the pai lab

the kinetics of gene regulation

About Us

Welcome to the Pai Lab in the RNA Therapeutics Institute at the University of Massachusetts Chan Medical School. We study the speed and efficiency at which RNA molecules are created and processed to ensure proper cellular functions.

Our lab combines high-dimensional computational analyses with state-of-the art genetic, molecular, and cellular genomics techniques to probe mechanisms of RNA maturation. We are looking for enthusiastic researchers interested in experimental and/or computational biology to JOIN US!

POSTDOC POSITION AVAILABLE! For more details, please see our advertisement and e-mail Athma for a casual inquiry or with requested application material.

news

Nov23 Congrats to Valeria Sanabria for winning the Zelda Haidak Scholarship in Cell Biology, awarded to a UMass Chan graduate student aiming to establish a research career in cell biology. Read more about the news here!

Nov23 We welcome Valeria Sanabria as a new graduate student in the lab! She will be developing projects focused on leveraging long read sequencing to understand cryptic splicing.

Oct23 Welcome to GSBS rotation students Christable Darko and Natalie Haas, who will be rotating with us through October! They will be working on long-read sequencing studies and cryptic splicing analyses, respectively!

Sep23 Congrats to Jesse Lehman, who was awarded a spot on the competitive UMass Chan Innate Immunity Training Program T32 grant!

Aug23 The lab has been a new R01 from NGHRI, which is the chapter in our long-standing collaboration with the Engelhardt lab at the Gladstone Institute/Stanford! We will work on developing a statistical framework to understand how gene regulatory kinetics underlie alternative RNA isoform expression. RECRUITING POSTDOCS TO JOIN THIS COLLABORATION!

July23 PREPRINT ALERT! Congrats to Ezequiel and Rachel, who toiled away at sysmetically assess the accuracy of identifying mRNA terminal ends from long read sequencing data - lots of insights, advice, and cautious tails (pun intended).

July23 PREPRINT ALERT! Congrats to Leslie, who completed a manuscript describing our new method to estimates rates of 3' end pre-mRNA cleavage - for the first time - and how/why cleavage rates vary in Drosophila S2 cells! Thanks to Ezequiel also for his contributions!

Jun23 Welcome back for Arvo Justice, our summer intern who just graduated high school and will spend the summer in our lab before leaving to start college at Johns Hopkins University!

031423 The Pai Lab Pi Day Pie Party has made a return - we were happy to take over the RTI monthly departmental tea time to share pie, pi jokes, and piRNA thoughts!

Mar23 Congrats to Jesse for passing his qualifying exam! He's back to lab with lots of excitement to pursue his thesis work on investigating the rates of transcription and splicing upon immune stimulation!

Mar23 The lab has been awarded a CAREER grant from the National Science Foundation! We're excited to use this funding to pursue our work on investigating the causes and consequences of cryptic splicing in mammalian cells!

Jan23 Lots of exciting collaborative papers have been published as the new year! Thanks to the Dekker (Valton et al. NSMB), Watts (Wang et al. NAR), and Fitzgerald (Vierbuchen et al. PNAS) labs on including us in their work and congrats to all the authors!

Jun22 We're excited to welcome Arvo Justice, a rising senior at Newton North High School, to the lab as a summer intern. He'll be working with Jesse on creating a lab resource for RNA-seq spikeins!

Mar22 Hannah and Yahui's study on circular isoforms of ANRIL, in collaboration with the Alonso lab at Weill Cornell, is now published in Scientific Reports! Congrats to all!

Mar22 We welcome a new graduate student, Jesse Lehman, who officially joined the lab after his recent rotation! He'll continue working on investigating RNA kinetics in the immune response, among other things we manage to excite him about!

31422 After a pandemic-induced break, we celebrated our third annual Pai Lab Pi Day Pie Party! Everyone brought in tasty pi pie goodies, with lots of creativity! Just within the lab for now, but hope to be back in a bigger way next year! #paipipie

Mar22 We bid farewell to Mustafa, who is leaving to pursue new adventures as a Research Scientist in the Weiss group at MIT.

Feb22 Welcome to GSBS rotation students Jesse Lehman and Vista Sohrab, who will be rotating with us through March! They will be working on investigating transcriptional kinetics in the immune response and the effects of U1 perturbation upon splicing kinetics, respectively.

