| 29 Apr 2026 | Our submission on “Generative modeling of multi-scale tissue remodeling dynamics with flow matching reveals niche-mediated drivers of cell state transitions” got accepted for a poster presentation at the 90th CSHL Symposium: AI in Biology, which will be held between 26-31 May. |
2026 |
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| 27 Apr 2026 | Co-organized the 1st Workshop on Generative AI in Genomics (Gen2): Barriers and Frontiers at ICLR 2026 in Rio de Janeiro, Brazil, which was a success! We will reflect on the themes and take-aways from our workshop and follow-up with a report. |
| 27 March 2026 | My BSRP intern, Erica Brown, accepted a PhD admitted to the Statistics PhD Program at the University of Michigan! Super thrilled! |
| 18 March 2026 | Gave an invited talk at the Workshop on Optimal Transport and Noise: OT meets (S)PDEs organized by the Weierstrass Institute for Applied Analysis and Stochastics (WIAS @ Berlin) on “Learning the drivers of continuous-time cell state and tissue-state dynamics via multi-marginal flow matching and OT”. |
2025 |
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| 16 Dec 2025 | My poster presentation was selected for an "Outstanding poster presentation award" at the Broad Retreat! It was one of 10 posters selected among 302 in total, and one of 2 selected among the 72 posters in the "Computational & Data Sciences" category |
| 15 Dec 2025 | Presented a poster on my ongoing work "Learning Tissue Remodelling Dynamics from Spatial Transcriptomic Snapshots with Biology-Aware Flow Matching" at the Broad Institute 21st Annual Retreat |
| 2 Dec 2025 | Our workshop proposal on "Generative AI in Genomics (Gen2): Barriers and Frontiers" was accepted at ICLR 2026. I'll be co-organizing this along with my co-organizers: Dongshunyi "Dora" Li (Broad), Maria Skoularidou (Broad), Renzo Soatto (Broad), Tamara Broderick (MIT), Valentin De Bortoli (Google DeepMind), Arnaud Doucet (Google DeepMind), Max Welling (CuspAI & University of Amsterdam) in April! |
| 25 Nov 2025 | Delivered a guest lecture in David Alvarez-Melis' COMPSCI2840 class on "Optimal Transport in " at Harvard University, covering some applications of optimal transport in computational biology and in ML for biology. I really admire David as a scientist, mentor and a person, so being part of his class truly meant a lot! |
| 1 June 2025 | Stepped down from my co-chair position in the Models, Inference & Algorithms (MIA) group to reduce (or rather, redirect) time dedicated to administrative work. |
2024 |
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| 26 Nov 2024 | Delivered an invited talk on “Identifying Regulatory Drivers of Cell State Transitions with Flow-Based Generative Models and Neural ODEs” at the University of Cambridge AI for Science Summit. Max Welling's talk was the highlight of the summit for me, bridging physics, materials science, machine learning, and generative modeling, which has a lot of parallels in biology. |
| 20 Nov 2024 | Delivered an invited talk at the Flatiron Institute and Simons Foundation "Workshop on Modeling Stochastic Processes in Cells" on my pas and recent work on optimal transport and neural ODEs for multi-modal single-cell data analysis and modeling the dynamics of cell state transitions. |
| 13-16 Nov 2024 | My BSRP intern Erica Brown, presented her research internship work at the 2024 Annual Biomedical Research Conference for Minoritized Scientists (ABRCMS), after receiving a travel award! Feeling very proud! :) |
| 30 Oct - 2 Nov 2024 | My BSRP intern Erica Brown, received a full travel award to present her research internship work at the 2024 (NDiSTEM SACNAS), after receiving a travel award! Feeling very proud! :) |
| 2 Aug 2024 | A bittersweet day as Erica Brown concludes her internship with me as part of the Broad Summer Research Program (BSRP). You can read her description of our work here. Erica is an incredibly smart, mature, and motivated researcher; her competence level was well beyond what one would expect from a rising junior. She’ll be applying for PhD programs in two years; keep an eye out for her application! We will miss her dearly but we will stay in touch. :) |
