News Archive

Jan 16, 2026 Jan 16, 2025 -- Jakub's paper "Towards interpretable prediction of recurrence risk in breast cancer using pathology foundation models" is published in npj Digital Medicine!

Jan 07, 2026 Jan 7, 2025 -- Jessica's paper on "Uncertainty-aware genomic deep learning with knowledge distillation" is published in npj Artificial Intelligence!

Jan 07, 2026 Jan 7, 2025 -- Sophia Chen and Arnav Pemmaraju are Regeneron STS Scholars! Congrats!

Dec 25, 2025 Dec 25, 2025 -- NTv3, co-led by Amber (Instadeep) with contributions by Chandana and Evan, is on bioRxiv -- great collab with InstaDeep, Koo Lab, Stark Lab, and Kuleshov Lab!

Dec 07, 2025 Dec 7, 2025 -- Chandana and Amber present LLMGEN at NeurIPS Workshop on Multi-modal Foundation Models and Large Language Models for Life Sciences!

Nov 07, 2025 Nov 7, 2025 -- Yijie and Evan give oral presentations at Genome informatics meeting!

Nov 03, 2025 Nov 3, 2025 -- Peter's Journal Club is published at Nature Reviews Genetics!

Oct 27, 2025 Oct 27, 2025 -- Vamsi Nallapareddy is joining the Koo Lab for 1 month as a visiting Grad Student from EPFL! Welcome Vamsi!

Oct 09, 2025 Oct 19, 2025 -- Evan's paper on SEAM is on bioRxiv!

Oct 07, 2025 Oct 7, 2025 -- Koo Lab starts a new Reading Group series on AI Agents!

Sep 19, 2025 Sep 19, 2025 -- Amber's gLM evaluation paper was covered as a Research Highlight at nature methods!

Sep 16, 2025 Sep 16, 2025 -- Yijie and Evan give great short talks at Keystone Meeting on AI and Molecular Biology at Santa Fe, NM!

Sep 10, 2025 Sep 10, 2025 -- Alan and Moon give a stellar talk at MLCB!

Sep 05, 2025 Sep 5, 2025 -- Summer is over and we say good by to Marta, Steven, Sophia, Chandana, Nirali, Evan, and Jessica.

Aug 27, 2025 Aug 27, 2025 -- Chandana Rajesh defended her thesis with flying colors! Congrats!

Aug 06, 2025 Aug 6, 2025 -- Da-Wei Lin joins lab as a postdoc! Welcome Da-Wei!

Jul 15, 2025 Jul 15, 2025 -- Amber's paper on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" is finally published in Genome Biology!

Jul 07, 2025 Jul 7, 2025 -- Alejandra Duran is a new postbac in the lab working with the Diffusion team! Welcome Alejandra!

Jun 09, 2025 June 9, 2025 -- Roma Nagle from UC Berkeley starts her Summer URP!

Jun 08, 2025 June 8, 2025 -- Shivani Muthukumar, High school researcher and PFF, will be going to Columbia College. Congrats!

Jun 06, 2025 June 6, 2025 -- Jessica's last day as postdoc! Good luck at Stripe!

Jun 01, 2025 June 1, 2025 -- Steven Yu (Columbia) is back at Koo lab to work with the Diffusion Team!

May 30, 2025 May 30, 2025 -- Trevor Christensen, SBS grad student, joins Koo Lab! Welcome Trevor!

May 20, 2025 May 20, 2025 -- Pablo Mantilla, SBS grad student, joins Koo Lab! Welcome Pablo!

May 17, 2025 May 17, 2025 -- Amber's paper on "Evauating the representational power of pre-trained DNA language models for regulatory genomics" is accepted at Genome Biology!

May 05, 2025 May 5, 2025 -- Book on "Machine Learning for Protein Science and Engineering" is now published! Edited in collaboration with Chistian Dallago, Ananthan Nambiar, and Kevin Yang.

Apr 28, 2025 Apr 28, 2025 -- Evan presents SEAM as an oral ICLR GEM Workshop! Jessica (DEGU), Anirban (D3) and Jack (PIONEER) present posters at various other ICLR Workshops!

Mar 03, 2025 Mar 3, 2025 -- Alan Murphy starts postdoc! Welcome Alan!

Feb 18, 2025 Feb 18, 2025 -- Collaborative paper with the Siepel lab on modeling transcription elongation is published in NAR!

