The Team

Ilyas Yildirim
Associate Professor

Department of Chemistry and Biochemistry

Charles E. Schmidt College of Science
Florida Atlantic University, Jupiter FL

Email : iyildirim [at] fau.edu

Phone : 561-799-832

Education:

Awards:

• BBSRC (UK) David Phillips Fellowship Finalist (2016).

• Postdoctoral Professional Development Travel Award, Northwestern University (2014).

• Physical Sciences-Oncology Centers (PS-OCs) Student Exchange Award, Northwestern University (2012). Title: Computational investigation of small molecule/ligand binding to RNA related human diseases caused by trinucleotide and tetranucleotide repeat expansions.

• Full Scholarship and Tuition Waiver for undergraduate study, Koc University (1994-1999).

• Honorable mention prize in Physics, the Scientific and Technological Research Council of Turkey (TUBITAK) (1992). Title: Noise absorption capacities of cheap and simple materials.

Referee / Reviewer:

• Journal of Physical Chemistry B

• Journal of Chemical Theory and Computation

• Journal of Chemical Information and Modeling

• Biochemistry

• PLoS ONE

• Nature Molecular Therapy-Nucleic Acids

• Nucleic Acids Research - Oxford Journals

• Scientific Reports

• Journal of Molecular Modeling

• Biophysical Journal

Current Members

Niransha Kumarachchi (Ph.D. Student), Fall 2019 - present

Department of Chemistry and Biochemistry, FAU

Project: RNA Force Fields

Mariam Ibrahim (Ph.D. Student), Fall 2021 - present

Department of Chemistry and Biochemistry, FAU

Project: Development of a Monte Carlo Simulator for RNA 3D Structure Prediction

Adam Burjan (Undergraduate Student), Spring 2022 - present

Harriet L. Wilkes Honors College, Department of Chemistry and Biochemistry, FAU

Project: Development of Computational Methods to Optimize Template Compounds Targeting RNA Motifs

Benjamin Carver (Undergraduate Student), Spring 2024 - present

Department of Electrical Engineering and Computer Science , FAU

Project: Properties of pre-MicroRNA Molecules in Homo Sapiens

Nicholas Ndreca (Undergraduate Student), Summer 2024 - present

Department of Chemistry and Biochemistry, FAU

Project: Morphological Properties of RNA using Computational Methods and Atomic Force Microscopy

Previous Members

Ivan Riveros, Honors and PrepCHEM Postbaccalaureate student in Chemistry and Biochemistry/FAU, Fall 2018 - Summer 2023

Honors Thesis Title: Computational Studies of RNA: From Stacking Properties to 3D Structure Prediction and Visualization

Projects Worked: Stacking/Unstacking Properties of RNA Dimers, and 3D Structure Prediction of RNA Tetraloops from Sequence

Current Position: Ph.D. student in MIT Chemistry

Maureen Tanner, Undergraduate student at Wilkes Honors College/FAU, Spring 2021 - Spring 2023

Project Worked: Properties of RNA Adenosine Bulges Using Computational Methods

Current Position: Master's student in Medical Physiology and Pharmacology, UF

Geoffrey Moody, PrepCHEM Postbaccalaureate student in Chemistry and Biochemistry/FAU, Spring 2022 - Summer 2023

Project Worked: Optimization of Lead Compounds Targeting RNA CUG Repeats Using Computational Methods

Current Position: MD student at Nova Southeastern University

Michael Cevallos, B.S. in Chemistry and Biochemistry/FAU, Spring 2022 - Spring 2023

Project Worked: 3D Structure Prediction of RNA Internal Loops from Sequence

Current Position: Master’s student in AI at FAU

Arjun Nair, Highschool/Undergraduate Student/FAU, Summer 2021 - Fall 2022

Project Worked: In Silico Drug Design for RNA.

Current Position: High School Student at A.D. Henderson University School & FAU High School

Julianna Lian, Highschool-Undergraduate Student/FAU, Spring 2020 - Summer 2022

Project Worked: Application of AFM on RNA CUG repeat expansion and Monte Carlo Simulator for RNA Structure Prediction.

Current Position: Undergraduate student at MIT, Chemistry and Computer Science

Riccardo D'Ambrosio, Cardinal Gibbons High School Student, Spring 2020 - Summer 2021

Project Worked: Development of a webserver for 'RNA folding' problem, and RUSTing RNA 3D Structure Prediction Algorithm

Current Position: Undergraduate student at FAU

Dr. Amirhossein Taghavi, Postdoctoral Researcher, May 2019 - July 2021

Project Worked: Application of computational methods in RNA and modified RNA systems

Current Position: Postdoc at UF-Scripps Research Institute Florida (Disney Lab)

Dr. Kye Won Wang, Postdoctoral Researcher, May 2019 - December 2020

Project Worked: Method development for small molecule-RNA binding

Current Position: Postdoc at Lehigh University (Im Lab)

James DeLoye, Atlantic Community High School Student, Summer 2019

Project Worked: Application of Dendrograms in small molecule-RNA binding studies

Current Position: Undergraduate student at UC Berkeley, College of Chemistry

Marina Nad, B.S. in Chemistry and Biochemistry/FAU, Spring 2018 - Spring 2019

Project Worked: Structural studies of microRNA in RNA Inducing Silencing Complex (RISC) using computational methods

Current Position: Research Associate at MODERNA