People
Principal Investigators
- Neocles Leontis, who passed away on December 8, 2020. Obituary. Remembrance.
- Craig Zirbel
Alumni
- Sri Devan Appasamy, developed R3DMCS to compare RNA motifs across many RNA 3D structures
- Zhicheng Ding, added DNA structures to the database and pipeline
- Xinyu Chu, improved websites and database management for the RNA 3D Motif Atlas, among many other things
- Patrick Nyadjo, created the 2024 release of the RNA Base Triple Database and worked on the Circular Diagram Server
- Mishty Malik, worked on RNA Alignment Interaction Diagrams (R3DAID)
- Adam Coger, helped to develop Python code behind the RNA 3D Motif Atlas and mapping other loops to Motif Atlas loops
- Alex Xu, developed code to map modified nucleotides to standard nucleotides
- Gul Bulbul, 2023 dissertation, modeled how local context can help to predict the mutation rate of an RNA nucleotide
- Jacob Mitchell, worked on base stacking, base-backbone, and core fr3d-python
- Deepthi Thammineni, worked on sequence variability across species, see R3DSVS
- Nicholas Kinyanjui, worked on standardized names for RNA chains
- Satya Upendra, worked on pairwise and multiple alignments of RNA chains
- Vy Nguyen, worked on the RNA 3D Motif Atlas
- Hima Namburu, worked on circular basepair diagrams
- Manisha Muthuluru, master's student, worked on sequence and structure alignments, see R3DSVS
- Syed Muhammed Abubaker, undergraduate, worked on circular basepair diagrams, now available at the Circular Diagram Server
- Bryan Li, high school student, worked on 3D structure alignments
- Karthik Jagilinki, PhD student, worked on reading DNA 3D structures
- Quinn Eberhard 2021 undergraduate, Goldwater scholar, worked on RNA-protein alignments
- Seyoung Ree, high school student, worked on RNA Motif Atlas code
- Kateland Sipe 2021 undergraduate, worked on RNA-protein interactions
- Malika Haver, undergraduate, worked on SASA calculations
- Aylin Tanriverdi, high school student, made WebFR3D instructional videos
- Chaska McGowan 2020 undergraduate, worked on the database
- Wyatt Brown 2019 undergraduate, studied RNA-protein interactions
- William Xi 2019 undergraduate, ported FR3D to Python
- Jamie Cannone 2019 research scientist
- Jim Roll 2019 dissertation
- Maryam Hosseini 2018 dissertation
- Poorna Roy 2017 dissertation
- Blake Sweeney 2016 dissertation
- Lorena Parlea 2015 dissertation
- Anton Petrov 2012 dissertation
- Emil Khisamutdinov 2012 dissertation
- Anton Alenko 2012 master's student
- Amal Abu Almakarem 2011 dissertation
- Stephen Dinda 2011 dissertation
- Irina Novikova 2010 dissertation
- Ryan Rahrig 2010 dissertation
- Jesse Stombaugh 2008 dissertation
- Kirill Afonin 2008 dissertation
- Meg Pirrung 2008 undergraduate, ported JAR3D to Java
- Jim Zubricky 2006 master's thesis
- Michael Sarver 2006 dissertation
- Ali Mokdad 2006 dissertation
- Kristina Csaszar Burch 2002 undergraduate, Goldwater Scholar, RNA sequence analysis
Updated: 10/22/2025 09:51AM