Technical Reports by Author
Theses by Author

2024 REPORT SERIES

CMU-CB-24-101
Explorations of Spatial Cellular Patterns at Proteomic Level
Huangqingbo (Paul) Sun, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-24-102
Automated hyper-parameter tuning and its applications in computational biology
Yihang Shen, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-24-103
Investigating the role of DNA damage in aging and neurodegeneration
Qiao "Cathy" Su, Ph.D. Thesis
Abstract, .pdf Pending

2023 REPORT SERIES

CMU-CB-23-101
Algorithmic Foundations of Genome Graph Construction and Comparison
Yutong Qiu, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-23-102
Spatio-Temporal Analysis of Single Cell Data
Dongshunui "Dora" Li, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-23-103
Conserved mammalian cell types and epigenomics of the striatum and cortex to identify targets and consequences of addiction genetic risk variants
BaDoi N. Phan, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-23-104
Principled Methods to Process Massive Datasets in Metabolomics
Mihir Mongia, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-23-105
Learning complex spatial relationships from tissue and cell images
Haoran Chen, Ph.D. Thesis
Abstract, .pdf Pending

2022 REPORT SERIES

CMU-CB-22-101
De novo design of new chemical entities with AI methods
Maria Korshunova, Ph.D. Thesis
Abstract, .pdf

CMU-CB-22-102
Deciphering the regulatory code underlying Alzheimer's Disease relevant brain and blood cell types
Easwaran Ramamurthy, Ph.D. Thesis
Abstract, .pdf

CMU-CB-22-103
Tumor Deconvolution Integrating Multiple Types of Genomic Data
Haoyuan Lei, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-22-104
Toward unsupervised visual proteomics: a deep learning framework for in situ cryo-ET structural pattern mining
Xiangrui Zeng, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-22-105
Charting the Landscape of 3D Genome Organization with Graph Representation Learning
Ruochi Zhang, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-22-106
Computational Methods for Discovering Polyketides by Integrating Genomic and Mass Spectral Data
Liu Cao, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-22-107
Modeling individual differences in the brain in the presence and absence of disease
Jennifer L. Williams, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-22-108
Algorithms and computational methods for transcriptome analysis
Laura H. Tung, Ph.D. Thesis
Abstract, .pdf Pending

CMU-CB-22-109
Application of Machine Learning Algorithms to Reveal 3D Genome Compartmentalization Patterns
Kyle Xiong, Ph.D. Thesis
Abstract, .pdf Pending

2021 REPORT SERIES

CMU-CB-21-101
Automated analysis of protein subcellular location in immunohistochemistry images for cancer diagnosis
Aparna Kumar, Ph.D. Thesis
Abstract, .pdf

CMU-CB-21-102
Computational methods for "atlas-scale" analysis of scRNA-seq data
Amir Alavi, Ph.D. Thesis
Abstract, .pdf

CMU-CB-21-103
Genome-Driven Personalized Medicine of Cancer via Machine Learning and Phylogenetic Models
Yifeng Tao, Ph.D. Thesis
Abstract, .pdf

2020 REPORT SERIES

CMU-CB-20-101
Detecting anomalies in inferred transcript sequences and expression from RNA-seq
Cong Ma, Ph.D. Thesis
Abstract, .pdf
Unavailable for Distribution

CMU-CB-20-102
Algorithms for the study of chromosomal structure variability
Natalie Sauerwald, Ph.D. Thesis
Abstract, .pdf

CMU-CB-20-103
Computational Methods for Multi-Species Comparison of 3D Genome Organization and Function
Yang Yang, Ph.D. Thesis
Abstract, .pdf

2019 REPORT SERIES

CMU-CB-19-101
Computational Methods for Image-derived Modeling of Cell Shape and Organization Dynamics
Xiongtao Ruan, Ph.D. Thesis
Abstract, .pdf
Unavailable for Distribution

2018 REPORT SERIES

2017 REPORT SERIES

2016 REPORT SERIES

CMU-CB-16-101
Modeling the Part, Present, and Future of Influenza
David Farrow, Ph.D. Thesis
Abstract, .pdf

CMU-CB-16-102
Computational methods for exploring gene regulation mechanisms using high-throughput sequencing data
Hao Wang, Ph.D. Thesis
Abstract, .pdf