Jan22 Welcome to Rachel Daniels, a senior researcher who is joining us from Harvard Chan School of Public Health. Rachel will be joint between the Pai and Karlsson labs - strengthening connections with BIB - and was recently awarded an R21 to study human hookworm genomics!

Jan22 Congrats to Hannah and Yahui for their preprint posted on bioRxiv, a great collaboration with the Alonso lab (formerly UMMS, now Weill Cornell)! We systematically identified, quantified, and characterized circular isoforms of ANRIL, a lncRNA involved in cardiometabolic disorders. And thanks to Ezequiel for his contributions!

Nov21 Welcome to GSBS rotation student Brad Class, who will be working on generation and analysis of nascent long-read data for the next two months!

May21 The lab's first pre-print is posted on bioRxiv, a great collaboration with our friends from the Fiszbein (BU) and Burge (MIT) labs! We describe the HITindex, a new method to classify exon categories using short-read RNA-seq, and how we used it to characterize hybrid internal-terminal exons. Congrats to Ezequiel, Athma, and all other authors!

Apr21 Congrats to Ezequiel for passing his qualifying exam! He's excited to continue work on the co-regulation of transcription and termination for his thesis research!

Jan21 Happy New Year! Here's hoping for a less crazy 2021! To help us achieve that, we welcome a new administrative coordinator, Kathy Sloan!

Nov20 Welcome to Mustafa Malik Ghulam, a postdoc joining us after completing his PhD at University of Sherbrooke in Quebec, Canada. Mustafa will be joint between the Pai and Sontheimer labs - strengthening connections with our next door neighbors!

Aug20 Congrats to Hannah and Leslie for passing their qualifying exams! They're excited to continue work on RNA processing kinetics - with Hannah focusing on mutation-altered kinetics in cancer cells and Leslie on how RNA processing might underlie the timing of the circadian clock for their respective thesis research.

May20 Welcome to MD/PhD rotation student Ayush Kumar, who will be working remotely with Eraj on noisy splicing analysis for the next month!

Apr20 Some good news among the whirlwind of 2020 - Ezequiel Calvo Roitberg has officially joined the lab for his thesis research! Welcome Ezequiel!

Mar20 Wet lab work has been put on pause due to the ongoing pandemic, but our computational work continues from home. Sadly the third annual Pai Lab Pi Day Pie Party has to be postponed - fingers crossed, we'll be back next year with a pie contest! #paipipie

Mar20 We've been funded by SLC6A1 Connect for a collaborative project with the Watts Lab to develop ASOs that target noisy splicing and up-regulate gene expression!

Feb20 We bid farewell to Paul Yan, who was instrumental to the lab's early days. We wish him well at his next adventure in industry!

Feb20 Welcome to GSBS rotation student Abigail Zeamer, who will be working on analysis and generation of nascent RNA-seq data for the next two months!

Dec19 Welcome to Eraj Khokhar, our first postdoc! Eraj comes to us after completing his PhD at The Jackson Laboratory in Maine.

Nov19 Welcome to GSBS rotation student Ezequiel Calvo, who will be working on optimizing our long-read nascent RNA-seq protocols over the next two months!

Sep19 We're excited to send Kevin off to graduate school! Luckily he's not going far - he just enrolled in the UMMS GSBS program, so we're looking forward to watching his graduate career bloom quite closely!

Jul19 The lab has our first Notice of Award! We have been awarded an R35 (MIRA) from NIH NIGMS to continue our work on investigating the temporal progression of RNA biogenesis and maturation!

Aug19 We were thrilled to contribute to a study developing Divalent-siRNA therapies for substantial huntingtin> knockdown as a therapeutic for Huntington's Disease, led by the Khvorova lab and now published in Nature Biotechnology.

Jul19 Congrats to Paul for passing his qualifying exam! He's excited to continue working on splicing kinetics over neuronal differentiation to understand molecular mechanisms underlying Huntington's Disease.

May19 Busy times in the Pai Lab this summer - Katy Monopoli (UMMS-WPI) will be joining us for a summer rotation and undergrads Parker Simpson (WPI) and Vista Sohrab (UMass Amherst) will be doing summer internships. Welcome!

Apr19 Hannah Macmillan and Leslie Torres Ulloa have officially joined the lab for their thesis research! We are excited to welcome them to lab!!

