Browse by CSHL Author

Paper

Siepel, Adam, Hassett, Rebecca, Staklinski, Stephen J (March 2026) VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies. bioRxiv. ISSN 2692-8205 (Submitted)

Staklinski, Stephen, Scheben, Armin, Brault, Lise, Hassett, Rebecca, Serio, Ryan, Xing, Jiawei, Nowak, Dawid, Siepel, Adam (September 2025) Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data. bioRxiv. ISSN 2692-8205 (Submitted)

Liu, Lingjie, Zhao, Yixin, Hassett, Rebecca, Toneyan, Shushan, Koo, Peter K, Siepel, Adam (February 2025) Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data. Nucleic Acids Research (NAR), 53 (4). ISSN 1362-4962 (Public Dataset)

Serio, Ryan N, Scheben, Armin, Lu, Billy, Gargiulo, Domenic V, Patruno, Lucrezia, Buckholtz, Caroline L, Chaffee, Ryan J, Jibilian, Megan C, Persaud, Steven G, Staklinski, Stephen J, Hassett, Rebecca, Brault, Lise M, Ramazzotti, Daniele, Barbieri, Christopher E, Siepel, Adam C, Nowak, Dawid G (July 2024) Clonal Lineage Tracing with Somatic Delivery of Recordable Barcodes Reveals Migration Histories of Metastatic Prostate Cancer. Cancer Discovery. ISSN 2159-8274

Zhao, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam (October 2023) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Research. ISSN 0305-1048

Conference or Workshop Item

Nowak, Dawid G, Serio, Ryan N, Brault, Lise M, Gargiulo, Domenic V, Hassett, Rebecca, Chaffee, Ryan J, Staklinski, Stephen J, Lu, Billy, Siepel, Adam C (April 2026) Rb1 loss defines distinct migration histories in metastatic prostate cancer subtypes. In: American Association for Cancer Research Annual Meeting 2026, 2026 Apr 17-22, San Diego, CA.