2015 REPORT SERIES

CMU-CB-15-101
Algorithms to Reconstruct Evolutionary Models of Tumor Progression
Salim Akhter Chowdhury, Ph.D. Thesis
Abstract, .pdf

CMU-CB-15-102
Image-derived generative modeling of complex cellular organization in both space and time
Devin P. Sullivan, Ph.D. Thesis
Abstract, .pdf

CMU-CB-15-103
Inferring and Analyzing the Present and the Past of Networks from Limited Information
Emre Sefer, Ph.D. Thesis
Abstract, .pdf

CMU-CB-15-104
Comparative Genomics Reveals Forces Driving the Evolution of Highly Iterated Palindrome-1 (HIP1) in Cyanobacteria
Minli Xu, Ph.D. Thesis
Abstract, .pdf

CMU-CB-15-105
Inferring Viral Capsid Self-Assembly Pathway from Bulk Experiment Measurement via Parameter Fitting Methods
Lu Xie, Ph.D. Thesis
Abstract, .pdf

Technical Reports by Author
Theses by Author

2014 REPORT SERIES (See also Lane Center for Computational Biology)

CMU-CB-14-101
Phenotype Inference from Genotype in RNA Viruses
Chuang Wu, Ph.D. Thesis
Abstract, .pdf

2013 REPORT SERIES

CMU-CB-13-101
Computational Study of Transcriptional Regulation
- From Sequence to Expression
Shan Zhong, Ph.D. Thesis
Abstract, .pdf

CMU-CB-13-102
Computational Methods for Learning Population History from Large Scale Genetic Variation Datasets
Ming-Chi Tsai, Ph.D. Thesis
Abstract, .pdf

CMU-CB-13-103
Spatiotemporal Modeling of Actin Cytoskeletal Mechanics Linked to Morphology and Mechanotransduction
John Kang, Ph.D. Thesis
Abstract, .pdf

CMU-CB-13-104
Efficient Modeling and Active Learning of Biological Responses: Learning without Prior Knowledge
Armaghan Naik, Ph.D. Thesis
Currently Unavailable

CMU-CB-13-105
Automated Construction of Dynamic Models of Subcellular Structure
Taráz E. Buck, Ph.D. Thesis
Abstract, .pdf

2012 REPORT SERIES

CMU-CB-12-101
Learning Generative Models of Microtubule Distributions
Aabid Shariff, Ph.D. Thesis
Abstract, .pdf

CMU-CB-12-102
Analysis of High Throughput Genomic Datasets Across Species
Guy E. Zinman, Ph.D. Thesis
Abstract, .pdf

CMU-CB-12-103
On the Identification and Investigation of Homologous Gene Families,
with Particular Emphasis on the Accuracy of Multidomain Families
Jacob M. Joseph, Ph.D. Thesis
Abstract, .pdf

CMU-CB-12-104
Generative Models for Super-Resolution Single Molecule
Microscopy Images of Biological Structures
Suvrajit Maji, Ph.D. Thesis
Abstract, .pdf

2011 REPORT SERIES

CMU-CB-11-101
The von Mises Graphical Model: Regularized Structure and Parameter Learning
Narges Razavian, Hetunandan Kamisetty, Christopher James Langmead
Abstract, .pdf
Also appears as CMU-CS-11-129

CMU-CB-11-102
The von Mises Graphical Model: Expectation Propagation for Inference
Narges Razavian, Hetunandan Kamisetty, Christopher James Langmead
Abstract, .pdf
Also appears as CMU-CS-11-130

CMU-CB-11-103
Using Visualization and Automation to Accelerate Genetics Discovery
Ross Eugene Curtis, Ph.D. Thesis
Abstract, .pdf

CMU-CB-11-104
Modeling the Space of Subcellular Location Patterns using Images and
other Sources of Information
Luis Pedro Coelho, Ph.D. Thesis
Abstract, .pdf

2010 REPORT SERIES

CMU-CB-10-101
A Framework for Inferring Protein Location as a Function of Condition
Shannon Quinn, M.S. Thesis
Abstract, .pdf

CMU-CB-10-102
Internal Dynamics and Energetics during Enzyme Catalysis
Arvind Ramanathan, Ph.D. Thesis
Abstract, .pdf

2009 REPORT SERIES

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