2026

• JANUARY: We're excited to welcome Kelly Cochran as a new postdoc in the lab, joint with the Schärfen lab! She is joining us after completing her PhD with Anshul Kundaje at Stanford, working on machine learning methods to predict transcriptional mechanisms.

2025

• DECEMBER: Happy to have been able to contribute to a new paper from the Dekker lab at UMass Chan, now out in Nature Cell Biology!
• DECEMBER: PREPRINT ALERT! As a companion to our recent study on cryptic splicing, the team developed a new approach called CRYPTID-exon to identify cryptic exons in short-read RNA-seq data.
• NOVEMBER: Sad to say goodbye to senior scientist, Rachel Daniels, who will not be going far! We wish her the best in her shift to being 100% in the Karlsson lab at UMass Chan and are happy we will still see and interact frequently!
• NOVEMBER: PREPRINT ALERT! As part of our efforts to develop RNA genomics methods, we present SPARK, a framework to simulate reads from various nascent RNA approaches. Excited to see this first output from our official collaboration with the Engelhardt lab at Gladstone.
• OCTOBER: NOW OUT in Science, our study describing the PITA phenomenon of coordinated transcription and 3' end processing, the result of a long-standing with the Fiszbein lab at BU! Congrats to Ezequiel and Christine!
• OCTOBER: Happy to have been able to contribute to a new paper from the Lee lab at UMass Chan, now out in Cell!
• SEPTEMBER: Congrats to Ezequiel Calvo-Roitberg, who won the 2025 Michael R. Green Award in Graduate Research from the UMass Chan Department of Molecular Cell and Cancer Biology for his contributions to the study of gene regulation. We're excited to attend his talk at the Michael Green Award Symposium!
• AUGUST: We're excited to welcome Ye Liu as a new postdoc in the lab! She is joining us after completing her PhD on biochemical mechanisms of splicing with Aaron Hoskins at UWisconsin.
• JULY: PREPRINT ALERT! A tour-de-force effort by Eraj and Kaitlyn on identifying and characterizing noisy splicing in human cells, as part of our long-standing collaboration with the Watts Lab at UMass Chan!
• FEBRUARY-JUNE: Lots of exciting collaborative papers have been published this year! Thanks to the Lien, Khvorova, and Galloway labs for including us in their work and congrats to all the authors!
• APRIL: Congrats to Eva and Joe for passing their qualifying exams! They're both back to lab with lots of excitement to dive into their thesis work!
• FEBRUARY: Congrats to Jesse Lehman for being awarded an NRSA Fellowship (F31) from NIAID to continue his work to understand the dynamics of transcription and splicing in the immune response. Read more about the news here!
• JANUARY: Welcome to GSBS rotation student Mary Likhite, who will be rotating with us through March and working to analyze nascent RNA long-read sequencing simulations and libraries.

2024

• NOVEMBER: We welcome Eva Jazbec as a new graduate student in the lab! She will be joint with the Sontheimer lab, working in collaboration to understand the dynamics of snRNA abundances in human cells.
• NOVEMBER: NOW OUT in Genome Research, Ezequiel and Rachel's perspective review on identifying and quantifying mRNA starts and ends from long-read sequencing data! Congrats to all!
• JULY: We welcome Sakshi Tembhurne as an intern this summer. Sakshi is part of the prestigious Khorana Scholars Program and is an undergraduate at Atria University in Bangalore!
• JULY: Excited to be involved in a collaboration, newly funded by NHGRI, with the Siepel and Koo labs at Cold Spring Harbor Labs to develop new machine learning models to study transcription elongation rates.
• JULY: Excited to be involved in a collaboration, newly funded by NIAID, with the Lien and Fitzgerald labs at UMass Chan to study the role of a splicing factor in innate immunity.
• MAY: Congrats to Ezequiel Calvo-Roitberg, who won the GSBS Mid-Thesis Research Award for his excellent progress in thesis research.
• MAY: We welcome Joe Paquette as a new graduate student in the lab! He will be working on projects investigating the regulation of long genes and RNA processing kinetics in neuronal cells.
• APRIL: CONGRATULATIONS to Dr. Hannah MacMillan, who successfully defended her PhD thesis entitled "Deciphering Splicing Anomalies in Pancreatic Islets and Cancer Cells"!! Hannah will be moving on to a computational biology position in industry or academic in the Boston area.
• APRIL: CONGRATULATIONS to Dr. Leslie Torres-Ulloa, who successfully defended her PhD thesis entitled "Kinetics of pre-mRNA 3’ end cleavage" as the FIRST PhD student from the lab!! Leslie will be moving on to postdoctoral position at Harvard University.
• MARCH: Welcome to GSBS rotation student Eva Jazbec, who will be rotating with us through June and working with Vale on optimizing nascent RNA long-read sequencing libraries.
• FEBRUARY: We're excited to welcome Marina Krykbaeva as a new postdoc in the lab! She is joining us after completing her PhD with Ollie Rando at UMass Chan.
• JANUARY: NOW OUT in RNA, Leslie's new method on estimating rates of 3' end pre-mRNA cleavage! Congrats to all!
• JANUARY: Welcome to GSBS rotation student Joe Paquette, who will be rotating with us through March! He will be working on investigating the dynamics of small RNAs upon immune stimulation.
• JANUARY: PREPRINT ALERT! A long labor of love from Ezequiel and Christine and a result of our long-standing collaboration with the Fiszbein lab at BU. We describe our discovery of widespread positional coordination in the usage of mRNA start and end sites. We call this phenomenon the Positional Initiation Termination Axis (PITA) and characterize the functional impacts + potential molecular causes in our new study. Thanks to all those involved and especially to Sergey & Job from the Dekker lab for their help in shedding some mechanistic insight!

