January 2024
Don defended his PhD thesis. Congratulations! Soumyadip Defended his MS thesis. Congratulations Soumyadip!
October 2023
Our lab was funded by DOE to develop deep learning foundation models for plant genomics (see DOE announcement).
March 2023:
Fahad’s paper on the role of transcription factors in the co-transcriptional regulation of intron retention has been published in Genome Biology as part of the special issue on interpretable deep learning in genomics.
December 2021:
I am a guest editor of a special issue on interpretable deep learning in genomics for the journal Genome Biology.
July 2021:
Yashwant defended his MS thesis. Congratulations Yashwanth! He is now a data scientist at GT Molecular.
March 2021:
Mridula defended her MS thesis. Congratulations Mridula! She is now a researcher at Pacific Northwest National Laboratory.
May 2020:
Fahad defended his PhD thesis. Congratulations Fahad!
April 2020:
Our lab was funded by NSF to develop tools for working with Oxford Nanopore direct RNA sequencing data (details here).
August 2019:
Gareth defended her MS thesis. Congratulations Gareth! She is now starting a Google engineering residency.
June 2019:
Our work with Prof. ASN Reddy from the Biology department was recognized at this year’s Celebrate! Colorado State Awards ceremony where we received the team Interdisciplinary Scholarship Award.
Sept 2017:

Swapnil Sneham defended her MS thesis: Machine learning models towards elucidating the plant intron retention code. Congratulations Swapnil! Swapnil has a job at ancestry.

Alex Fout defended his MS thesis: Protein interface prediction using graph convolutional networks. Congratulations Alex! Alex is now a PhD student at the statistics department at CSU. Also congratulations for the NIPS paper that is based on this work.

May 2016:

Indika Kahanda defended his PhD thesis: Large scale automated function prediction. Congratulations Indika!

Our work “A survey of the sorghum transcriptome using single-molecule long reads.” was accepted in Nature Communications. Check out the PacBio isoform assembly program TAPIS.

Asa was awarded the Graduate Student Council Advising and Mentorship Award.

July 2015:
I am organizing a computational and systems biology symposium to be held at CSU July 21st.
April 2015:
CSU was awarded a grant from NSF to start a new interdisciplinary program on the interface of biology and computer science/engineering/statistics/math on which I’m co-lead. Here’s the NSF announcement and the CSU Source story. We are seeking applicants for the GAUSSI program. Each year eight one-year NSF fellowships will be awarded.
April 2014:
Asa has received the College of Natural Sciences award for Faculty Excellence in Graduate Education & Mentoring.
February 2014:
Fayyaz Minhas has defended his PhD thesis. Congratulations Fayyaz! He is now at the Department of Computer and Information Sciences at the Pakistan Institute of Engineering and Applied Sciences (PIEAS).
November 2013:
DOE has funded the continued collaboration with ASN Reddy’s lab on alternative splicing. Here’s the press release. See also a CSU Today story.
February 2013:
The CAFA evaluation paper finally came out in Nature Methods.
June 2012:
Michael Hamilton will present our work on discovery of splicing regulatory elements at the ISMB alternative splicing SIG.
April 2012:
Kiley Graim defended her Master’s thesis. She was accepted to UC Santa Cruz’s Biomolecular Engineering program for her PhD.
August 2011:
Artem Sokolov defended his PhD thesis. He is now at Josh Stuart’s lab at UC Santa Cruz.
July 2011:

GOstruct did very well in the CAFA automatic function prediction competition. Details coming soon!

SpliceGrapher was presented at the ISMB late breaking research session.

May 2010:

The GOstruct project was funded by NSF

Michael Hamilton and Adam Labadorf have defended their master’s theses. Adam is now at the Fraenkel lab at MIT.

November 2008:

A tutorial on using SVMs for biological sequence analysis published by PLoS Computational Biology (joint work with C-S. Ong, S. Sonnenburg, B. Schoelkopf, and G. Raetsch).

CSU bioinformatics retreat co-organized with the folks at the CSU bioinformatics center and supported by ISTeC.

June 2008:
Todd iverson defended his PhD thesis. Todd is now an assistant professor at the department of mathematics and statistics at Saint Mary’s University
March 2008:
The lab’s collaboration with Reddy’s lab on alternative splicing in plants was funded by NSF.