31419 Second annual Pai Lab Pi Day Pie Party was thrown in conjunction with the Garber Lab during the 3/18 RTI Teatime. Thanks to our many colleagues for showing up to enjoy pi[e] with us! #paipipie

Feb19 Welcome to rotation students Han Zhang (GSBS), Hannah Macmillan (GSBS), Jocelyn Pettito (WPI-UMMS), and Shaimae Elhajjajy (UMMS-WPI)! We will have a full house through March!

Dec18 Welcome to GSBS rotation students Leslie Torres Ulloa and Alex Park, both of whom will be working on computational rotations with us through January!

Sep18 Welcome to GSBS rotation student Wenjia Huang, who will be working with Paul for the month.

Sep18 New review on the dynamics of RNA processing upon perturbation of cellular conditions now published in WIREs RNA!

Aug18 Our paper on recursive splicing has been published in PLOS Genetics, with Paul and Athma as authors! Note the sister paper by Zhiping Weng's group in the same issue.

Jun18 Paul Yan joins the lab as our first graduate student! Paul has an undergraduate degree from UMass Lowell and is pursuing a Ph.D. in the UMass Med GSBS program.

Apr18 Kevin Fortier joins us as a research associate, previously having worked with Sean Ryder at UMMS! Kevin will be working on optimizing experimental protocols and ultimately automation of our basic workflow.

Apr18 Welcome to rotation students Eleni, Garhom, and Paul - looking forward to exploring exciting potential projects over the next couple months!

31418 First annual Pai Lab Pi Day Pie Party served as our lab warming. Thanks to our many colleagues for showing up to enjoy pi[e] with us! #paipipie

Jan18 Nida Javeed joins as our first lab member. Welcome Nida!

Jan18 The Pai Lab is officially open! Plenty of boxes to be unpacked and files to be moved!

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research

Distribution of mean splicing half-lives across bins of RIME (θ axis) and deciles of joint intron and exon lengths (r axis). While 60-70nt introns are spliced more efficiently, putative exon-defined introns are spliced faster than intron-defined introns in flies. [1]

Phenotypic variation in humans is driven by coordinated changes in gene regulation that allow a continuum of gene expression levels to arise from the same genome sequence. Recent studies have provided unprecedented insight into how individual molecular mechanisms regulate changes in mRNA levels and revealed that substantial transcriptome diversity arises from the differential processing of nascent RNAs. Many studies of gene expression focus on characterizing steady-state mRNA levels, even though living systems are inherently dynamic. Thus, a key unanswered question underlying functional genomics is: how do the dynamics of individual molecular processes combine to influence the cellular transcriptome?

Our lab seeks to answer this question by investigating how the kinetics of disparate steps of gene regulation are regulated synergistically to influence steady-state mRNA levels. In particular, we focus on characterizing the speed and efficiency of essential steps in the life-cycle of an RNA molecule - transcriptional elongation, pre-mRNA splicing, and cleavage and polyadenylation - to profile how these steps are coordinated to create mature mRNA molecules. We do this using a experimental techniques to isolate newly created nascent RNA, followed by high-throughput sequencing and computational and mathematical modeling approaches to simultaneously measure the rates of each RNA processing step along a gene body. Genome-wide measurements provide us with the ability to learn about the cellular logic and regulatory grammer involved in efficient RNA processing. We have previously used these methods to study the rates of mRNA splicing in flies, which provided insights about genomic features that influence variability in rates and mechanistic choices made during intron recognition for mRNA splicing.

[1] (view) The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture. Pai AA, Henriques T, McCue K, Burkholder A, Adelman K, Burge CB. eLife 2017, 6, e32537

Distribution of deltaPSI values for each RNA processing category after infection with either Listeria or Salmonella bacteria. Negative values represent less inclusion, while positive values represent more inclusion, as defined by the schematic exon representations. There are striking global shifts towards increased inclusion of skipped exons and the shortening of 3' UTRs following infection with either bacteria. [1]

Changes in gene regulation have long been known to play an important role in any cellular response, with many previous studies extensively characterizing transcriptional response pathways. However, post-transcriptional mechanisms, especially those involved in mRNA process and alternative splicing, remain understudied despite gaining prominence as crucial regulators of cellular defense systems.

