PhD Students
- Apurva Kalia
- Vlad Porokhin
- Margaret Martin
- Frederick Zhang
- Yan Zhou Chen
- Yinkai Wang
- Alberto Naveira
Current MS/BS Students
- Brandon Mukadziwashe
- Guangyu Lin
- Sammie Chum
Those who have moved on - PhDs, and last known whereabouts!
- Xinmeng Li (Computer Science) -Developing Machine Learning Models with Heterogeneous Data for
Biological Engineering Applications, May 2022, Montai, Cambridge
- Sara Amin (Computer Science) - Advancing the Prediction of Unexpected Cellular Behavior Due to Enzyme Promiscuity and Enzyme Solubility, May 2019, Amazon
- Neda Hassanpour (Computer Science) - Computational Methods to Advance Directed Evolution of Enzymes and Metabolomics Data Analysis, May 2018, Takadata, Cambridge, MA
- Mona Yousofshahi (Computer Science) - Computational Methods for Pathway Synthesis and Strain Optimization, December 2014, Apple, CA
- Ehsan Ullah (Computer Science) - Pathway Analysis of Metabolic Networks Using Graph Theoretical Approaches, August 2014, Researcher, Qatar Computing Research Institute, Qatar
- Brad Gaynor (Electrical and Computer Engineering) - Simulation of FinFET Electrical Performance Dependence on Fin Shape and TSV and Back-Gate Noise Coupling in 3-D Integrated Circuits, May 2014, STR (Systems & Technology Research)
- Gautham Sridharan (Chemical and Biological Engineering) (Co-advised with Kyongbum Lee) - Modularity Analysis of Metabolic Networks Based on Shortest Retroactive Distances (ShReD), May 2013, Alnylam, Cambridge, MA
- Nauman Khan (Computer Science), Noise Analysis and Power Grids for 3D ICs, August 2011, Intel, OR
- Brian Swahn (Electrical and Copmuter Engineering), CAD for FinFETs, August 2006, Analog Devices
Completed Masters Project or Credit, and last known whereabouts!
- Ramtin Hosseini (Inference for metabolomics), Fall 2018-Fall 2019
- Alex Tong (Inference for metabolomics), Spring 2017, Yale, grad school
- Doug Weaver (Modularity analysis), Fall 2009
- Jesse Craig (Simulation and Modeling of Neuro-Mechanical Control in Soft Material), back to IBM, Fall 2008
- Jinhai Qiu (Delay Estimation) Master's, August 2007, at Synopsys
- Meera Thiagarajan (regularity extraciton, timing analysis) Master's, Dec. 2002; Sr. Manager Corporate Applications at Synopsys
- Julie Hernandez (architectural synthesis), Master's, May 2002.
- Jiong Xie (functional customization), Master's, May 2002, at Mathworks.
- Eduardo Calvillo Gámez (timing analysis), Master's, May 2001
- Basil Darwish (network processors), Master's, May 2001, MBA at Wharton
- Christophe Cromer (timing analysis, network processors), Master's, May 2001, MBA at Wharton
- Grace Nam (regularity extraction), Master's, May 1999.
Completed Undergraduate Projects, graduation year, and last known whereabouts!
- Haneen Abderrazzaq -- Using graph explainability to derive reaction rules
- Vickie Liu -- Metaboloics analysis
- Jyoti Bhardwaj - Using GNNs on the RaMP database
- Leo Kaluzhny - Using GNNs on the RaMP database
- Elizabeth Cucuzzella -- Data processing of BRENDA data
- Kamil Krukowski - Machine learning for protein-molecule interaction
- Jacob Bryan - Novel metabolic reactions for promsicous products in E. coli; REU student finishing up undergrad at UC Berekely
- Lexi Shewchuk - Predicting Enzyme Function and Similarity Based on Fingerprints
- Aayushma Gautam - Machine Learning to Characterize Metabolic Pathway Activities
- Gian Marco Visani - Enzyme Classification on Molecules, May 2021, PhD at UW! Go Huskies!
- Olivia Gillma- Using PROXIMAL to predict metabolic products of durgs, May 2023
- Nick Sokol - Using PROXIMAL to predict metabolic products of durgs, May 2023
- Michael Simpson - biotransformation considering chirality, May 2023
- Tina Ma - biotransformation considering chirality, May 2023
- Tom McNulty- perBRENDA: a tool for extracting BRENDA data in a format suitable for machine learning, May 2024
- Caroline Vanderlee - A web interface for PROXIMAL, May 2022
- Julie Jiang - Using Graph Embedding to Predict Enzyme Prmiscuity, May 2019, PhD at USC
- Nicole Kennedy - Computing Chemical Derivatives, May 2020
- Jeremy Marcus (thesis) - Mining for Functional Abortives in E. coli, May 2016
Draper Labs; UC Berkeley
- Andrew Li - GPU programming, May 2014, Tufts Medical School
- Russell Stern - Model and Constraint Checking for Biochemical Networks, May 2013
- Steven Halstead - Sytems Bio project, May 2012
- Calvin Hopkins (thesis) - Analysis of Metabolic Pathways; Kinetic Function Estimation, May 2012 (Microsoft)
- Sean Kelly -- Generalized Kinetic Expression Estimation, May 2012
- Richard Mondello - Modularity Algorithms for Biochemical networks, May 2012 (Apple)
- Marshal Moutenot - Modularity Algorithms for Biochemical networks
- Stephen Bidwell - Modularity Algorithms for Biochemical networks
- Michelle Ichinco - random walk for biochemical networks
- Shilpa Nadimpalli, BS, May 2011
- Neha Uppal, BA Child Development, May 2009
- Laurent Lanster, BA Art History, May 2010
- Brandon Lucia, BS, May 2007; Phd at UW; Now Prof at CMU
- Nick Foti, BS, May 2007; PhD at Dartmouth
- Eli Marschner, BS, May 2007
- Alana Fu, BS, May 2003
- Laura Weyland, VLSI Design Project, BS, May 2003
- Lisa Lafleur, BS, May 2002, Post Doc at UW
REU Students
Nikki Rejai, UCSD, Summer 2022)
Jacob Bryan,
Summer 2019Elizabeth Chavez, UNC, Summer 2018
Emily Chicklis, Simmons, Summer 2017 |
image credit: https://sammykatta.com/diversity
