuuliel_lab

1 year

Happy and honored to receive the Göran Gustafsson prize in molecular biology! It's always inspiring to see our work recognized. Special thanks to current and former lab members and collaborators for making this possible.

Göran Gustafssonpriser till forskning om allt från molnbildning till tarmsjukdomar - Kungl....

Göran Gustafssonpriser till forskning om allt från molnbildning till tarmsjukdomar

www.kva.se

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Lappalainen Lab

@tuuliel_lab

4 years

Five years ago I switched from buggy Endnote to Papers to manage references, and now Papers has become just as bad. What next? Any recommendations? Compatibility with Google Docs would be a major plus now that many papers/grants are written there.

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Lappalainen Lab

@tuuliel_lab

2 years

A new preprint from the lab, with @mollymozzarella @stephanecastel and others! We developed methods for RNA-seq from non-invasive biospecimens. TL;DR: hair follicles and urine have major potential for large-scale transcriptomics. 🧵👇

Noninvasive, low-cost RNA-sequencing enhances discovery potential of transcriptome studies

Transcriptomic studies lend insight into the biology of genetic regulation and bear promise in furthering the goals of precision medicine. However, the cost of RNA-sequencing and types of tissues...

www.biorxiv.org

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Lappalainen Lab

@tuuliel_lab

1 year

Excited to share a new preprint from my lab, led by @silvakasela ✨, analyzing cellular and environmental modifiers of regulatory variants in the TOPMed multi-omics pilot data from the MESA cohort. 🧵

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Lappalainen Lab

@tuuliel_lab

7 months

Ten years ago I started my lab. What a time it's been - working with great people (👇 & more 🙏), exciting science, interesting times. I still don't quite understand how I've been so lucky. I got everything that I ever wanted and probably more than I dared to dream of.

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Lappalainen Lab

@tuuliel_lab

3 years

We're looking for a new faculty colleague at the New York Genome Center! We welcome applications in all areas of human genetics or genomics. Please feel free to reach out to me or other faculty to chat; applications by April 1:

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Lappalainen Lab

@tuuliel_lab

3 years

We're hiring! @david_a_knowles and I at @nygenome are looking for a jointly mentored postdoc to work on functional genomics and/or statistical genetics. We offer top notch data, great environment & a fun city! Happy to chat informally, please RT.

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Lappalainen Lab

@tuuliel_lab

3 months

We're recruiting postdocs! Join our lab at @scilifelab @KTHuniversity in Stockholm to work on functional genomics at the experimental and/or computational intersection of CRISPR/scRNA-seq/genetics approaches. Close links to our team at @nygenome . 1/

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Lappalainen Lab

@tuuliel_lab

3 years

I'm hiring!

Tuuli Lappalainen

@tuuliel

3 years

I'm hiring staff & postdocs for my Stockholm lab! Cool projects in experimental/computational functional population genomics, cutting-edge environment at @scilifelab @KTHuniversity in lovely Stockholm, close interactions with my lab at @nygenome . Please RT

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Lappalainen Lab

@tuuliel_lab

1 year

Our Revio has arrived!

NGI Sweden

@ngisweden

1 year

The @PacBio #Revio has arrived in Uppsala at @scilifelab @ngisweden !!!🥳 Now time for unpacking...🎁 then on to installation and testing!

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Lappalainen Lab

@tuuliel_lab

3 years

Beautiful preprint from @jkpritch and Alex Marson labs. The insights from CRISPR + single cell have huge potential in uncovering regulatory networks underlying functional genetic architecture of human traits. This type of data will be transformative.

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture...

Complex gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed it can lead to disease. To understand how gene expression...

www.biorxiv.org

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Lappalainen Lab

@tuuliel_lab

8 months

Looking for suggestions for modern textbooks in areas that my diverse lab covers - to help lab members quickly build a foundation in an area where they have less background. Popgen, human genetics, func genomics, molbio, modern biostats & bio data science... Help!

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Lappalainen Lab

@tuuliel_lab

2 years

We're looking for a postdoc in Stockholm! Co-mentored position at the intersection of biology/genomics and ML. Fantastic environment at @KTHuniversity & @scilifelab 's Data Driven Life Science community, with strong international networks. Please RT!