In collaboration with Luis Barreiro's lab at the University of Montreal, we have been studying the dynamics of transcriptional and post-transcriptional regulation in response to infection by naturally occuring pathogens (Listeria monocytogenes and Salmonella typhimeurium), with a particular focus on investigating the role of mRNA processing during cellular reponses. In an initial study[1], we discovered thousands of changes in isoform usage following infection. Immune response was characterized by specific changes in mRNA splicing and polyadenylation site choice, with global shifts towards increased inclusion of cassette exons and a widespread usage of upstream polyadenylation sites in genes upregulated after infection. Favoring shorter 3' UTRs after infection likely allows immune-relevant transcripts to escape repression by miRNAs activated in response to infection. We are continuing work on the mechanisms of mRNA processing dynamics during the immune response and mapping genetic loci that influence inter-individual differences in immune response through mRNA processing pathways.

For a broader perspective on the dynamics of mRNA processing, we investigated mRNA processing changes across a panel of cellular responses to environmental and drug stimulii in collaboration with the labs of Francesca Luca and Roger Pique-Regi at Wayne State University[2]. Simular to immune response, we see clear signatures of directed shifts in particularly RNA processing mechanisms, in a stimulus-dependent manner. Combined with functional genomic data and knowledge of regulated pathways, we are able to identify trans-acting factors that influence RNA isoform usage, particularly for alternative transcription start sites. Overall, our work clearly demonstrates the ubiquity of post-transcriptional mRNA changes related to gene expression response to the environment, including for key functions like the innate immune response and drug response.

[1] (view) Widespread Shortening of 3' Untranslated Regions and Increased Exon Inclusion Are Evolutionarily Conserved Features of Innate Immune Responses to Infection. Pai AA, Baharian G, Sabourin A, Brinkworth JF, Nédélec Y, Foley JW, Grenier J, Siddle KJ, Dumaine A, Yotova V, Johnson ZP, Lanford RE, Burge CB, Barreiro LB. PLOS Genetics 2016, 12(9), e1006338

[2] (view) Environmental perturbations lead to extensive directional shifts in RNA processing. Richards AL, Watza D, Findley A, Alazizi A, Wen X, Pai AA, Pique-Regi R, Luca F. PLOS Genetics 2017, 13(10), e1006995

people

Athma was born in Stamford, CT, once called the "Research City" due to it's bustling innovation-driven economy. She was fascinated by science at an early age, inspired by her father's demonstrations of bright chemiluminescent displays and working her way through all the science fiction books in the local library. In high school, she discovered genetics by reading Matt Ridley's Genome: An Autobiography of a Species in 23 Chapters.

At the University of Pennsylvania, Athma managed to simultaneously pursue her interests in genetics, chemistry, and evolution by majoring in Biochemistry and Anthropology and doing research in an anthropological genetics lab studying the genetic signatures of human migration. Continuing in this vein, she pursued graduate work in human and comparative genomics in the Department of Human Genetics at the University of Chicago. Working with Yoav Gilad and collaborating closely with Jonathan Pritchard's group, Athma applied both experimental and computational approaches to understanding how gene regulatory variation in humans and closely related primates established gene expression signatures. One primary focus of her work was to map molecular quantitative trait loci (QTLs) in humans for many transcriptional regulatory mechanisms.

To gain more experience in understanding the molecular details of gene regulatory mechanisms, Athma did postdoctoral research as a Jane Coffin Childs Fellow at MIT working with Christopher Burge. She focused on understanding the changes in mRNA splicing and RNA processing mechanisms after immune response and developing methods to measure the dynamics of such processes. Her transition to an RNA systems geneticist complete, Athma assumed her current position as an Assistant Professor in the RNA Therapeutics Institute at UMMS in January 2018. Her research focuses on developing and applying methods to study the kinetics of RNA processing and understanding how various steps in RNA maturation are coordinated through the lifecycle of an RNA molecule. In her spare time, Athma enjoys traveling, racquet sports, experimenting with molecular gastronomy, and finding the best ice cream in New England.

