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!
Continue reading...April 24, 2024 — Six out of 57 accepted RECOMB24 papers are authored by current or former Kingsford group members. These include 2 papers authored by current Ph.D. students, and 4 authored by former trainees of the group.
April 10, 2024 — Yihang Shen has successfully defended his Ph.D. Congratulations Dr. Shen!
Continue reading...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.”
Continue reading...
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!
Continue reading...June 10, 2023 — In order to survey the current frontier of the interface between AI methodology and biology and to chart future directions and challenges, we held an "NSF-NIH Joint Workshop on Emerging AI in Biology" in June 2023 that gathered approximately 40 experts on the intersection of research in AI and biology.
Continue reading...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!
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.
Continue reading...October 28, 2022 — Laura Tung successfully defended her Ph.D. thesis. She will join Gaurdant Health, Inc. Congratulations, Dr. Tung!
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.
Continue reading...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.
Continue reading...October 12, 2020 — Cong Ma has successfully defended her Ph.D. Congratulations Dr. Ma! Cong will join Princeton University as a postdoc.
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.
Continue reading...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.
Continue reading...November 10, 2019 — Congratulations to Natalie Sauerwald, 5th-year CPCB Ph.D. student, for having one of her papers:
selected as one of the “Top 10 Reading Papers“ at RECOMB/ISCB Regulatory & Systems Genomics 2019.
The paper developed a method to compare genome structure
September 10, 2019 — The paper ‘Practical Universal k-mer Sets for Minimizer Schemes’, was awarded best student paper at the ACM-BCB 2019 conference in Niagara Falls, NY.
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!
November 10, 2017 — Dan DeBlasio has published a book with his Ph.D. advisor covering his research on learning the best way to run algorithms for multiple sequence alignment.
Dan is a member of the Kingsford Group and a Lane Fellow in the Computational Biology Department at Carnegie Mellon.
August 16, 2017 — Response to Blog Post About Salmon.
August 10, 2017 — A Ph.D. might span ~240 weekends. If we assume that 1 weekend / month is spent relaxing, watching movies and TV and running errands, 1 weekend / month is spent working 😁, and 4 weekends per year are spent traveling, that leaves about 100 weekends to explore Pittsburgh, if you are a student here.
April 16, 2017 — Lane Fellow Mingfu Shao was interviewed on the inaugural episode of the The Bioinformatics Chat podcast! He talks about his new transcriptome assembler, Scallop.
Listen to hear all about Mingfu’s work!