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Lappalainen Lab

@tuuliel_lab

7 months

Six weeks left until the abstract deadline for Biology of Genomes at CSHL #BoG24 ! We have a stellar lineup of keynotes and discussion leaders (=~invited speakers), and look forward to another brilliant meeting in May 7-11. Abstract submission & info:

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Lappalainen Lab

@tuuliel_lab

2 years

John Morris @johnomix , postdoc with me & @nevillesanjana at @nygenome at #bog22 : Systematic targeting and inhibiting of noncoding GWAS loci with single-cell sequencing. This is an update (with lots of new data & insights) of our preprint.

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Lappalainen Lab

@tuuliel_lab

5 months

My department at @KTHuniversity @scilifelab is recruiting an Assistant Professor in computational biology! Fantastic academic environment, top notch infra, colleagues and students, international vibe, Sweden is a lovely place to live. More info 👇

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Lappalainen Lab

@tuuliel_lab

3 years

Open postdoc position in my lab! Functional genetic variation with computational or experimental focus, cutting-edge data & tech, fantastic environment in Stockholm at @scilifelab , interactions & opportunity to spend time in the New York lab. Please RT!

Postdoc in Genomics

Job description Professor Tuuli Lappalainen’s research group is looking for a postdoctoral researcher to work on functional effects of genetic variants in humans. This position is suitable for both

kth.varbi.com

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Lappalainen Lab

@tuuliel_lab

4 months

Happy to receive the Wallenberg Scholar funding from @KAWstiftelsen !

Knut and Alice Wallenberg Foundation grants SEK 2.1 billion to 118 of Sweden's top researchers |...

kaw.wallenberg.org

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Lappalainen Lab

@tuuliel_lab

1 year

New work from Linda Kvastad in my lab - using spatial transcriptomics + GWAS data to identify disease-relevant tissue structures. #ESHG2023

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Lappalainen Lab

@tuuliel_lab

10 months

One week left to apply for junior faculty positions in the Data Driven Life Science program in Sweden! Competitive startup, big program with a strong peer+mentorship networks, great country with strong science, international vibe and nice quality of life.

DDLS Fellows recruitment

Fellows recruitment The practice of life science is continuously becoming more data-dependent. The amount and complexity of data is growing exponentially, and more scientific discoveries are enabled...

www.scilifelab.se

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Lappalainen Lab

@tuuliel_lab

3 months

I've been coming to #bog24 since 2007 (I think), and I see many other veterans and old friends at Grace now. One of the best things about this meeting is all the new faces. Here's my protips for the meeting:

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Lappalainen Lab

@tuuliel_lab

4 months

New preprint 🎉 led by @AervaI 👇! We introduce an approach to prioritize biological driver genes by recalibrating differential expression fold changes with population variance. This extracts new meaning out of DE analysis, which is a cornerstone of computational biology!

Philipp Rentzsch

@AervaI

4 months

Very happy to share our latest work from my postdoc with @tuuliel_lab on recalibrating gene expression changes relative to natural dosage variance:

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Lappalainen Lab

@tuuliel_lab

1 year

Folks at #BoG23 and others - I'm recruiting postdocs to my Stockholm and New York teams. Reach out if interested - experimental or computational opportunities in gene expression dosage (talk #39 ), GWAS+CRISPR+molQTLs, developmental GTEx, etc.

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens

High-throughput single-cell CRISPR screens help in the understanding of noncoding human genetic variants for blood cell traits.

www.science.org

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Lappalainen Lab

@tuuliel_lab

1 year

Please take the brevity, awkwardness, mistakes and typos in my emails as a compliment: I wrote them myself.

Dr Max Liboiron

@MaxLiboiron

1 year

I asked ChatGPT to write me a "no thanks" email to requests for my time and people are responding to it so much better than when I wrote it myself. That machine is better at emotional labour than I am (maybe it's the repetition)? The text in question:

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Lappalainen Lab

@tuuliel_lab

4 years

Hello world! It's Tuuli. This is my new strictly science account for the genetics/genomics community 🤓. You'll find #scicomm , policy, life, etc. tweets for a more general audience at @tuuliel 😎. I'll cross-tweet sometimes.