| 3 June 2024 | Serving as a research mentor for the “Broad Summer Research Program (BSRP)” this year! Started working with Erica Brown, who is an undergraduate student from my PhD granting institution, Brown University. Super excited!! :) |
| 3 Jan 2024 | Started serving as a co-chair at Models, Inference and Algorithms Initiative (MIA) at the Broad, along with Orr Ashenberg! :) |
| 3 May 2024 | Presented our accepted paper "Breaking isometric ties and introducing priors in Gromov-Wasserstein distance" as a poster at the International Conference on Artificial Intelligence and Statistics (AISTATS) in beautiful Valencia, Spain, soaking in the sun. |
2023 |
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| 21 Nov 2023 | Joined a panel on "opportunities and challenges for foundation models in biology" at the "Schmidt Center - Helmhotz Institute, ML in Genomics Collaboration Kick-off" event. Some points of convergence with other panelists: current benchmarks are too simplistic and circular, yet we do not really know as a field how to robustly evaluate these models outside of specialized applications; dataset availability is not nearly there in single-cell genomics for "scaling laws" to be leveraged to the same extent as in natural language and computer vision aplications. Despite these, everyone seems excited and optimistic about the future of these models! |
| 31 Oct 2023 | Delivered an invited talk at the Ohio State University, Topology, Geometry, and Data Analysis Seminar , presenting my doctoral work on developing optimal transport-based algorithms for single-cell multi-modal data integration. Many thanks to Aziz Burak Gulen for the invitation! Aziz is a super approachable, humble, and wickedly smart Ph.D. student working with Facundo Mémoli, a giant in the field on whose shoulders we stand. Facundo Mémoli is the mathematician that proposed the Gromov-Wasserstein distance, and was just as approachable and humble discussing OT together. So this was a truly surreal day! |
| 11 Oct 2023 | Delivered an invited "lightning whiteboard talk" (along with 3 other postdocs / scientists) at the Models, Inference and Algorithms (MIA) Seminar at the Broad, based on our latest "Augmented Gromov Wasserstein" work. Here is the recording. |
| 6-7 Oct 2023 | Feeling incredibly inspired after attending SorinFest!, a celebration held to honor my doctoral co-advisor, Sorin Istrail, on his 70th birthday. We celebrated his legacy as a computer scientist, who led the development of the sequencing read assembly algorithms used for the Human Genome Project at Celera. Many of the pioneers who made the HGP a success, including Michael Waterman and Craig J. Venter, reflected on the progress made (and the promises yet to be reached) in the ~20 years since its completion, and retold stories of this ambitious undertaking, with all its struggle, competition, and glory. It was moving to learn more about Sorin’s journey as an immigrant from Romania, the hardships he overcame, contributions he made across multiple fields (e.g. ), the communities he established for computational biology (e.g. the RECOMB conference), and the difference he's made in others' through his generosity of spirit. It is humbling to be co-advised by such a warm person and a capable scientist! |
| 4 Sep 2023 | Joined the steering committee of the Models, Inference and Algorithms (MIA) Initiative at the Broad Institute, many thanks to the invitation by the current co-chair Salil Bhate! MIA was an invaluable community and resource for me during my doctoral years, exposing me to branches of computational biology and biomedicine outside of the scope of my graduate department. I got to meet several brillian and kind scientists through MIA and even found opportunities through connections there. So, it feels wonderful to be contributing to this community as part of the steering committee now! |
| 17 July 2023 | Started my postdoctoral fellowship at the Eric and Wendy Schmidt Center at the Broad Institute of MIT and Harvard. I’m looking forward to the next three years as I work to establish my independent research agenda, collaborating with and learning from some of the scientists I have long admired! Unsurprisingly, after multiple RECOMB conferences and workshops, I ran into Donghsunyi "Dora" Li again, who is also starting her postdoc fellowship here! |