Jan 10, 2025 Jan 10, 2025 -- Jakub's new tool SpinPath, which enables fast and easy specimen-level inference in computational pathology is out on preprint!

Jan 06, 2025 Jan 6, 2025 -- Marta Lemanczyk joins lab as a visiting graduate student from the Renard Lab at Hasso-Plattner-Institute!

Jan 02, 2025 Jan 2, 2025 -- Yash was awarded the best Master's project at IIT Kharagpur for his work with the Koo Lab on data distillation! Congrats Yash!

Dec 12, 2024 Dec 12, 2024 -- Peter is promoted to Associate Professor! Yahooooo!

Dec 05, 2024 Dec 5, 2024 -- Nirali was awarded the best poster presentation at Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS) conference! Woohoo!

Dec 05, 2024 Dec 12, 2025 -- Peter is promoted to Associate Professor! Yahooooo!

Dec 05, 2024 Dec 5, 2024 -- Nirali was awarded the best poster presentation at Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS) conference! Woohoo!

Nov 17, 2024 Nov 17, 2024 -- Jessica's manuscript on "Uncertainty-aware genomic deep learning with knowledge distillation" is on bioRxiv! Congrats Jessica!

Nov 16, 2024 Nov 16, 2024 -- Jessica and Peter give oral presentations at Biological Data Science Conference! Evan and Shivani gave poster presentations!

Nov 04, 2024 Nov 4, 2024 -- Brian Schilder starts postdoc! Welcome Brian!

Sep 23, 2024 Sep 23, 2024 -- Shushan wins the International Birnstiel Award for her PhD thesis research! Congrats Shush!

Sep 19, 2024 Sep 19, 2024 -- CREME is published in Nature Genetics! Congrats Shush!

Sep 05, 2024 Sep 5, 2024 -- Anirban presents D3 and Jessica presents ensemble distillation at MLCB!

Sep 04, 2024 Sep 4, 2024 -- HIPPO is now a preprint! Congrats Jakub!

Jul 24, 2024 Jul 24, 2024 -- Koo lab has its first lab retreat!

Jul 13, 2024 Jul 13, 2024 -- Peter presents CREME and Jessica presents ensemble distillation at ISMB!

Jun 21, 2024 Jun 21, 2024 -- SQUID is published in Nature Machine Intelligence! Congrats Evan!

May 24, 2024 May 24, 2024 -- Anirban's new work on "Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion" is on bioRxiv!

May 20, 2024 May 20, 2024 -- Moon Nagai, SBS grad student, joins Koo Lab! Welcome Moon!

May 10, 2024 May 10, 2024 -- Alessandro gives oral presentation at Biology of Genomes on how active learning can be used to design optimal training data for genomic deep learning!

May 02, 2024 May 2, 2024 -- Evan is awarded the NIH F32 (Ruth L. Kirschstein Postdoctoral Individual National Research Service Award)!

Apr 24, 2024 Apr 24, 2024 -- Amber passes her thesis defense! Congrats Dr. Ziqi Tang!

Apr 17, 2024 Apr 17, 2024 -- Shush passes her thesis defense! Congrats Dr. Shushan Toneyan!

Apr 04, 2024 Apr 4, 2024 -- Pretty is awarded the NSF Graduate Research Fellowship! Congrats!

Mar 08, 2024 Mar 8, 2024 -- EvoAug-TF is published in Bioinformatics here.

Mar 04, 2024 Mar 4, 2024 -- Amber's work on "Evaluating the representational power of pre-trained DNA language models for regulatory genomics" in on bioRxiv!

Jan 18, 2024 Jan 18, 2024 -- EvoAug-TF preprint is out! Check it out here.

Jan 10, 2024 Jan 10, 2024 -- Aayush, PFF student and summer researcher from Half Hallow Hills High, is a Regeneron STS Scholar (Top 300)! Congrats!

Dec 07, 2023 Dec 7, 2023 -- Evan presents SQUID at CSHL's Genome Informatics meeting!

Nov 17, 2023 Nov 17, 2023 -- Evan's work on "Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models is now on bioRxiv!

Nov 10, 2023 Nov 10, 2023 -- Shush gets green light from thesis committee! Congrats!

Nov 08, 2023 Nov 8, 2023 -- Amber gets green light from thesis committee! Congrats!