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Lappalainen Lab

@tuuliel_lab

2 years

We introduce the largest long-read transcriptome sequencing data from human tissues from @gtexportal . The @nanopore technology provided an opportunity for improved analysis of the real biological units of the transcriptome: transcripts - not just genes or splice junctions. 2/7

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Lappalainen Lab

@tuuliel_lab

2 years

Xiaoting Li from the Bussemaker lab at Columbia presenting our collaborative project: Identifying genetic regulatory variants that affect transcription factor activity. New method for estimating TF activity from expression data applied to GTEx for GWAS mapping #BoG22

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Lappalainen Lab

@tuuliel_lab

2 years

Thrilled to receive the ERC Consolidator grant - the first big external grant for my rapidly growing Swedish lab! We'll be digging deep into variation in gene expression dosage and its role in genetic architecture of human diseases. 🎉🥳

KTH Royal Institute of Technology

@KTHuniversity

2 years

KTH-forskarna Madeleine Balaam, Ricardo Vinuesa, Tuuli Lappalainen och Lisa Prahl Wittberg får omkring två miljoner euro vardera i ERC Consolidator Grants från Europeiska Forskningsrådet.

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Lappalainen Lab

@tuuliel_lab

4 years

I'm excited to share our new preprint, led by my postdoc @g_dafni and @beryl_bbc in collaboration with Garrett Garborcauskas, @dgmacarthur , @nanopore and others: Transcriptome variation in human tissues revealed by long-read sequencing. Thread here:

Transcriptome variation in human tissues revealed by long-read sequencing

Regulation of transcript structure generates transcript diversity and plays an important role in human disease. The advent of long-read sequencing technologies offers the opportunity to study the...

www.biorxiv.org

Tuuli Lappalainen

@tuuliel

4 years

I'm excited to share our new preprint, led by my postdoc @g_dafni and @beryl_bbc in collaboration with Garrett Garborcauskas, @dgmacarthur , @nanopore and others: Transcriptome variation in human tissues revealed by long-read sequencing. Thread 👇

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Lappalainen Lab

@tuuliel_lab

3 years

The truly sweet part of the move for us is getting closer to family who live in Finland and Sweden. It’s been an awesome adventure of 12 years since I finished my PhD and left Finland; 7 years in NYC. But now it’s time to go home to Scandinavia - next chapter of the adventure.

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Lappalainen Lab

@tuuliel_lab

4 years

There is also a large number of companion papers from the consortium that dig deeper into specific questions and introduce novel data sets and methods. Full list here, and keep an eye on updates as additional papers get published.

The Genotype-Tissue Expression Project | Collections | AAAS

www.science.org

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Lappalainen Lab

@tuuliel_lab

1 year

Junior PI positions in computational biology in Sweden! A fantastic opportunity to join a rich community.

SciLifeLab

@scilifelab

1 year

Interested in engaging in research using data-driven approaches? The SciLifeLab and Wallenberg National Program for Data-Driven Life Science ( #DDLS ) is now recruiting 19 new high-profile young researchers as DDLS Fellows. @KAWstiftelsen #SciLifeLab

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Lappalainen Lab

@tuuliel_lab

3 years

A new preprint from the lab! We dug into transcription factors as drivers of eQTL activity and its variation across individuals and tissues, using GTEx and other data sets. Led by the brilliant @EliseScience whose thread summarizes the approach and the findings 👇

Elise Flynn

@EliseScience

3 years

Excited to share that our preprint on transcription factors and eQTLs is out!

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Lappalainen Lab

@tuuliel_lab

2 years

We identified about 100K novel transcripts that typically validate well in proteome MS data. They're enriched for tissue-specific expression - maybe that's why they were missed before. We see a lot of potential for transcript annotation in humans and other organisms. 3/7

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Lappalainen Lab

@tuuliel_lab

11 months

Great to see this paper published! @xiaoting_l and @HarmenBussemkr developed a really creative way to robustly quantify TF activity, which we then used as a phenotype in GWAS.

