Raluca Mihaela Gordan | Scholars@Duke

Raluca Mihaela Gordan
Associate Professor in Biostatistics & Bioinformatics

Current Appointments & Affiliations

Associate Professor in Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2019
Associate Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2019
Associate Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2019
Associate Professor of Cell Biology, Cell Biology, Basic Science Departments 2022
Member of the Duke Cancer Institute, Duke Cancer Institute, Institutes and Centers 2022

Contact Information

101 Science Drive, 2179 CIEMAS, Durham, NC 27708
Duke Box 3382, Durham, NC 27710
raluca.gordan@duke.edu (919) 684-9881
Gordan Lab Website

Background
Education, Training, & Certifications
- Ph.D., Duke University 2009
Previous Appointments & Affiliations
- Assistant Professor in Molecular Genetics and Microbiology, Molecular Genetics and Microbiology, Basic Science Departments 2012 - 2019
- Assistant Professor in Biostatistics & Bioinformatics, Biostatistics & Bioinformatics, Basic Science Departments 2011 - 2019
- Assistant Professor of Computer Science, Computer Science, Trinity College of Arts & Sciences 2011 - 2019
Recognition
In the News
- JAN 13, 2021 Duke Research Blog
  
  A Computer Scientist Investigating the Source Code of Life
- OCT 21, 2020
  
  Transcription Factors May Inadvertently Lock in DNA Mistakes
- FEB 18, 2014
  
  Five Science Faculty Win Sloan Fellowships
Awards & Honors
- Sloan Research Fellowship-Molecular Biology. Alfred P. Sloan Foundation. 2014
Expertise
Subject Headings
Research
Selected Grants
- University Training Program in Biomolecular and Tissue Engineering awarded by National Institutes of Health 1994 - 2027
- Cell and Molecular Biology Training Program awarded by National Institutes of Health 2021 - 2026
- Design, prediction, and prioritization of systematic perturbations of the human genome awarded by National Institutes of Health 2021 - 2026
- Beyond GWAS: High Throughput Functional Genomics & Epigenome Editing to Elucidate the Effects of Genetic Associations for Schizophrenia awarded by National Institutes of Health 2021 - 2026
- Genetic and Genomics Training Grant awarded by National Institutes of Health 2020 - 2025
- Training Program in Bioinformatics at the Intersection of Cancer Immunology and Microbiome awarded by National Institutes of Health 2020 - 2025
- Uncovering novel gene regulatory mechanisms underlying glucocorticoid response phenotypes through targeted mutagenesis of an essential transcription factor awarded by National Institutes of Health 2022 - 2025
- Helix-distorting DNA damages at transcription factor binding sites: causes and effects awarded by US-Israel Binational Science Foundation 2020 - 2024
- The role of transcription factor proteins in mutagenesis at their binding sites awarded by National Institutes of Health 2020 - 2024
- Role of DNA structural dynamics in mutagenesis and oncogenesis awarded by National Institutes of Health 2010 - 2023
- The Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of disease awarded by National Institutes of Health 2020 - 2023
- Preparing Genetic Counselors for Genomic Medicine Research awarded by National Institutes of Health 2017 - 2023
- IRES Track 1 IRTG Engaged in Dissecting and Reengineering the Regulatory Genome awarded by National Science Foundation 2019 - 2023
- Discovery of DNA determinants of transcription factor binding and function in photoreceptors awarded by Washington University School of Medicine 2017 - 2022
- Determining Mechanisms of Rewiring of the Eukaryotic Cell Cycle by a Virus awarded by North Carolina State University 2018 - 2022
- Bioinformatics and Computational Biology Training Program awarded by National Institutes of Health 2005 - 2021
- HARDAC-M: Enabling memory-intensive computation for genomics awarded by North Carolina Biotechnology Center 2020 - 2021
- Differential effects of genomic context on the binding specificity of paralogous transcription factors awarded by National Science Foundation 2017 - 2021
- New methods for quantitative modeling of protein-DNA interactions awarded by National Institutes of Health 2015 - 2020
- Genetics Training Grant awarded by National Institutes of Health 1979 - 2020
- A hands-on, integrative next-generation sequencing course: design, experiment, and analysis awarded by National Institutes of Health 2016 - 2020
