News

November 2024

A paper led by Sahar Attar and featuring contributions from Val Browning, Mary Krebs, Yuzhen Liu, and Eva K. Nichols—Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER—is published in Nature Methods. Congrats all!
A preprint led by David Shechner's lab in which Elliot Hershberg participated—Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA—goes online at bioRxiv. Congrats all!

October 2024

A paper led by David Shechner's lab in which Elliot Hershberg participated—Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping—is published in Nature Methods. Congrats, Elliot!

September 2024

Nicolas Longhi starts in his new role as a research assistant in the lab. Welcome back, Nico!
Madison Sanchez-Forman joins the lab as a MSDS Master's student. Welcome, Madison!
Eric Lian joins the lab as an undergraduate researcher. Welcome, Eric!
A preprint co-led by Eva K. Nichols and featuring contributions from Val Browning, Nico Longhi, and Conor Camplisson—Predicting cell cycle stage from 3D single-cell nuclear-stained images—goes online at bioRxiv. Congrats all!

July 2024

A preprint co-led by Yuzhen Liu and featuring contributions from Mary Krebs, Conor Camplisson, and David Nwizugbo—DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci—goes online at bioRxiv. Congrats all!
The lab goes on a hike to Keekwulee Falls!

Conor Herlihy joins the lab as a postdoctoral fellow (joint with the Schweppe Lab). Welcome, Conor!

June 2024

Nicole Hang and Jaden Mattison join the lab as summer REU researcher. Welcome, Jaden and Nicole!

March 2024

A paper co-led by Monika Perez and Conor Camplisson—Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP—is published in Methods in Molecular Biology. Congrats, Conor and Monika!
Eanya Devasagayam joins the lab as an undergraduate researcher. Welcome, Eanya!
Lidan Li joins the lab as a postdoctoral fellow. Welcome, Lidan!

January 2024

A paper led by Robin Aguilar and featuring contributions from Conor Camplisson and Chelsey Lin—Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes—is published in Nature Communications. Congrats all!
Our new high performance image analysis workstation, "Ozymandias", arrives! The team is excited to circle lots of objects...

December 2023

The lab journeys down the Burke Gilman trail for an end of quarter outing to Dough Zone.

The lab gets an early holiday present!

November 2023

Robin Aguilar starts their new position as a Science Communication Specialist at A-Alpha Bio. Congrats, Robin—and farewell!

October 2023

Robin Aguilar successfully defends their thesis. Congrats, Dr. Aguilar!
Hunter Jung (UW French) joins the lab as an undergraduate researcher (joint with the Schweppe Lab). Welcome, Hunter!

September 2023

Lawrie Brunswick joins the lab as a MSDS Master's student. Welcome, Lawrie!
Matthew Chaw (GS) joins the lab as a rotation student for the fall quarter. Welcome, Matt!
Nicolas Longhi returns to the lab as a undergraduate researcher. Welcome back, Nico!
Chelsey Lin starts in her new role as a joint research assistant in the Shechner and Beliveau Labs. Welcome back, Chelsey!
David Nwizugbo starts in his new role as a research assistant in the lab. Welcome back, David!
Caleb Kono departs to start as a PhD student in the UW BPSD program. Congrats, Caleb—and farewell!

August 2023

The lab wins a Lab Safety award in our annual inspection. Big thanks to Sahar (lead), Conor K., Mary, and Val for leading our safety and compliance efforts.

We have our annual lab retreat! Dumplings were consumed. Pins were felled.

July 2023

Vincent Chau joins the lab as a Bioinformatics Intern. Welcome, Vincent!
Chandler Ault starts his new position as an intern at Exponential. Congrats, Chandler—and farewell!

June 2023

Nicolas Longhi (UW Bioengineering) joins the lab as a UW GS Summer REU researcher. Welcome, Nicolas!
Conor Camplisson is awarded a Environmental Pathology/Toxicology predoctoral training grant. Congrats, Conor!
Sahar Attar (GS), Conor Kelly (GS), and Monika Perez (GS) join the lab for their dissertation research. Welcome, Monika, Conor, and Sahar!

May 2023

The lab goes ice skating

March 2023

Stephen Gonzalez (GS) joins the lab as a rotation student for the spring quarter. Welcome, Stephen!
A preprint led by Robin Aguilar and featuring contributions from Conor Camplisson and Chelsey Lin—Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes—goes online at bioRxiv. Congrats all!

February 2023

A preprint led by Sahar Attar and featuring contributions from Val Browning, Yuzhen Liu, and Eva K. Nichols—Efficient and highly amplified imaging of nucleic acid targets in cellular and histopathological samples with pSABER—goes online at bioRxiv. Congrats all!

January 2023

A preprint led by David Shechner's lab in which Elliot Hershberg participated—Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.—goes online at bioRxiv. Congrats, Elliot!
A paper in collaboration with Bernhard Payer's lab in which Elliot Hershberg participated in, Cohesin controls X chromosome structure remodeling and X-reactivation during mouse iPSC-reprogramming, is published in PNAS. Congrats, Elliot!
Conor Kelly (GS) and Connor Finkbeiner (GS) join the lab as rotation students for the winter quarter. Welcome, Connor and Conor!

