August 26, 2024 — Haotian Teng has successfully defended his Ph.D. dissertation. Teng was co-advised by Carl Kingsford and Ziv Bar-Joseph. Congratulations Dr. Teng!

Haotian Teng (2024) Improving performance on unsupervised biological tasks with hybrid models. Ph.D. Thesis Tech Report.

April 10, 2024 — Yihang Shen has successfully defended his Ph.D. Congratulations Dr. Shen!

Yihang Shen (2024) Automated hyper-parameter tuning and its applications in computational biology. Ph.D. Thesis (CMU-CB-24-100).

March 8, 2024 — Carl Kingsford, Herbert A. Simon Professor of Computer Science in the Ray and Stephanie Lane Computational Biology Department, has been elected as a Fellow of the International Society of Computational Biology (ISCB).

The ISCB notes that Carl has been chosen for this honor because he “is a trailblazer in computational molecular biology, showcasing sustained innovation in scalable algorithmic approaches.”

October 16, 2023 — Minh Hoang has successfully defended his Ph.D. dissertation, which is titled “Practical Methods for Automated Algorithm Design in Machine Learning and Computational Biology.” He will join Princeton University as a postdoc. Congratulations Dr. Hoang!

Minh Hoang (2023) Practical Methods for Automated Algorithm Design in Machine Learning and Computational Biology. Ph.D. Thesis.

May 5, 2023 — Yutong Qiu, a CPCB Ph.D. student, successfully defended her dissertation titled “Algorithmic Foundations of Genome Graph Construction and Comparison.” She will join Illumina, Inc. Congratulations, Dr. Qiu!

Yutong Qiu (2023) Algorithmic Foundations of Genome Graph Construction and Comparison. Ph.D. Thesis CMU-CB-23-101.

Pangenomic studies have enabled a more accurate depiction of the human genome landscape. Genome graphs are suitable data structures for analyzing collections of genomes due to their efficiency and flexibility of encoding shared and unique substrings from the population of encoded genomes.

October 28, 2022 — Laura Tung successfully defended her Ph.D. thesis. She will join Gaurdant Health, Inc. Congratulations, Dr. Tung!

Laura H. Tung (2022) Algorithms and computational methods for transcriptome analysis . Ph.D. (CMU-CB-22-108).

February 24, 2022 — Hongyu Zheng successfully defended his Ph.D. thesis. He will joint Princeton University as a postdoc. Congradulations, Dr. Zheng!

Hongyu Zheng (2022) Theory and Practice of Low-Density Minimizer Sketches. Ph.D. Dissertation.

Sequence sketch methods generate compact fingerprints of large string sets for efficient indexing and searching. Minimizers are one of such sketching methods, sampling k-mers from a string by selecting the minimal k-mer from each sliding window with a predetermined ordering. Minimizers sketches preserve information to detect sufficiently long substring matches.

February 5, 2021 — CPCB Ph.D. student Yutong Qiu has been awarded an SCS Cancer Research Fellowship. Yutong works on computational methods for understanding the human genome, including methods to identify variants within single genomes and populations of genomes. Her recent work is focused on construction and use of genome graphs for applications in cancer, especially more accurate subtyping of cancers from genomic features.

February 4, 2021 — Carl will receive the Herbert A. Simon Professorship of Computer Science in a virtual ceremony at 5:30 p.m. on Thursday, Feb. 4, 2021.

October 12, 2020 — Cong Ma has successfully defended her Ph.D. Congratulations Dr. Ma! Cong will join Princeton University as a postdoc.

Cong Ma (2020) Detecting anomalies in inferred transcript sequences and expression from RNA-seq. Ph.D. Thesis.

Anomalies are data points that do not follow established or expected patterns. When measuring gene expression, anomalies in RNA-seq are observations or pat- terns that cannot be explained by the inferred transcript sequences or expressions. Transcript sequences and expression are key indicators for cell status and are used in many phenotypic and disease analyses.

Natalie Sauerwald (2020) Algorithms for the study of chromosomal structure variability . Ph.D. Dissertation.

October 5, 2020 — The last two decades have introduced several experimental methods for studying three-dimensional chromosome structure, opening up a new dimension of genomics. Studies of these new data types have shown great promise in explaining some of the open questions in gene regulation, but the experiments are indirect and imperfect measurements of the underlying structure, requiring rigorous computational methods.

April 11, 2019 — Laura Tung, a Ph.D. student in the CPCB Computational Biology Program at Carnegie Mellon University has been awarded a NSF Graduate Research Fellowship. This highly competitive fellowship will partially fund her research for 3 years.

Congratulations!

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