Nov 06, 2023 Nov 6, 2023 -- Shush's submission on CREME is selected for Oral presentation at MLCB 2023! Chandana's and Amber's submission on unusual inits was accepted as a poster! Congrats!

Oct 23, 2023 Oct 23, 2023 -- Yinan Dong leaves lab to join Meta as a Research Scientist! Good luck!

Oct 02, 2023 Oct 2, 2023 -- Jessica Zhou and Yinan Dong join lab as postdocs! Welcome!

Sep 25, 2023 Sep 25, 2023 -- Peter gives oral presentation on SQUID and Shush presents poster on CREME at Kipoi Summit in Munich!

Sep 12, 2023 Sep 13, 2023 -- Yash Mundewadi joins lab remotely from IIT Kharagpur to work on Master's Thesis!

Sep 06, 2023 Sep 6, 2023 -- Koo's Booze Cruise 2 Boozed 2 Lose takes 3rd place at CSHL Annual Raft Race (but is immortalized on new plaque at Blackford Bar for most creative name)!

Sep 01, 2023 Sep 1, 2023 -- Kaeli passes quals! Congrats!

Aug 25, 2023 Aug 25, 2023 -- Summer research has ended. Thanks for your contribution and great summer Tianhao and Steven!

Aug 01, 2023 Aug 1, 2023 -- Koo lab is awarded a new NIH R01 from NIGMS! $$Woohoo$$

Aug 01, 2023 Aug 25, 2023 -- Summer research has ended. Thanks for your contribution and great summer Tianhao and Steven!

Jul 29, 2023 Jul 29, 2023 -- Amber present's work on "Building foundation models for regulatory genomics requires rethinking large language models" at 2023 ICML Workshop on Computational Biology!

Jul 05, 2023 Jul 5, 2023 -- Katie Engel and Shivani Muthukumar, motivated high schoolers, start research projects in Koo Lab!

Jul 04, 2023 Jul 4, 2023 -- Shush's work on "Interpreting Cis-Regulatory Interactions from Large-Scale Deep Neural Networks for Genomics" in now on bioRxiv!

Jun 22, 2023 Jun 22, 2023 -- Nika Chuzhoy, an undergrad at CalTech CS, starts summer research!

Jun 21, 2023 Jun 21, 2023 -- Pretty Garcia joins lab as a PREP Scholar!

Jun 09, 2023 Jun 9, 2023 -- Tianhao Luo, an undergrad at UPenn Statistics, starts summer research!

May 30, 2023 May 30, 2023 -- Jakub's paper entitled "ChampKit A framework for rapid evaluation of deep neural networks for patch-based histopathology classification" is published in Computer Methods and Programs in Biomedicine!

May 17, 2023 May 17, 2023 -- Kaeli Rizzo officially joins lab! Woohoo!

May 09, 2023 May 9, 2023 -- Paper entitled "Correcting gradient-based interpretations of deep neural networks for genomics" is published in Genome Biology!

May 04, 2023 May 4, 2023 -- Paper entitled "EvoAug, improving generalization and interpretability of genomic deep neural networks with evolution-inspired data augmentations" is published in Genome Biology!

Apr 14, 2023 Apr 14, 2023 -- Anirban Sarkar joins lab as a postdoc! Welcome Anirban!

Apr 10, 2023 Apr 10, 2023 -- Maha Syed, a CSHL grad student, starts rotation. Welcome Maha!

Mar 27, 2023 Mar 27, 2023 -- Alessandro Crnjar joins lab as a postdoc! Welcome Alessandro!

Feb 13, 2023 Feb 13, 2023 -- June He, a grad student in SBU Genetics, starts rotation. Welcome June!

Jan 19, 2023 Jan 19, 2023 -- Collaborative paper on "ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation" led by Yuan Gao of the Vakoc Lab is accepted for publication in Nature Cell Biology. Congrats to all authors, including Shush.

Jan 09, 2023 Jan 9, 2023 -- Kaeli Rizzo, a CSHL grad student, starts rotation. Welcome Kaeli!

Dec 23, 2022 Dec 23, 2022 -- Antonio's and Chandana's paper "Selecting deep neural networks that yield consistent attribution-based interpretations for genomics" is published in the Proceedings of the 17th Machine Learning in Computational Biology meeting.

