From Fold Recognition to Homology Modeling: An Analysis of Protein Modeling Challenges At Different Levels of Prediction Complexity. - Krzysztof A. Olszewski; Lisa Yan; David Edwards; Tina Yeh (Comput. Chem., 2000)

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds. - Carl S. Ewig; Rajiv Berry; Uri Dinur; Jörg-Rüdiger Hill; Ming-Jing Hwang; Haiying Li; Chris Liang; Jon Maple; Zhengwei Peng; Thomas P. Stockfisch; Thomas S. Thacher; Lisa Yan; et al. (J. Comput. Chem., 2001)

Functional annotation of proteomic sequences based on consensus of sequence and structural analysis. - David H. Kitson; Azat Ya. Badretdinov; Zhan-yang Zhu; Mikhail Velikanov; David J. Edwards; Krzysztof A. Olszewski; Sándor Szalma; Lisa Yan (Briefings Bioinform., 2002)

An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems. - Shenghua Shi; Lisa Yan; Yang Yang; Jodi Fisher-Shaulsky; Tom Thacher (J. Comput. Chem., 2003)

A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. - W. Jim Zheng; Velin Z. Spassov; Lisa Yan; Paul K. Flook; Sándor Szalma (Comput. Biol. Chem., 2004)

Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method. - Jurgen Koska; Velin Z. Spassov; Allister J. Maynard; Lisa Yan; Nic Austin; Paul K. Flook; C. M. Venkatachalam (J. Chem. Inf. Model., 2008)

A VoD System for Massively Scaled, Heterogeneous Environments: Design and Implementation. - Kangwook Lee 001; Lisa Yan; Abhay Parekh; Kannan Ramchandran (MASCOTS, 2013)

High Speed Networks Need Proactive Congestion Control. - Lavanya Jose; Lisa Yan; Mohammad Alizadeh; George Varghese; Nick McKeown; Sachin Katti (HotNets, 2015)

Compiling Packet Programs to Reconfigurable Switches. - Lavanya Jose; Lisa Yan; George Varghese; Nick McKeown (NSDI, 2015)

A pH-dependent computational approach to the effect of mutations on protein stability. - Velin Z. Spassov; Lisa Yan (J. Comput. Chem., 2016)

Learning Networking by Reproducing Research Results. - Lisa Yan; Nick McKeown (Comput. Commun. Rev., 2017)

TMOSS: Using Intermediate Assignment Work to Understand Excessive Collaboration in Large Classes. - Lisa Yan; Nick McKeown; Mehran Sahami; Chris Piech (SIGCSE, 2018)

Pensieve: Feedback on Coding Process for Novices. - Lisa Yan; Annie Hu; Chris Piech (SIGCSE, 2019)

The PyramidSnapshot Challenge: Understanding Student Process from Visual Output of Programs. - Lisa Yan; Nick McKeown; Chris Piech (SIGCSE, 2019)

Learning Networking by Reproducing Research Results. - Lisa Yan (P-RECS@HPDC, 2020)

Co-Teaching Computer Science Across Borders: Human-Centric Learning at Scale. - Chris Piech; Lisa Yan; Lisa Einstein; Ana Saavedra; Baris Bozkurt; Eliska Sestáková; Ondrej Guth; Nick McKeown (L@S, 2020)

Unique Exams: Designing Assessments for Integrity and Fairness. - Gili Rusak; Lisa Yan (SIGCSE, 2021)

Scaling and Adapting a Program for Early Undergraduate Research in Computing. - Christine Alvarado; Joe Hummel; Diba Mirza; Renata A. Revelo; Lisa Yan (SIGCSE (1), 2022)

Developing a Tool to Automate Extensions to Support a Flexible Extension Policy. - Jordan Schwartz; Madison Bohannan; Jacob Yim; Yuerou Tang; Dana Benedicto; Charisse Liu; Armando Fox; Lisa Yan; Narges Norouzi (CoRR, 2023)

WIP: Automated Flexible Extensions for Improving Learning Equity in Large Scale Computing Classrooms. - Dana Benedicto; Jordan Schwartz; Narges Norouzi; Lisa Yan (FIE, 2024)

WIP: Examining the Impact of a Flexible Extension Policy on Student Learning Experience in a Large-Scale Computing Course. - Charisse Liu; Yuerou Tang; Narges Norouzi; Lisa Yan (FIE, 2024)

EIT: Earnest Insight Toolkit for Evaluating Students' Earnestness in Interactive Lecture Participation Exercises. - Mihran Miroyan; Shiny Weng; Rahul Shah 003; Lisa Yan; Narges Norouzi (SIGCSE (1), 2024)

Automated Support for Flexible Extensions. - Jordan Schwartz; Madison Bohannan; Jacob Yim; Yuerou Tang; Dana Benedicto; Charisse Liu; Armando Fox; Lisa Yan; Narges Norouzi (SIGCSE (2), 2024)

Supporting Mastery Learning with Flexible Extensions. - Yuerou Tang; Jacob Yim; Jordan Schwartz; Madison Bohannan; Dana Benedicto; Charisse Liu; Armando Fox; Lisa Yan; Narges Norouzi (SIGCSE (2), 2024)

What Gets Them Talking? Identifying Catalysts for Student Engagement Within a Computing Ethics Course. - Carol Li; Su Min Park; Jedidiah Tsang; Lisa Yan (SIGCSE (2), 2025)

Supporting Students at Scale: Profiling Student Behaviors on Usage and Impact of the Student Support System. - Teresa Luo; Chenkun Sheng; Lisa Yan (SIGCSE (2), 2025)

Challenging the Status Quo in a Computing Ethics Course, One Water Cooler Conversation at a Time. - Su Min Park; Carol Li; Jedidiah Tsang; Lisa Yan (SIGCSE (2), 2025)

Exploration of Undergraduate Teaching Assistant Identity and Teaching Goals in Data Science Courses. - Krina Patel; Abigail Brooks-Ramirez; Rebecca Dang; Bryan Adolfo Ventura Benitez; Lisa Yan (SIGCSE (2), 2025)

On a Time Crunch: Examining Learning Outcomes Within a One Unit Computing Ethics Course. - Jedidiah Tsang; Carol Li; Su Min Park; Lisa Yan (SIGCSE (2), 2025)

Using LLMs to Detect the Presence of Learning Outcomes in Submitted Work Within Computing Ethics Courses. - Jedidiah Tsang; Carol Li; Su Min Park; Lisa Yan (SIGCSE (2), 2025)

Teaching Our Teacher Assistants to Thrive: A Reflexive, Inclusive Approach to Scalable Undergraduate Education. - Lisa Yan (SIGCSE (1), 2025)