CPCB@ISMB
The Joint 91视频-Pitt Ph.D. Program in Computational Biology (CPCB) had a strong presence at the annual international conference on, the flagship conference of the International Society for Computational Biology.
22 current students and 24 faculty contributed to papers, talks, and posters presented at the conference, highlighting the breadth of computational biology research across the program.
Presentations with current CPCB students
- Using Interpretable Latent Representations of Spatial Transcriptomic Datasets to Identify Molecular Mechanisms of Immunomodulation
Authors: Hanxi Xiao, Niranjana Natarajan, Javad Rahimikollu, Partha Dutta, Jishnu Das
Presenter: Hanxi Xiao
CSI, July 13 - A signaling-informed sequence-to-function model identifies mechanisms of cytokine-specific gene regulation
Authors: Anamarie Martinez-Turak, Yaxuan Yang, Ali Tugrul Balci, Laura F. Strube, Caroline I. Larkin, Neha Cheemalavagu, Karsen E. Shoger, James R. Faeder, Maria Chikina, Rachel A. Gottschalk
Presenter: Anamarie Martinez-Turak
CSI, July 13 - Topology-Based Analysis of Gene Tree Heterogeneity with Applications to Incomplete Lineage Sorting and Introgression
Authors: Tanjeem Zaman, Yuting Xiao, Maureen Stolzer, Dannie Durand
Presenter: Tanjeem Zaman
EvolCompGen, July 15 - Bounding mutations for a subsampling-placement strategy to reconstruct clonal lineage trees for somatic evolution
Authors: Nishat Anjum Bristy, Russell Schwartz
Presenter: Nishat Anjum Bristy
EvolCompGen, July 16 - In Pursuit of Forbidden Protein Domain Architectures
Authors: Yu-Hsiang Chen, Xiaoyue Cui, Maureen Stolzer, Dannie Durand
Presenter: Yu-Hsiang Chen
EvolCompGen, July 16 - SpaReg: Sparsity-based scalable reconstruction of three-dimensional microenvironments at subcellular resolution
Authors: Rajdeep Pawar, Thomas Jacob, Rebecca Raphael, Elaine Byrnes, Simon Watkins, T. Rinda Soong, Aatur Singhi, Shikhar Uttam
Presenter: Rajdeep Pawar
GenCompBio, July 16 - seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences
Authors: Gün Kaynar, Carl Kingsford
Presenter: Gün Kaynar
iRNA, July 14; Published in Proceedings - RAmpSim: A Thermodynamic Simulator for Hybridization Capture in Metagenomic Sequencing
Authors: Aidan Zhang, Christina Boucher, Noelle Noyes, Yun William Yu
Presenter: Aidan Zhang
MICROBIOME, July 13; Published in Proceedings - Characterizing Functional Microniches with SpaceTravLR
Authors: Alyson Wang, Koushul Ramjattun, Amanda Poholek, Youjin Lee, Jishnu Das
Presenter: Alyson Wang
MLCSB, July 15 - SpiderNet reveals a meta-interaction basis for cell-cell communication in tissues
Authors: Junjie Tang, Shaoheng Liang, Shahul Alam, Jian Ma
Presenter: Junjie Tang
RegSys, July 13 - FIREFate: Functional and Interpretable Regulatory Encoding of Fate determination
Authors: Swapnil Keshari, Jishnu Das
Presenter: Swapnil Keshari
RegSys, July 13
Posters with current CPCB students
- A-163 — Quantum Closest-Pair Search for Biological Sequences via k-mer Distribution Statistics
Authors: Zhezheng Xander Song, Carl Kingsford
HiTSeq, Session A - A-225 — ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering
Authors: Jiayi Li, Hong-Sheng Lai, Litian Liang, Shiyi Du, Shijie Tang, Carl Kingsford
MLCSB, Session A - A-359 — SpiderNet reveals a meta-interaction basis for cell-cell communication in tissues
Authors: Junjie Tang, Shaoheng Liang, Shahul Alam, Jian Ma
RegSys, Session A - A-367 — FIREFate: Functional and Interpretable Regulatory Encoding of Fate determination
Authors: Swapnil Keshari, Zarifeh Rarani, Akanksha Sachan, Nicholas Pease, Jingyu Fan, Harinder Singh, Jishnu Das
RegSys, Session A - B-060 — Intron Variant Identification in Mass Spectrometry
Authors: Benjamin Krummenacher, David Koes, Robin Lee
CompMS, Session B - B-124 — CNVeil enables haplotype-resolved copy number inference and clonal analysis in single-cell tumor genomes from single-cell DNA sequencing data
Authors: Weiman Yuan, Can Luo, Yunfei Hu, Liting Zhang, Zihang Wen, Yichen Henry Liu, Xian Mallory, Xin Maizie Zhou
HiTSeq, Session B - C-187 — sPotts: Soft Probabilistic modeling for de novo cellular phenotyping of complex tissue microenvironments
Authors: Chris Andersen, Shikhar Uttam
MLCSB, Session C - C-319 — Augmenting Electronic Health Records for Adverse Event Detection
Authors: Gün Kaynar, Zhaoyi You, Richard D. Boyce, Takahiro Yakoh, Carl Kingsford
TransMed, Session C - C-323 — A Tumor Classification Framework for Computational Pathology in Hepatocellular Carcinoma
Authors: Mst Shaila Afrin, Tyler M. Yasaka, Yu-Chiao Chiu
TransMed, Session C - C-397 — Agent-driven development of a validated open-source statistical genetics toolkit on genotype representation graphs
Authors: Seyed Alireza Rasoulzadeh Hosseini, Richard Border
VarI, Session C - D-106 — Analysis of Gene Tree Heterogeneity with Applications to Incomplete Lineage Sorting and Introgression
Authors: Yuting Xiao, Tanjeem Zaman, Maureen Stolzer, Dannie Durand
EvolCompGen, Session D - D-178 — Alignment Metadata Leakage Enables Re-identification and Variant Calling in Secure Read Mapping Pipelines
Authors: Navid Bin Hasan, Yun William Yu
GenCompBio, Session D