Dec 22, 2022 Dec 22, 2022 -- Amber's and Chandana's collaborative paper with Risa Kawaguchi and the Gillis Lab entitled "Learning single-cell chromatin accessibility profiles using meta-analytic marker genes" is finally published in Briefings in Bioinformatics!

Dec 05, 2022 Dec 5, 2022 -- Shush's and Amber's paper "Evaluating deep learning for predicting epigenomic profiles" is finally published in Nature Machine Intelligence!

Dec 03, 2022 Dec 3, 2022 -- Antonio leaves lab to go back to finance, now as an ML researcher in Bloomberg LP. Good luck!

Nov 09, 2022 Nov 9, 2022 -- Collaborative paper on "Learning single-cell chromatin accessibility profiles using meta-analytic marker genes" led by Risa and the Gillis Lab is accepted for publication in Briefings in Bioinformatics. Congrats to all authors, including Amber, Chandana, and Rohit!

Nov 03, 2022 Nov 3, 2022 -- Antonio and Chandana's jointly led paper on "Selecting deep neural networks that yield consistent attribution-based interpretations for genomics" is accepted for an Oral presentation at MLCB!

Oct 25, 2022 Oct 25, 2022 -- Shush's collaborative work with the Vakoc lab is accepted for publication in Nature Cell Biology.

Oct 07, 2022 Oct 7, 2022 -- The Koo lab team of summer high school students places 7th in the 2022 DREAM Challenge on Predicting Gene Expression Using Millions of Random Promoter Sequences (Team name - High Schoolers is All You Need)

Sep 16, 2022 Sep 16, 2022 -- Koo's Booze Cruise wins the 2022 CSHL Raft Race! Great team work Jakub, Amber, Chandana, and Craig!

Sep 11, 2022 Sep 11, 2022 -- Rohan and Ethan leave for college. Columbia and Caltech are lucky to have you, good luck!

Sep 05, 2022 Sep 6, 2022 -- Amanda Nemshin, a senior at Cold Spring Harbor High, joins the lab through the PFF program.

Jul 19, 2022 Jul 19, 2022 -- Peter is recognized as an Outstanding reviewer for ICML (Top 10%).

Jul 08, 2022 Jul 8, 2022 -- Rohit leaves for staff position in Jackson Lab. Good luck Rohit!

Jun 14, 2022 Jun 14, 2022 -- Jakub releases preprint on Evaluating histopathology transfer learning with ChampKit.

Jun 08, 2022 Jun 8, 2022 -- Phillip Zhou, an undergrad at Amherst College, joins us as a researcher for the summer (Jointly mentored with David McCandlish). Welcome Phillip!

May 01, 2022 May 1, 2022 -- Antonio releases preprint on Statistical correction of input gradients for black box models trained with categorical input features.

May 01, 2022 May 1, 2022 -- Shush and Amber release preprint on Evaluating deep learning for predicting epigenomic profiles.

Apr 13, 2022 Apr 13, 2022 -- Lucia Tellez Pérez, a CSHL grad student, starts rotation. Welcome Lucia!

Mar 11, 2022 Mar 11, 2022 -- Shush is awarded a NVIDIA Academic Hardware Grant!

Mar 07, 2022 Mar 7, 2022 -- Evan Seitz, from the Frank lab at Columbia, starts postdoc (jointly advised with Justin Kinney)!

Mar 01, 2022 Mar 1, 2022 -- Thomas Huffstutler, a masters student in Applied Math and Statistics at Stony Brook University, starts rotation.

Jan 20, 2022 Jan 22, 2022 -- Rohan is a 2022 Regeneron STS Finalist!

Jan 06, 2022 Jan 6, 2022 -- Ethan and Rohan are 2022 Regeneron STS Scholars, the nation's oldest and most prestigious science and math competition for high school seniors.

Dec 13, 2021 Dec 13, 2021 -- Rohan wins the BEST PAPER AWARD at the 2021 NeurIPS Workshop on AI for Science!

Dec 01, 2021 Dec 1, 2021 -- Scott Feltman and Joon-Hyun Song, PhD students in Applied Math and Statistics at Stony Brook University, start rotations.

Nov 22, 2021 Nov 22, 2021 -- Antonio's oral presentation on "Statistical correction of input gradients for black box models trained with categorical input features" is today at MLCB!