Research in Progress

The RIP series provides an informal forum for computational biologists to keep abreast of colleagues' projects, to help students and postdocs hone their presentation skills, and to get expert feedback on new projects. The forum is targeted towards anyone working at the interface of Biology and Analytical sciences. CBBG students are strongly encouraged to present. These meetings will be held in room #4105 Brendan Iribe Center (#432) Thursdays from 3-4pm, unless otherwise noted. There will be two presentations, approximately 30 minutes each with time for open discussion and socializing. Sign up here.

**If you are interested in speaking on an open date, or if you need to cancel or reschedule, please contact Max Leiserson and inform Barbara Lewis when you are scheduled to give a presentation.
CBCB Fall 2014 RIP Schedule

Summer Semester 2019





Topic & Abstract

Time (if other than 3pm)


Cindy Li


Leiserson Lab

Imputing genetic interaction using matrix completion models
Abstract: Genetic interaction (GI), the phenomenon that unexpected phenotypes occur under the co-mutation of two genes, is essential for characterizing gene functions and provides critical insights in targeted cancer therapy. In cancer cells, where specific genes are mutated more frequently than in normal cells, targeting the negative GI partners of these genes leads to cancer cell death while leaving healthy cells intact. However, not much is known regarding human GI profile. While it is possible to continue experimentally testing for all 200 million possible interactions, a more efficient approach is to take a computational “shortcut” and make biologically meaningful predictions for GI profiles of genes with little or no reported GI data. Here, I will (1) introduce Kernelized Probabilistic Matrix Factorization (KPMF), our chosen model of predicting GI, (2) present our preliminary results of using KPMF to make GI predictions under different scenarios of missing values, and (3) discuss my proposed model of transfer knowledge of GI across species using matrix factorization and matrix clustering to make prediction for species (e.g. human) with very sparse GI data.

Room 4105 Iribe Center


Muzi Li


Liu/Mount Lab

Comparative Analysis of Peach and Apple Transcriptomes from Early Developing Fruit
Absract: Rosaceae is a single plant family with 3,000 species including several economically important fruits (apple, peach, strawberry, and raspberry). Peach and apple are two species from the same subfamily of Rosaceae (Spireaeoidae) with publicly available high-quality genomes. Peach and apple share a basic flower structure of five sepals, five petals, and numerous stamens. However, distinct part of their flower develops into the fruit flesh after fertilization. In peach, the mesocarp enlarges and becomes the fruit flesh and the endocarp lignifies to form a hard stone surrounding the seeds. In apple, the fruit flesh is developed from the hypanthium. There has been a lot of research on flower development. However, genetic mechanisms specifying the fruit identity is not known. To understand the evolution of fleshy fruit diversity, we dissected three specific floral compartments (ovary wall, hypanthium, and ovule) at four critical early stages (0, 5/6, 12, and 18/20 days post-anthesis (DPA)) of peach and apple fruit development in triplicate. Subsequently, a total of 72 RNA-seq libraries were made and sequenced. We have examined differentially expressed genes and developed peach and apple consensus networks to identify the genes that are involved in fertilization-induced cell division. What’s more, our study has revealed that hypanthium and ovary wall develop and grow coordinately in apple. In contrast, peach hypanthium expression pattern deviates from ovary wall.

Room 4105 Iribe Center