- Statistical/Computational Methods for Pharmacogenomics and Individualized Therapy awarded by University of North Carolina - Chapel Hill 2015 - 2020
- Determining mechanisms of rewiring of the eukaryotic cell cycle by a virus without disrupting network function awarded by National Science Foundation 2018
- Collaborative Research: Experimental and Computational Studies of DNA Binding by Human Paralogous Transcription Factors awarded by National Science Foundation 2014 - 2017
- HARDAC+:Reproducible HPC for next-generation genomics awarded by North Carolina Biotechnology Center 2016 - 2017
- Alfred P. Sloan Research Fellow awarded by Alfred P. Sloan Foundation 2014 - 2016
External Relationships
- Weizmann Institute of Science
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Mielko, Zachery, Yuning Zhang, Harshit Sahay, Yiling Liu, Matthew A. Schaich, Brittani Schnable, Abigail M. Morrison, et al. “UV irradiation remodels the specificity landscape of transcription factors.” Proc Natl Acad Sci U S A 120, no. 11 (March 14, 2023): e2217422120. https://doi.org/10.1073/pnas.2217422120.
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  - Sun, Tianai, Chien-Kuang Cornelia Ding, Yuning Zhang, Yang Zhang, Chao-Chieh Lin, Jianli Wu, Yasaman Setayeshpour, et al. “MESH1 knockdown triggers proliferation arrest through TAZ repression.” Cell Death Dis 13, no. 3 (March 10, 2022): 221. https://doi.org/10.1038/s41419-022-04663-6.
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  - Barrera, Julio, Lingyun Song, Julia E. Gamache, Melanie E. Garrett, Alexias Safi, Young Yun, Ivana Premasinghe, et al. “Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.” Mol Neurodegener 16, no. 1 (August 24, 2021): 58. https://doi.org/10.1186/s13024-021-00481-0.
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  - Zhang, Yuning, Tiffany D. Ho, Nicolas E. Buchler, and Raluca Gordân. “Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions.” Genome Res 31, no. 7 (May 11, 2021): 1216–29. https://doi.org/10.1101/gr.275145.120.
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  - Liu, Mo, Arnoud Boot, Alvin W. T. Ng, Raluca Gordân, and Steven G. Rozen. “Mutational processes in cancer preferentially affect binding of particular transcription factors.” Sci Rep 11, no. 1 (February 8, 2021): 3339. https://doi.org/10.1038/s41598-021-82910-0.
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  - Afek, Ariel, Honglue Shi, Atul Rangadurai, Harshit Sahay, Alon Senitzki, Suela Xhani, Mimi Fang, et al. “DNA mismatches reveal conformational penalties in protein-DNA recognition.” Nature 587, no. 7833 (November 2020): 291–96. https://doi.org/10.1038/s41586-020-2843-2.
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  - Ilic, Stefan, Shira Cohen, Ariel Afek, Raluca Gordan, David B. Lukatsky, and Barak Akabayov. “DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling.” J Vis Exp, no. 152 (October 8, 2019). https://doi.org/10.3791/59737.
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  - Belo, Yael, Zachery Mielko, Hila Nudelman, Ariel Afek, Oshrit Ben-David, Anat Shahar, Raz Zarivach, Raluca Gordan, and Eyal Arbely. “Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.” Biochim Biophys Acta Gen Subj 1863, no. 9 (September 2019): 1343–50. https://doi.org/10.1016/j.bbagen.2019.05.019.
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  - Martin, Vincentius, Jingkang Zhao, Ariel Afek, Zachery Mielko, and Raluca Gordân. “QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants.” Nucleic Acids Res 47, no. W1 (July 2, 2019): W127–35. https://doi.org/10.1093/nar/gkz363.
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  - Innocenti, Federico, Chen Jiang, Alexander B. Sibley, Amy S. Etheridge, Ace J. Hatch, Stefanie Denning, Donna Niedzwiecki, et al. “Genetic variation determines VEGF-A plasma levels in cancer patients.” Sci Rep 8, no. 1 (November 5, 2018): 16332. https://doi.org/10.1038/s41598-018-34506-4.
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  - Innocenti, F., K. Owzar, C. Jiang, A. S. Etheridge, R. Gordân, A. B. Sibley, F. Mulkey, et al. “The Vitamin D receptor gene as a determinant of survival in pancreatic cancer patients: Genomic analysis and experimental validation.” Plos One 13, no. 8 (August 1, 2018). https://doi.org/10.1371/journal.pone.0202272.