| 10 Apr 2023 | Defended my PhD thesis! I feel really grateful to my primary doctoral advisor, Ritambhara Singh, who has been such a great role model and an empathetic leader throughout my doctoral journey. |
| 12 Feb 2023 | Presented our on "Unbalanced CO-Optimal Transport" at the AAAI Conference on Artificial Intelligence in Washington, D.C. |
2022 |
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| 9 Dec 2022 | Virtually presented our work-in-progress "Joint alignment of cells and genomic features of single-cell multi-omic datasets with co-optimal transport" at the NeurIPS Workshop on Learning Meaningful Representations of Life (LMRL). |
| 21 Nov 2022 | Virtually presented our work-in-progress "Joint alignment of cells and genomic features of single-cell multi-omic datasets with co-optimal transport" at the Machine Learning in Computational Biology (MLCB) conference, both as a spotlight talk and a poster. The recording for the full day of presentations is available online on the MLCB YouTube channel |
| 5 Nov 2022 | Delivered an invited talk at the SigmaXi iFoRE Conference "The Convergence of Data, Geometry, and Biology: Insights from the ‘shape’ of biological data" session, describing our efforts to leverage dataset geometry to integrate disparate single-cell multi-modal data with optimal transport. Many thanks to Dhananjay Bhaskar, who organized this session, for the invitation! |
| 10 Nov 2022 | Attended the CSHL Biological Data Science Meeting and presented our poster on "Joint alignment of cells and genomic features of single-cell multi-omic datasets with co-optimal transport." It was exciting meeting so many top researchers in person, whom I previoiusly only known through their publications! :) |
| 27 Oct 2022 | I attended the Rising Stars in EECS Workshop at the University of Texas at Austin! This was quite an informative workshop to attend to learn more about academic job applications and the nature of a faculty position. I also got to meet other brilliant scientists from my field, such as Donghsunyi "Dora" Li from CMU, whom I quite frequently run into at conferences as our paths cross naturally!, and Yi Zhang from DFCI. Happy to have a good representation for computational biology at this EECS workshop! :) |
| 7 June 2022 | Honored to be selected to the 2022 cohort of Rising Stars in EECS by the University of Texas at Austin. Feeling grateful to my Ph.D. advisor, Ritambhara Singh, for nominating me! |
| 7 June 2022 | Delivered an invited virtual talk on Biologically Annotated Neural Networks at Kundaje Lab, Stanford University, by invitation from Gokcen Eraslan. It was quite stimulating to discuss the technical difficulties we ran into as we tried to incorporate Bayesian variable selection into neural networks (lots of work to be done here, but there are many alternative approaches that I would rather use today), and brainstorm possible other applications of a similar approach Thank you, Gokcen! |
| 6 June 2022 | Started a summer research internship at Microsoft Research (Health Futures) |
| 22 May 2022 | Gave an oral presentation at the RECOMB conference on Unsupervised integration of single-cell multi-omics datasets with disparities in cell-type representation. Some of the highlights for me were: |
| 12 Apr 2022 | Received the 2022 RECOMB Travel Fellowship |
2021 |
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| 14 Dec 2021 | Delivered a keynote talk at the Optimal Transport in Machine Learning Workshop at 2021 Conference on Neural Information Processing Systems (NeurIPS).. I got to e-meet Gabriel Peyre and Marco Cuturi, whose book Computational Optimal Transport gave me an introduction to this field. |
| 10 Dec 2021 | Delivered an invited talk on Biologically Annotated Neural Networks at the Translational Bioinformatics Journal Club at Brown University. |
| 21 Oct 2021 | Delivered an invited talk at the University of Connecticut Bioinformatics Seminar, organized by Derek Aguiar, on single-cell multi-omic dataset alignment. |