Ezequiel Calvo Roitberg
Graduate Student
Rachel Daniels
Research Assistant Professor
Nida Javeed
Research Associate
Eraj Khokhar
Postdoctoral Researcher
Jesse Lehman
Graduate Student
Hannah Macmillan
Graduate Student
Athma Pai
Principal Investigator
Valeria Sanabria
Graduate Student
Leslie Torres Ulloa
Graduate Student
Postdoctoral Researchers

Mustafa Malik Ghulam (2020-22, joint with Sontheimer lab), now Research Scientist @ Weiss Lab, MIT

Graduate Students

Paul Yan (2018-20), now Senior Research Associate @ Arbor Biotechnologies

Research Associates

Kevin Fortier (2018-19), now graduate student in UMMS/WPI joint program (Weng lab)

Pre-graduate Interns

Akash Koul, undergrad at Union College (Winter 2018-19)
Parker Simpson, undergrad at WPI (Summer 2019)
Vista Sohrab, undergrad at UMass Amherst (Summer 2019, Winter 2019-20)
Arvo Justice, high-school student at Newton North High School (Summers of 2022 & 2023)

Rotation Students

Eleni Jaecklein, GSBS (Spring 2018)
Jiahong Li, GSBS (Spring 2018)
Paul Yan, GSBS (Spring 2018)
Wenjia Huang, GSBS (Fall 2018)
Alexander Park, GSBS (Winter 2019)
Leslie Torres Ulloa, GSBS (Winter 2019)
Shaimae Elhajjajy, UMMS/WPI joint program (Spring 2019)
Hannah Macmillan, GSBS (Spring 2019)
Han Zhang, GSBS (Spring 2019)
Jocelyn Petitto, UMMS/WPI joint program (Spring/Summer 2019)
Katy Monopoli, UMMS/WPI joint program (Summer 2019)
Ezequiel Calvo Roitberg, GSBS (Winter 2020)
Abigail Zeamer, GSBS (Spring/Summer 2020)
Ayush Kumar, MD/PhD (Summer 2020)
Brad Class, GSBS (Winter 2022)
Jesse Lehman, GSBS (Spring 2022)
Vista Sohrab, GSBS (Spring 2022)

Graduate Students: We are actively recruiting graduate students from the GSBS doctoral program at UMass Chan Medical School in Worcester. Prospective students should apply directly to this program and current students are welcome to e-mail Athma to discuss rotation projects! Graduate students will have the chance to learn techniques spanning experimental genomics to computational biology and mathematical modeling with the goal of understanding fundamendal molecular mechanisms and their mis-regulation in human diseases.

Postdoctoral Scholars: We are currently looking for 1-2 enthusiastic and creative postdoctoral scholars. The ideal candidate will have experience in both experimental and computational genomics, but we welcome all applicants with an interest in expanding their skill-sets in RNA biology, genomics and computational biology. For more details, please see our advertisement and e-mail Athma with the necessary material.

Other positions: We encourage inquiries from undergraduate researchers from the New England area or visiting scientists from any discipline. Please email Athma to see whether there are any such opportunities available in the lab at the moment.

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publications

# Abstract Authors Title Journal Year

Photos from Lab


contact

The Pai Lab
RNA Therapeutics Institute
UMass Chan Medical School
368 Plantation Street, AS5-2057
Worcester, MA 01605

wet-lab: AS5-2003/2004
dry-lab: AS5-2053/2055

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Athma Pai

athma.pai@umassmed.edu

B.A. Biochemistry & Anthropology, U. of Penn (2007)
Ph.D. Human Genetics, U. of Chicago (2012)
Jane Coffin Childs Postdoctoral Fellow, MIT (2012-17)
Google Scholar | PubMed

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Kathy Drolet

kathryn.drolet@umassmed.edu

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Nida Javeed

nida.javeed@umassmed.edu

B.S. Microbiology, U. of California, Davis (2012)

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Hannah Macmillan

hannah.macmillan@umassmed.edu

B.S. Biotechnology, Florida Gulf Coast University (2015)
M.S. Biology, New York University (2018)

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Leslie Torres Ulloa

leslie.torresulloa@umassmed.edu

B.S. Biology & Philosophy, U. of Massachusetts, Boston (2018)

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Eraj Khokhar

eraj.khokhar@umassmed.edu

B.S. Biology, SBASSE @ Lahore University of Management Sciences, Lahore, Pakistan (2013)
Ph.D. Biomedical Sciences, The Jackson Laboratories & University of Maine (2019)