October 2022

A paper led by Jay Shendure's lab in which Eva K. Nichols and Melissa Phung-Rojas participated, Optimized single-nucleus transcriptional profiling by combinatorial indexing, is published in Nature Protocols. Congrats, Melissa and Eva!
Chandler Ault joins the lab as a MSDS Master's student. Welcome, Chandler!

September 2022

Sahar Attar (GS) and Monika Perez (GS) join the lab as rotation students for the fall quarter. Welcome, Monika and Sahar!
Thomas A. Perkins, Jr. joins the lab as a research assistant. Welcome, Thomas!
Mary Krebs joins the lab as a research assistant. Welcome, Mary!

July 2022

We have our annual lab retreat (in 2 parts) with visits to the Seattle Art Museum and the Van Gogh Immersive Experience!

A paper led by Lily Deng—An open source 16-channel fluidics system for automating sequential fluorescent in situ hybridization (FISH)-based imaging—is published in HardwareX. Congrats, Lily!

June 2022

Caleb Kono (UW Biochemistry) joins the lab as a UW GS Summer REU researcher. Welcome, Caleb!
Chelsey Lin (UW Physiology) joins the lab as an undergraduate researcher. Welcome, Chelsey!
Saurabh Shukla starts his new position at Perscryptive Health as a Data Scientist. Congrats, Saurabh—and farewell!
The lab goes out for coffee and pastries to send off Saurabh!

May 2022

Robin Aguilar's artwork is featured on the cover of ACS Chemical Biology. Congrats, Robin!
Melissa Phung-Rojas (Case Western Reserve University, Biology and Cognitive Science) returns to the lab as joint summer undergraduate researcher with the Shendure Lab. Welcome back, Melissa!
A paper in collaboration with Jonathan Liu's lab in which Eva K. Nichols participated in, A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues, is published in Nature Methods. Congrats, Eva!

April 2022

David Nwizugbo (UW Biochemistry) joins the lab as an undergraduate researcher. Welcome, David!

March 2022

Ben Mallory (GS) joins the lab as a rotation student for the spring quarter. Welcome, Ben!
Lily Deng starts her new position at RareCyte as a Computational Biology Scientist. Congrats, Lily—and farewell!
A preprint led by Lily Deng—An open source 16-channel fluidics system for automating sequential fluorescent in situ hybridization (FISH)-based imaging—goes online at bioRxiv. Congrats, Lily!

February 2022

Sahar Attar is accepted to and decides to enroll in the Genome Sciences PhD program. Congrats, Sahar!

January 2022

Chris Hsu's CMAP Research and Education training fund application is selected for funding. Congrats, Chris!
Malvika Tejura (GS) joins the lab as a rotation student for the winter quarter. Welcome, Malvika!

December 2021

Robin Aguilar has an abstract chosen for a poster presentation at the 2022 HHMI Investigator Science Meeting. Congrats, Robin!

November 2021

Eva K. Nichols has an abstract chosen for a plenary "Blue Sky Ideas" session talk at the 4DN Annual Meeting. Congrats, Eva!
Robin Aguilar and Eva K. Nichols have abstracts chosen for poster presentations at the 4DN Annual Meeting. Congrats, Eva and Robin!
Valentino (Val) Browning joins the lab as a research assistant (joint with the Shendure Lab). Welcome, Val!

October 2021

A preprint led by Jay Shendure's lab in which Eva K. Nichols and Melissa Phung-Rojas participated—An optimized protocol for single cell transcriptional profiling by combinatorial indexing—goes online at arXiv. Congrats, Eva and Melissa!
Eva K. Nichols is awarded a WRF Postdoctoral Fellowship. Congrats, Eva!

September 2021

Shruti Jain (GS) and Connor Kubo (GS) join the lab as rotation students for the fall quarter. Welcome, Connor and Shruti!
Eva K. Nichols is named a poster award finalist at the 2021 Genome Sciences Retreat. Congrats, Eva!
Yuzhen Liu crushes the General Exam and officially becomes a PhD candidate. Congrats, Yuzhen!
A preprint in collaboration with Jonathan Liu's lab in which Eva K. Nichols participated—A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues—goes online at bioRxiv. Congrats, Eva!
Chris Hsu is awarded a Genome Training Grant predoctoral fellowship. Congrats, Chris!
Conor Camplisson is awarded a Genome Training Grant predoctoral fellowship. Congrats, Conor!

August 2021

We have our second (and all outdoor) lab retreat!

July 2021

Saurabh Shukla joins the lab as a visiting postdoctoral scholar (joint with the De Yoreo Lab). Welcome, Saurabh!

June 2021

A paper co-led by Elliot Hershberg and Conor Camplisson and featuring contributions from Sahar Attar, Yuzhen Liu, and Ryan Chern—PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments—is published in Nature Methods. Congrats all!
Conor Camplisson crushes the General Exam and officially becomes a PhD candidate. Congrats, Conor!
Sneh Gupta (UW Molecular and Cellular Biology) joins the lab as an undergraduate researcher. Welcome, Sneh!
Caleb Bower (UC Davis Biochemistry and Molecular Biology) joins the lab as a UW GS Summer REU researcher. Welcome, Caleb!
Chris Hsu joins the lab for his dissertation research. Welcome, Chris!
Robin Aguilar is awarded an HHMI Gilliam Fellowship. Congrats, Robin!