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  - Afek, A., L. Tagliafierro, O. C. Glenn, D. B. Lukatsky, R. Gordan, and O. Chiba-Falek. “Toward deciphering the mechanistic role of variations in the Rep1 repeat site in the transcription regulation of SNCA gene.” Neurogenetics 19, no. 3 (August 2018): 135–44. https://doi.org/10.1007/s10048-018-0546-8.
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  - Afek, A., S. Ilic, J. Horton, D. B. Lukatsky, R. Gordan, and B. Akabayov. “DNA Sequence Context Controls the Binding and Processivity of the T7 DNA Primase.” Iscience 2 (April 27, 2018): 141–47. https://doi.org/10.1016/j.isci.2018.03.019.
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  - Shen, Ning, Jingkang Zhao, Joshua L. Schipper, Yuning Zhang, Tristan Bepler, Dan Leehr, John Bradley, John Horton, Hilmar Lapp, and Raluca Gordan. “Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.” Cell Syst 6, no. 4 (April 25, 2018): 470-483.e8. https://doi.org/10.1016/j.cels.2018.02.009.
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  - Manandhar, Dinesh, Lingyun Song, Ami Kabadi, Jennifer B. Kwon, Lee E. Edsall, Melanie Ehrlich, Koji Tsumagari, Charles A. Gersbach, Gregory E. Crawford, and Raluca Gordân. “Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.” Nucleic Acids Res 45, no. 20 (November 16, 2017): 11684–99. https://doi.org/10.1093/nar/gkx773.
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  - Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, et al. “Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.” Cancer Discov 7, no. 10 (October 2017): 1116–35. https://doi.org/10.1158/2159-8290.CD-17-0368.
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  - Joh, Daniel Y., Angus M. Hucknall, Qingshan Wei, Kelly A. Mason, Margaret L. Lund, Cassio M. Fontes, Ryan T. Hill, et al. “Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood.” Proc Natl Acad Sci U S A 114, no. 34 (August 22, 2017): E7054–62. https://doi.org/10.1073/pnas.1703200114.
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  - Shats, Igor, Michael Deng, Adam Davidovich, Carolyn Zhang, Jungeun S. Kwon, Dinesh Manandhar, Raluca Gordân, Guang Yao, and Lingchong You. “Expression level is a key determinant of E2F1-mediated cell fate.” Cell Death Differ 24, no. 4 (April 2017): 626–37. https://doi.org/10.1038/cdd.2017.12.
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  - Sparks, Erin E., Colleen Drapek, Allison Gaudinier, Song Li, Mitra Ansariola, Ning Shen, Jessica H. Hennacy, et al. “Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.” Dev Cell 39, no. 5 (December 5, 2016): 585–96. https://doi.org/10.1016/j.devcel.2016.09.031.
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  - Schipper, Joshua L., and Raluca M. Gordân. “Transcription Factor-DNA Binding Motifs in Saccharomyces cerevisiae: Tools and Resources.” Cold Spring Harb Protoc 2016, no. 11 (November 1, 2016). https://doi.org/10.1101/pdb.top080622.
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  - Medina, E. M., J. J. Turner, R. Gordân, J. M. Skotheim, and N. E. Buchler. “Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.” Elife 5, no. MAY2016 (May 10, 2016). https://doi.org/10.7554/eLife.09492.001.
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  - Medina, Edgar M., Jonathan J. Turner, Raluca Gordân, Jan M. Skotheim, and Nicolas E. Buchler. “Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi.” Elife 5 (May 10, 2016). https://doi.org/10.7554/eLife.09492.
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  - Barrera, Luis A., Anastasia Vedenko, Jesse V. Kurland, Julia M. Rogers, Stephen S. Gisselbrecht, Elizabeth J. Rossin, Jaie Woodard, et al. “Survey of variation in human transcription factors reveals prevalent DNA binding changes.” Science 351, no. 6280 (March 25, 2016): 1450–54. https://doi.org/10.1126/science.aad2257.
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  - Frank, Christopher L., Dinesh Manandhar, Raluca Gordân, and Gregory E. Crawford. “HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.” Epigenetics Chromatin 9 (2016): 15. https://doi.org/10.1186/s13072-016-0065-5.
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  - Afek, Ariel, Hila Cohen, Shiran Barber-Zucker, Raluca Gordân, and David B. Lukatsky. “Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.” Plos Comput Biol 11, no. 8 (August 2015): e1004429. https://doi.org/10.1371/journal.pcbi.1004429.
