Model-based deconvolution of genome-wide DNA binding. - David J. Reiss; Marc T. Facciotti; Nitin S. Baliga (Bioinform., 2008)

Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis. - Marc T. Facciotti; Wyming Lee Pang; Fang-Yin Lo; Kenia Whitehead; Tie Koide; Ken-ichi Masumura; Min Pan; Amardeep Kaur; David J. Larsen; David J. Reiss; Linh Hoang; Ewa Kalisiak; et al. (BMC Syst. Biol., 2010)

Mauve Assembly Metrics. - Aaron E. Darling; Andrew J. Tritt; Jonathan A. Eisen; Marc T. Facciotti (Bioinform., 2011)

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs. - Phillip Seitzer; Elizabeth G. Wilbanks; David J. Larsen; Marc T. Facciotti (BMC Bioinform., 2012)

Improved Motif Detection in Large Sequence Sets with Random Sampling in a Kepler workflow. - Sven Köhler 003; Phillip Seitzer; Marc T. Facciotti; Bertram Ludäscher (ICCS, 2012)

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. - Phillip Seitzer; Tu Anh Huynh; Marc T. Facciotti (BMC Bioinform., 2013)

Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution. - Tobias Warnecke; Erin A. Becker; Marc T. Facciotti; Corey Nislow; Ben Lehner (PLoS Comput. Biol., 2013)

Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. - Christopher L. Plaisier; Fang-Yin Lo; Justin Ashworth; Aaron N. Brooks; Karlyn D. Beer; Amardeep Kaur; Min Pan; David J. Reiss; Marc T. Facciotti; Nitin S. Baliga (BMC Syst. Biol., 2014)

Using Student Annotated Hashtags and Emojis to Collect Nuanced Affective States. - Amy X. Zhang; Michele Igo; Marc T. Facciotti; David R. Karger (L@S, 2017)

Classifying and visualizing students' cognitive engagement in course readings. - Eran Yogev; Kobi Gal; David R. Karger; Marc T. Facciotti; Michele Igo (L@S, 2018)

#Confused and beyond: detecting confusion in course forums using students' hashtags. - Shay A. Geller; Nicholas Hoernle; Kobi Gal; Avi Segal; Amy X. Zhang; David R. Karger; Marc T. Facciotti; Michele Igo (LAK, 2020)

Seeding Course Forums using the Teacher-in-the-Loop. - Einat Shusterman; Hyunsoo Gloria Kim; Marc T. Facciotti; Michele Igo; Kamali Sripathi; David R. Karger; Avi Segal; Kobi Gal (LAK, 2021)

New Methods for Confusion Detection in Course Forums: Student, Teacher, and Machine. - Shay A. Geller; Kobi Gal; Avi Segal; Kamali Sripathi; Hyunsoo Gloria Kim; Marc T. Facciotti; Michele Igo; Nicholas Hoernle; David R. Karger (IEEE Trans. Learn. Technol., 2021)

#lets-discuss: Analyzing Student Affect in Course Forums Using Emoji. - Ariel Blobstein; Kobi Gal; David R. Karger; Marc T. Facciotti; Hyunsoo Gloria Kim; Jumana Almahmoud; Kamali Sripathi (EDM, 2022)

Spotlights: Designs for Directing Learners' Attention in a Large-Scale Social Annotation Platform. - Jumana Almahmoud; Farnaz Jahanbakhsh; Marc T. Facciotti; Michele Igo; Kamali Sripathi; Kobi Gal; David R. Karger (Proc. ACM Hum. Comput. Interact., 2022)

Enhancing User Engagement in Large-Scale Social Annotation Platforms: Community-Based Design Interventions and Implications for Large Language Models (LLMs). - Jumana Almahmoud; Marc T. Facciotti; Michele Igo; Kamali Sripathi; David R. Karger (CoRR, 2025)

How Adding Metacognitive Requirements in Support of AI Feedback in Practice Exams Transforms Student Learning Behaviors. - Mak Ahmad; Prerna Ravi; David R. Karger; Marc T. Facciotti (CoRR, 2025)