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Rachel Daniels

rachel.daniels@umassmed.edu

Joint with Karlsson Lab @ UMMS
B.Sc. Biology, Brandeis University (2002)
Ph.D. Biological and Biomedical Sciences, Harvard University (2013)
Postdoctoral Researcher, Harvard University (2014)

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Ezequiel Calvo Roitberg

ezequiel.calvo@umassmed.edu

Licenciatura Biological Sciences (B.S/M.S. equivalent),
Universidad Nacional de Buenos Aires (2019)

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Jesse Lehman

jesse.lehman@umassmed.edu


B.S. Biology & Biotechnology, Worcester Polytechnic Institute (2015)

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Valeria Sanabria

valeria.sanabria@umassmed.edu


M.D. equivalent Medicine, Universidad de Buenos Aires Medical School (2021)

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You?

We have open opportunies to join us! Please see details here.

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The Pai lab at UMass Chan Medical School is seeking a postdoctoral candidate in the field of RNA biology and functional genomics with relevant experience in experimental and/or computational biology. Our research combines high-dimensional computational analyses with state-of-the-art genetic, molecular, and cellular genomic techniques to probe the molecular mechanisms of RNA maturation (including transcription, splicing and 3' end processing). We specifically focus on characterizing the kinetics of RNA processing steps to understand the overall speed and efficiency at which RNA molecules are created and processed to ensure proper cellular functions.

Ideal applicants will have a strong background in RNA biology, functional genomics, systems biology, or computational biology/bioinformatics. We desire a candidate with both experimental and computational skills, but encourage applications from scientists motivated to expand their skillset to include both approaches. Applicants must be self-motivated, creative, and able to work in a highly collaborative and interdisciplinary environment.

Responsibilities include:

  • Develop and/or apply new molecular, biochemical, and/or computational approaches, perform data analyses, and supervise/train technicians or graduate students.
  • Take a strong lead in project design and management for multiple research projects, generate and interpret data, and collaborate with other team members.
  • Report results by regularly presenting at scientific conferences and writing scientific manuscripts.
  • Tackle cutting-edge problems in biomedical science, interact with world class scientists, and gain experiences or develop skillsets for her/his next career stage.

Desired qualifications:

  • Ph.D. in biological sciences (e.g. molecular or cellular biology, genetics, biochemistry), computational sciences (e.g. bioinformatics, computer science, statistics) or related discipline. Ph.D. candidates anticipating thesis defense are encouraged to apply for hire after completion of Ph.D.
  • Relevant experimental and/or computational biology research experience, preferably with strong scientific knowledge in eukaryotic RNA biology, gene regulation, or genetics and genomics.
  • Experience with high-throughput sequencing data generation or analysis, preferably for genome- or transcriptome-wide datasets (e.g. RNA-seq, nascent RNA-seq, ChIP-seq, DNase/ATAC-seq, CLIP-seq).
  • Familiarity with Unix/Linux shell and at least one of the following programming languages: C++, PERL, Python, or R.
  • Excellent oral and written communication skills in Engish.
  • Previous record of independent research, including conference presentations and first-/co-author publications.
  • Excellent teamwork, time management, and organizational skills, with the ability to meet deadlines and multi-task across multiple research projects.

To apply, please e-mail the following to Athma Pai at athma.pai@umassmed.edu:

  1. Curriculum vitae, including complete list of publications and pre-prints.
  2. Contact information for three referees.
  3. Summary of your present research (1 page max).
  4. Outline of your future research interests (1 page max).

This position is in the RNA Therapeutics Institute at the University of Massachusetts Chan Medical School in Worcester, MA. To learn more about the Pai lab, please visit our website. The RNA Therapeutics Institute is an exceptional training environment, with many interactive and highly collaborative research groups uniting researchers studying fundamental RNA mechanisms with the active development of RNA-based therapeutic strategies. The department has strong intellectual and proximity-based links with neighboring groups in Bioinformatics and Integrative Biology and the Program in Systems Biology at UMass Chan Medical School, creating a stimulating interdisciplinary research environment with world-class expertise in many disciplines relevant for our work.

UMass Chan Medical School is committed to being an equal opportunity and affirmative action employer and recognizes the power of a diverse community. We encourage applications from protected veterans, individuals with disabilities and those with varied experiences, perspectives and backgrounds to consider UMass Chan Medical School as their employer of choice.

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