| 29 Aug 2021 | Presented Gromov–Wasserstein Optimal Transport to Align Single-Cell Multi-Omics Data at the 25th Annual International Conference on Research in Computational Biology (RECOMB) . |
| 11 Aug 2021 | Our work on multi-scale genomic inference has been accepted for publication at PLOS Genetics! |
| 27 May 2021 | Passed my qualifying exam, defended my dissertation proposal, and advanced to candidacy! |
| 2 March 2021 | My Ph.D. co-adviser, Sorin Istrail., has been named an International Society for Computational Biology (ISCB) fellow for his foundational contributions to computational biology! |
| 17 Feb 2021 | Established my thesis committee with Ritambhara Singh (as my primary doctoral thesis advisor), Sorin Istrail (as my secondary doctoral thesis advisor and concurrent masters advisor), Erica Larschan (as the chair of my thesis committee) and Lorin Crawford. We held an exploratory meeting to discuss my Ph.D. dissertation proposal. |
2020 |
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| 18 Dec 2020 | Our work on single-cell multi-omic data integration has been accepted at the 25th Annual International Conference on Research in Computational Biology (RECOMB) |
| 24 Nov 2020 | Delivered a talk on our paper "Gromov-Wasserstein optimal transport to align single-cell multi-omics data" at the 2020 Machine Learning in Computational Biology (MLCB) conference. The recording for talks is available here. |
| 10 Nov 2020 | Poster presentation, jointly delivered with my co-first author and friend, Rebecca Santorella, on applications of optimal transport to single-cell multi-omics at the Workshop on Optimal Control, Optimal Transport, and Data Science hosted by University of Minnesota Institute for Mathematics and Its Applications (IMA). |
| 28 Oct 2020 | Served as a reviewer for the Machine Learning in Computational Biology (MLCB) conference. |
| 23 Sept 2020 | My Ph.D. adviser, Ritambhara Singh, Ph.D. presented our work titled "Unsupervised manifold alignment for single-cell multi-omics data" at the 2020 ACM-BCB conference. |
| 18 Sept 2020 | Last day of my internship at Microsoft Research. Had a really nice time with the Genomics Team! |
| 17 July 2020 | Received the 2020 ICML WCB Fellowship award. |
| 17 July 2020 | Spotlight talk (by me) and poster presentation (by Rebecca Santorella) on our work on single-cell multi-omics integration at the 2020 International Conference in Machine Learning (ICML) - Workshop on Computational Biology). Poster presentation received the Best Poster Award. |
| 15 July 2020 | Berk Alpay presented our paper "Combinatorial and statistical prediction of gene expression from haplotype sequence" at the 28th Conference on Intelligent Systems in Molecular Biology (ISMB). Video here. |
| 14 July 2020 | Presented our work on single-cell multi-omics integration at the 28th Conference on Intelligent Systems in Molecular Biology (ISMB). Video for poster presentation (by me) is here and the video for talk (by Rebecca Santorella) is here |
| 29 June 2020 | Delivered a talk on optimal transport theory applications on single-cell multi-omics integration at the 2020 Brown Unconference on Computational Intelligence and Applications. |
| 15 June 2020 | Started my summer internship at Microsoft Research with the Genomics Team. |
| 13 Apr 2020 | Our paper "Combinatorial and statistical prediction of gene expression from haplotype sequence" got accepted for publication and presentation at the 28th Conference on Intelligent Systems in Molecular Biology (ISMB) |
2019 |
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| 30 Oct 2019 | Delivered an invited talk on Bayesian hierarchical models for multi-scale genomic association at the 2019 CCV-Con. |
| 02 July 2019 | Our paper on my work at MIT, "Rapid Accumulation of Motility-Activating Mutations in Resting Liquid Culture of Escherichia coli" got accepted for publication at the Journal of Bacteriology |
| 02 July 2019 | Our paper on my work at MIT, "Rapid Accumulation of Motility-Activating Mutations in Resting Liquid Culture of Escherichia coli" got accepted for publication at the Journal of Bacteriology |
Pinar Demetci