Harmen Bussemaker

@HarmenBussemkr

11 months

Excited to share that our paper came out in Cell Genomics last week. We developed a model to estimate TF regulatory activity from GTEx RNA-seq data and mapped genetic variants (“aQTLs”) predictive of this virtual trait.

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Lappalainen Lab

@tuuliel_lab

2 years

#bog22 here we gooooo! Awesome to be back and see old friends and new faces. Fighting my jetlag but excited about the functional genomics session (including the talk by our very own @johnomix !)

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Lappalainen Lab

@tuuliel_lab

10 months

FYI to those unfamiliar with the Swedish system, PhD students take courses alongside their research projects, but you apply directly to a lab instead of a program. These are employed positions with benefits - no need to put your life on hold for 4 years to pursue a PhD!

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Lappalainen Lab

@tuuliel_lab

1 year

Join us at SciLifeLab & KTH! Great environment, heavy investment in computational biology, tons of data being produced, international atmosphere. Sweden also has a great culture for work/life balance. A couple of weeks left to apply.

SciLifeLab

@scilifelab

1 year

Recruiting SciLifeLab Fellow (Assistant Professor) in #MachineLearning in Computational Biology, employed by @KTHuniversity The position comes with generous financial support for recruiting a team and sustaining research activities Learn more and apply↓

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Lappalainen Lab

@tuuliel_lab

7 months

This work is now published in @AJHGNews ! Congrats @silvakasela and others. This link should provide full access:

Lappalainen Lab

@tuuliel_lab

1 year

Excited to share a new preprint from my lab, led by @silvakasela ✨, analyzing cellular and environmental modifiers of regulatory variants in the TOPMed multi-omics pilot data from the MESA cohort. 🧵

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Lappalainen Lab

@tuuliel_lab

8 months

Excited to have our paper published! Congrats @mollymozzarella and others.

Lappalainen Lab

@tuuliel_lab

2 years

A new preprint from the lab, with @mollymozzarella @stephanecastel and others! We developed methods for RNA-seq from non-invasive biospecimens. TL;DR: hair follicles and urine have major potential for large-scale transcriptomics. 🧵👇

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Lappalainen Lab

@tuuliel_lab

2 years

@nomad421 @GarmireGroup This. Also, this is a way for everyone to know what their lab mates are actually working on - otherwise is it a team or just a bunch of individuals sitting in the same office?

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Lappalainen Lab

@tuuliel_lab

1 year

A major use case for ChatGPT: digesting looong emails from funding agencies to tell me if there are any real action items or necessary information.

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Lappalainen Lab

@tuuliel_lab

10 months

This was great news! My first rodeo renewing our national funding as the @ngisweden director.

SciLifeLab

@scilifelab

10 months

Congrats to @ngisweden , @NBISwe , @BioMS_Sweden , NMI (National Microscopy Infrastructure), Ancient DNA ( @SciLifeLab_ADF (Part of Archlab)) and everyone else who has been awarded grants within the call Research infrastructure of national interest! 🌟

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Lappalainen Lab

@tuuliel_lab

4 years

In the main paper, co-led with @francoisaguet and @KArdlie , we introduce the data set of eQTLs and sQTLs in cis and trans from >15K samples from 49 tissues, analyze functional mechanisms, tissue- and cell-type specificity, GWAS interpretation, and more.

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Lappalainen Lab

@tuuliel_lab

1 year

@shyam_lab @anshulkundaje I have the exact same if not higher standards for our preprints - I'd endanger my professional reputation in the eyes of the entire community (not just a few ppl) if I posted utter crap. And that reputation, rather than papers, is the real currency that makes or breaks careers.

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Lappalainen Lab

@tuuliel_lab

1 year

Our first NovaSeqX has arrived!

Jessica Nordlund

@Jessie_no

1 year

I spy with my little eye a new instrument arriving at @ngisweden in Uppsala! #novaseqXplus 🧬

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Lappalainen Lab

@tuuliel_lab

2 years

New preprint from our lab! We dug deeper into interpretable splicing changes linked to common genetics variants, including predicted changes in protein structure w #alphafold2 . Huge thanks to @EinsonJ for driving this this project and writing the thread 👇 !