May 2021

Melissa Phung-Rojas (Case Western Reserve University, Biology and Cognitive Science) joins the lab as joint summer undergraduate researcher with the Shendure Lab. Welcome, Melissa!

April 2021

Robin Aguilar has an abstract chosen for a poster presentation at the CSHL Biology of Genomes conference. Congrats, Robin!
Eva K. Nichols is awarded a Genome Training Grant postdoctoral fellowship. Congrats, Eva!

March 2021

Lincoln Harris (GS) joins the lab as a rotation student for the spring quarter. Welcome, Lincoln!
Jackson Zariski graduates and prepares to head off to the University of Arizona Applied Mathematics PhD program. Congrats, Jackson—and farewell!
Alisa Tvorun-Dunn graduates and prepares to head off to the Dartmouth Quantitative Biomedical Sciences MS program. Congrats, Alisa—and farewell!

Feburary 2021

Robin Aguilar's Career Column article, Breaking the binary by coming out as a trans scientist, is published in Nature. Congrats!

January 2021

Shayan Avanessian (MCB) and Chris Hsu (GS) join the lab as rotation students for the winter quarter. Welcome, Chris and Shayan!

October 2020

Robin Aguilar has an abstract chosen for a poster presentation at the CSHL Biological Data Science meeting. Congrats, Robin!
Leah Anderson (GS) and Aidan Keith (GS) join the lab as rotation students for the fall quarter. Welcome, Aidan and Leah!

September 2020

Robin Aguilar is named a poster award finalist at the 2020 Genome Sciences Retreat. Congrats, Robin!
Robin Aguilar has an abstract chosen for a poster presentation & lightning talk at the T2T / HPRC 2020. Congrats, Robin!

July 2020

A paper in collaboration with the Ting Wu and Marc Marti-Renom labs in which Elliot Hershberg participated, 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing, is published in Nature Methods. Congrats!
Robin Aguilar wins the General Computational Biology – Best Poster Award at ISMB 2020. Congrats, Robin!
A preprint led by Elliot Hershberg and featuring contributions from Conor Camplisson, Sahar Attar, Yuzhen Liu, and Ryan Chern—PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments—goes online at bioRxiv. Congrats all!
Eva K. Nichols joins the lab as a postdoctoral fellow (joint with the Shendure Lab). Welcome, Eva!

June 2020

Ryan Chern is awarded a Herschel Roman Scholarship. Congrats, Ryan!
Jumana Fathima (UW Bioengineering) joins the lab as a summer undergraduate researcher. Welcome, Jumana!
Conor Camplisson (GS) and Yuzhen Liu (MCB) join the lab for their dissertation research. Welcome, Yuzhen and Conor!
Robin Aguilar crushes the General Exam and officially becomes a PhD candidate. Congrats, Robin!

May 2020

Robin Aguilar has an abstract chosen for a poster presentation at ISMB 2020. Congrats, Robin!

April 2020

A paper in collaboration with Prof. Massimiliano Pagani's lab in which Elliot Hershberg participated, OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment, is published in Nucleic Acids Research. Congrats!

March 2020

Ryan Chern is awarded a Mary Gates Research Scholarship. Congrats, Ryan!
Elliot Hershberg is accepted to and decides to enroll in the Stanford Genetics PhD program. Congrats, Elliot!
Zorian Thornton (GS) joins the lab as a rotation student for the spring quarter. Welcome, Zorian!

February 2020

Alisa Tvorun-Dunn is accepted to the RNA Bioscience Initiative Summer Internship Program at University of Colorado Denver. Congrats, Alisa!
Sahar Attar joins the lab as a research assistant (joint with the Akliesh Lab). Welcome, Sahar!

December 2019

We obtain some important new lab equipment.

Haitham Shaban visits the lab for a week as part of the Research Exchange Program. Welcome, Haitham!

October 2019

Elliot, Robin, Lily, and Brian travel to the Pairing Hoedown in Cleveland!

Lab potluck to welcome Soyeon, Yuzhen, and Conor!

September 2019

Conor Camplisson (GS), Yuzhen Liu (MCB), and Soyeon Showman (MCB) join the lab as rotation students for the fall quarter. Welcome all!

August 2019

We have our first lab retreat!

A preprint from the Kelley Harris lab in which Robin Aguilar participated—Selection against archaic DNA in human regulatory regions—is posted on bioRxiv. Congrats, Robin!
Lily Deng has an abstract chosen for a talk at GRC Genome Architecture in Cell Fate and Disease 2019. Congrats, Lily!

July 2019

Robin Aguilar has an abstract chosen for a poster presentation at ASHG 2019. Congrats, Robin!
Jackson Zariski is awarded a Herschel Roman Scholarship. Congrats, Jackson!
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News

Lab potluck to welcome Soyeon, Yuzhen, and Conor!