2023

• NOVEMBER: 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!
• NOVEMBER: 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.
• OCTOBER: 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!
• SEPTEMBER: Congrats to Jesse Lehman, who was awarded a spot on the competitive UMass Chan Innate Immunity Training Program T32 grant!
• AUGUST: 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!
• JULY: 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).
• JULY: 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!
• JUNE: 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!
• MARCH: 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!
• MARCH: 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!
• JANUARY: Lots of exciting collaborative papers have been published as the new year begins! 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!

2022

• JUNE: 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!
• MARCH: 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!
• MARCH: 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
• MARCH: We bid farewell to Mustafa, who is leaving to pursue new adventures as a Research Scientist in the Weiss group at MIT.
• FEBRUARY: 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.
• JANUARY: 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!
• JANUARY: 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!

2021

• NOVEMBER: 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!
• MAY: 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!
• APRIL: 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!
• JANUARY: Happy New Year! Here's hoping for a less crazy 2021! To help us achieve that, we welcome a new administrative coordinator, Kathy Sloan!

2020

• NOVEMBER: 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!
• AUGUST: 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.
• MAY: Welcome to MD/PhD rotation student Ayush Kumar, who will be working remotely with Eraj on noisy splicing analysis for the next month!
• APRIL: Some good news among the whirlwind of 2020 - Ezequiel Calvo Roitberg has officially joined the lab for his thesis research! Welcome Ezequiel!
• MARCH: 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
• MARCH: 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!
• FEBRUARY: 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!
• FEBRUARY: 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!

2019

• DECEMBER: Welcome to Eraj Khokhar, our first postdoc! Eraj comes to us after completing his PhD at The Jackson Laboratory in Maine.
• NOVEMBER: 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!
• SEPTEMBER: 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!
• JULY: 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!
• AUGUST: 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.
• JULY: 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.
• MAY: 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!
• APRIL: Hannah Macmillan and Leslie Torres Ulloa have officially joined the lab for their thesis research! We are excited to welcome them to lab!!
• 031419: 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
• FEBRUARY: 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!

2018

• DECEMBER: Welcome to GSBS rotation students Leslie Torres Ulloa and Alex Park, both of whom will be working on computational rotations with us through January!
• SEPTEMBER: Welcome to GSBS rotation student Wenjia Huang, who will be working with Paul for the month.
• SEPTEMBER: New review on the dynamics of RNA processing upon perturbation of cellular conditions now published in WIREs RNA!
• AUGUST: 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.
• JULY: 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.
• APRIL: 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.
• APRIL: Welcome to rotation students Eleni, Garhom, and Paul - looking forward to exploring exciting potential projects over the next couple months!
• MARCH: 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
• JANUARY: Nida Javeed joins as our first lab member. Welcome Nida!
• JANUARY: The Pai Lab is officially open! Plenty of boxes to be unpacked and files to be moved!