Jonah Einson

@EinsonJ

2 years

Excited to announce that my paper entitled "The impact of genetically controlled splicing on exon inclusion and protein structure" is finally out on bioRxiv! #bioRxiv #biorxiv_genomic

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Lappalainen Lab

@tuuliel_lab

2 years

3 days left to apply for our postdoc position in Stockholm! Co-mentored project at the intersection of genomics and ML. Fantastic environment at @KTHuniversity & @scilifelab 's Data Driven Life Science community, with strong international networks.

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Lappalainen Lab

@tuuliel_lab

10 months

Apparently on this platform posts with links get deprioritized - here's the link:

Doctoral student in genomics

Project description Third-cycle subject: Biotechnology Professor Tuuli Lappalainen’s research group is looking for a PhD student for an ERC-funded research project that links variation in gene dosag

kth.varbi.com

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Lappalainen Lab

@tuuliel_lab

9 months

Finally made it to #ASHG2023 ! Looking forward to great science and catching up with everyone.

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Lappalainen Lab

@tuuliel_lab

11 months

We're looking for a postdoc! Cool ERC-funded project digging into gene dosage variation with CRISPR+sc+computational methods. Dynamic environment at KTH / SciLifeLab Stockholm campus, plus interactions with our New York team. Apply or email for more info:

Postdoktor inom genomik

Arbetsuppgifter Projektet kombinerar experimentellt arbete med CRISPR teknologin och encells-sekvensering med beräkningsanalys. Det specifika projektet kommer att skräddarsys efter postdoktorns intr

kth.varbi.com

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Lappalainen Lab

@tuuliel_lab

7 months

Excited to share a new preprint from my lab, led by brilliant student @mariia_minaeva !

Mariia Minaeva

@mariia_minaeva

7 months

Exciting news! My first paper, "Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs," is now out on bioRxiv! Check it out: #biorxiv_bioinfo 1/5 🧵

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Lappalainen Lab

@tuuliel_lab

2 years

...and here is the accessible link to the paper

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Lappalainen Lab

@tuuliel_lab

4 years

Wow, this looks impressive. Congrats @manoliskellis et al!

Manolis Kellis

@manoliskellis

4 years

Our #SingleCell dissection of #Schizophrenia genes/pathways, a new #TranscriptionalResilience cell type, target genes at #GWAS loci, and upstream #MasterRegulators is out @medRxivPreprint #PsychENCODE #BradRuzicka @Mohammadi_PhD #JoseDavila @NIMHgov

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Lappalainen Lab

@tuuliel_lab

5 months

We detected transcriptional effects of dosage modulation of 3 TFs. Nonlinear responses are common and distinct for up/downregulation - which makes biological sense, but highlights the difficulty of capturing this without gradual dosage modulation. 3/

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Lappalainen Lab

@tuuliel_lab

2 years

This is a subtweet.

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Lappalainen Lab

@tuuliel_lab

1 year

@AdamRutherford I had an argument about this with a very high-ranking genetics professor 10 years ago - he thought that the probabilistic perspective is just intellectual laziness and all genetics worth studying is deterministic. 🤯😂

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Lappalainen Lab

@tuuliel_lab

3 months

Anyone? We've done some work looking at expression level vs eQTL effect size across tissues for GWAS loci (see GTEx 2020. TL;DR it's complicated). We didn't look specifically for these situations though; my gut feeling is that it's rare.

Brandon Logeman

@brandon_logeman

3 months

I’m looking for examples where a gene is normally expressed in cell type A but a GWAS/QTL hit contains a variant that causes ectopic expression in cell type B. All examples welcome, plz RT! @jkpritch @doctorveera @SashaGusevPosts @dgmacarthur @tuuliel @anshulkundaje

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Lappalainen Lab

@tuuliel_lab

1 year

Excited to share a new preprint from the lab! We dug into splicing QTLs as modifiers of penetrance of rare deleterious variants in their target exons, using data from GTEx, TOPMed, SSC. See thread from @EinsonJ (and the preprint!) for more details 👇

Jonah Einson

@EinsonJ

1 year

I'm very excited to announce another preprint from my PhD that's (finally) live on BioRxiv!

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Lappalainen Lab

@tuuliel_lab

8 months

Excited to see this review paper out! Thanks to all co-authors.

AJHG

@AJHGNews

8 months

@khmiga @EichlerEE The next article in the series comes from @tuuliel_lab @ee_reh_neh & colleagues 📰Increasing diversity of functional genetics studies to advance biological discovery and human health

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Lappalainen Lab

@tuuliel_lab

2 years

@Eric_Fauman @pfizer Very nice! And astonishingly good agreement with analysis we did for eQTLs in the GTEx main paper of 2017 (using allele-specific signal to separate cis/trans). The good old 1 Mb threshold for cis effects is 💎

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Lappalainen Lab

@tuuliel_lab

2 years

@nilshomer Not sure if I can call myself a bioinformatician but: Start from simple analyses/methods - you'll learn about the data, which will help you to pursue more ambitious approaches. And quite often you'll find that simple approaches - when used with care - are sufficient.

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Lappalainen Lab

@tuuliel_lab

2 years

There seems to be a method to the madness. For me, moving/setting up a lab has been like: -6mo: the thrill of a twitter announcement, -3-0mo: moving stress and admin confusion, 0-3mo: total chaos and lots of excitement, 3-6mo: vague understanding of how things work.

Tina Termini

@CterminiPhD

2 years

Week 2: So thrilled our piece, “The transition phase: preparing to launch a laboratory” is out in @TrendsBiochem ! We created this resource to guide incoming group leaders. Thank you to my dream team collaborators @karalmckinley @DrDidychuk @QuinaScience

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Lappalainen Lab

@tuuliel_lab

4 years

Huge thanks & congrats to my coauthors - above all @francoisaguet and also other lead analysts Alvaro Barbeira @rodbonazzola @arnsbr @stephanecastel Brian Jo @silvakasela @skimhellmuth @yanyu_liang Meritxell Oliva & @princyparsana . And @KArdlie @hakyim @alexisjbattle !

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Lappalainen Lab

@tuuliel_lab

2 years

I have work email & Slack on my phone, but notifications turned off. No email notifications on laptop either, and only selectively for Slack. Also, I've taught myself to feel no guilt when I've chosen not to work. When I'm out, I'm out.

Brit Will Made It

@DrBritWilliams

2 years

I am making a list of new boundaries to change my life. The first will start next week: I am taking my work email off my cell phone. Faculty folx who’ve done the workplace unravel but are still faculty, what else do you recommend? Other folx?

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Lappalainen Lab

@tuuliel_lab

5 months

We were able to gradually up-and downregulate gene expression by sgRNA tiling around TSS in K562 cells with either CRISPRa or CRISPRi. Readout with ECCITE-seq with targeted scRNA-seq for high-quality quantifications. This is a scalable approach that is easy to apply. 2/

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Lappalainen Lab

@tuuliel_lab

2 years

This is very cool. Also highlights the value of the transcriptome as a multi-dimensional, highly informative readout.

Josh Welch

@LabWelch

2 years

Is it possible to draw a picture of a cell based on the genes it expresses? In our new preprint, @hojaeklee shows that you can! 🧵(1/6)

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Lappalainen Lab

@tuuliel_lab

1 year

Fun with data access renewals! Why does the NIH have 17 different login systems?

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Lappalainen Lab

@tuuliel_lab

2 years

To analyze genetic effects by allele-specific expression and transcript structure analysis, we first developed a new tool, LORALS, to extract these data from long reads in a scalable manner, accounting for specific properties of these data. LORALS is available in github. 4/7

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Lappalainen Lab

@tuuliel_lab

2 years

Finally, we demonstrate potential in better interpretation of rare variants, both by improved transcript annotation and by describing how rare variants disrupting transcript structure manifest in long-read transcriptome data. 6/7

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Lappalainen Lab

@tuuliel_lab

4 years

I also want to thank people who built this consortium: @KArdlie , @dermitzakis @NancyGenetics @RodericGuigo , the analysis group over the years, @GTExPortal @NIH , sample collection & sequencing folks, above all donor families, & many others. It's been a pleasure and a privilege!

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Lappalainen Lab

@tuuliel_lab

2 years

Busy posters today for people in my lab: @JuliaDiumenge @EinsonJ Brielin Brown #BoG22

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Lappalainen Lab

@tuuliel_lab

2 years

Summary data are available in , and the sequencing data are available via GTEx protected access. I hope to see many further uses for these data and also the technology - lots of potential for further discovery and applications! 7/7

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Lappalainen Lab

@tuuliel_lab

1 year

@PetrovADmitri @arjunrajlab This is one of the craziest science-Twitter craziness’s I’ve seen in a while.

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Lappalainen Lab

@tuuliel_lab

10 months

This resource is an absolute 💎 and it’s great to see it develop and grow!

Nurlan Kerimov

@kerimovOn

10 months

🎉 Exciting update on our work with the eQTL Catalogue! We're diving deep into understanding genetic variants associated with complex traits in non-coding regions of the genome.

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Lappalainen Lab

@tuuliel_lab

3 years

Very cool work! I've been thinking that this is probably the case, and it's fantastic to see data 👏👏👏

Nathan Abell

@n_s_abell

3 years

It is a major challenge to fine-map causal variants within genetic associations due to linkage, so a common assumption is that a single variant drives a given signal. But how many variants could really be causal? Check out our new paper from @sbmontgom lab

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Lappalainen Lab

@tuuliel_lab

1 year

This is an incredible loss to the entire community.

UPenn GCB

@UPennGCB

1 year

It is with great sadness that we share the news that Dr. Casey Brown passed away on Saturday, March 18. He was a friend, colleague, and mentor to so many in the GCB and CAMB communities, as well as the scientific community as a whole, and will be deeply missed.

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Lappalainen Lab

@tuuliel_lab

2 years

@ceclindgren @timfrayling @pnatarajanmd @dgmacarthur @RoyalPapworth @Cambridge_Uni @bdi_oxford @HumanGeneticsOx European universities should invest in support staff, allowing researchers to focus on research instead of admin. In the US universities could do more to support a healthy combination of family/personal life with a research career (although these problems are society-wide).

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Lappalainen Lab

@tuuliel_lab

5 months

After many struggles with the sparsity of allelic series in genetic insights to the dosage-to-function question, I'm very excited about our new molecular biology approach to this question. This is just a pilot study, and we're continuing this line of work in the lab. 6/6

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Lappalainen Lab

@tuuliel_lab

1 year

@vagar112 IDK. If graduate student or a postdoc works their ass off for years to produce a data set, and then someone who’s quicker at analysis publishes the key discoveries the trainee has been dreaming to pursue…even if they get a data set citation and credit, is that a great outcome?

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Lappalainen Lab

@tuuliel_lab

3 years

I’m thrilled to join one of the strongest biomedical hubs in Europe, continue my research at @KTHresearch with new collaborations, and contribute to the fantastic technology hub that @scilifelab is. I’ll be recruiting staff, postdocs and students to my new lab - stay tuned!

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Lappalainen Lab

@tuuliel_lab

3 years

@dgmacarthur Obviously it refers to the secret call centers in the basement of each research institute ☎️

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Lappalainen Lab

@tuuliel_lab

3 years

The bittersweet part is leaving Columbia and transitioning from a Core to Associate Faculty at NYGC. It’s been amazing, with great research environment & colleagues, but all good things come to an end. But I’ll still have a lab at NYGC and I’ll be around in NYC quite a lot!

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Lappalainen Lab

@tuuliel_lab

4 years

Interesting sequel in the series of seemingly binary behavior in single cells that are shown to be largely artifacts.

Dr. Liana Lareau

@lianafaye

4 years

Now in eLife! Single-cell RNA-seq led to a surprising model of alternative splicing: individual cells make one isoform or the other, but rarely both in one cell. Carlos Buen Abad Najar, with Nir Yosef and me, shows this is an artifact of low mRNA recovery.

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Lappalainen Lab

@tuuliel_lab

11 months

Very interesting work by @xinlixl lab! Gene dosage sensitivity deserves a lot more attention.

AJHG

@AJHGNews

11 months

💫New @AJHGNews from Dong et al. 📰An RNA-informed dosage sensitivity map reflects intrinsic functional nature of genes 👇

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