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  - Zhou, Tianyin, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard S. Mann, Harmen J. Bussemaker, Raluca Gordân, and Remo Rohs. “Quantitative modeling of transcription factor binding specificities using DNA shape.” Proc Natl Acad Sci U S A 112, no. 15 (April 14, 2015): 4654–59. https://doi.org/10.1073/pnas.1422023112.
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  - Boyd, J Lomax, Stephanie L. Skove, Jeremy P. Rouanet, Louis-Jan Pilaz, Tristan Bepler, Raluca Gordân, Gregory A. Wray, and Debra L. Silver. “Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.” Curr Biol 25, no. 6 (March 16, 2015): 772–79. https://doi.org/10.1016/j.cub.2015.01.041.
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  - Afek, Ariel, Joshua L. Schipper, John Horton, Raluca Gordân, and David B. Lukatsky. “Protein-DNA binding in the absence of specific base-pair recognition.” Proc Natl Acad Sci U S A 111, no. 48 (December 2, 2014): 17140–45. https://doi.org/10.1073/pnas.1410569111.
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  - Slattery, Matthew, Tianyin Zhou, Lin Yang, Ana Carolina Dantas Machado, Raluca Gordân, and Remo Rohs. “Absence of a simple code: how transcription factors read the genome.” Trends Biochem Sci 39, no. 9 (September 2014): 381–99. https://doi.org/10.1016/j.tibs.2014.07.002.
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  - Munteanu, Alina, Uwe Ohler, and Raluca Gordân. “COUGER--co-factors associated with uniquely-bound genomic regions.” Nucleic Acids Res 42, no. Web Server issue (July 2014): W461–67. https://doi.org/10.1093/nar/gku435.
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  - Siggers, Trevor, and Raluca Gordân. “Protein-DNA binding: complexities and multi-protein codes.” Nucleic Acids Res 42, no. 4 (February 2014): 2099–2111. https://doi.org/10.1093/nar/gkt1112.
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  - Yang, Lin, Tianyin Zhou, Iris Dror, Anthony Mathelier, Wyeth W. Wasserman, Raluca Gordân, and Remo Rohs. “TFBSshape: a motif database for DNA shape features of transcription factor binding sites.” Nucleic Acids Res 42, no. Database issue (January 2014): D148–55. https://doi.org/10.1093/nar/gkt1087.
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  - Guo, Jiannan, Tiandao Li, Joshua Schipper, Kyle A. Nilson, Francis K. Fordjour, Jeffrey J. Cooper, Raluca Gordân, and David H. Price. “Sequence specificity incompletely defines the genome-wide occupancy of Myc.” Genome Biol 15, no. 10 (2014): 482. https://doi.org/10.1186/s13059-014-0482-3.
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  - Mordelet, Fantine, John Horton, Alexander J. Hartemink, Barbara E. Engelhardt, and Raluca Gordân. “Stability selection for regression-based models of transcription factor-DNA binding specificity.” Bioinformatics 29, no. 13 (July 1, 2013): i117–25. https://doi.org/10.1093/bioinformatics/btt221.
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  - Gordân, Raluca, Ning Shen, Iris Dror, Tianyin Zhou, John Horton, Remo Rohs, and Martha L. Bulyk. “Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.” Cell Rep 3, no. 4 (April 25, 2013): 1093–1104. https://doi.org/10.1016/j.celrep.2013.03.014.
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  - Munteanu, A., and R. Gordân. “Distinguishing between genomic regions bound by paralogous transcription factors.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7821 LNBI (April 3, 2013): 145–57. https://doi.org/10.1007/978-3-642-37195-0_12.
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  - Gordân, Raluca, Saumyadipta Pyne, and Martha L. Bulyk. “Identification of cell cycle-regulated, putative hyphal genes in Candida albicans.” Pac Symp Biocomput, 2012, 299–310.
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  - Gordân, Raluca, Kevin F. Murphy, Rachel P. McCord, Cong Zhu, Anastasia Vedenko, and Martha L. Bulyk. “Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.” Genome Biol 12, no. 12 (December 21, 2011): R125. https://doi.org/10.1186/gb-2011-12-12-r125.
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  - Miller, Heather B., Timothy J. Robinson, Raluca Gordân, Alexander J. Hartemink, and Mariano A. Garcia-Blanco. “Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.” Rna 17, no. 4 (April 2011): 665–74. https://doi.org/10.1261/rna.2462011.
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  - Gordân, Raluca, Leelavati Narlikar, and Alexander J. Hartemink. “Finding regulatory DNA motifs using alignment-free evolutionary conservation information.” Nucleic Acids Res 38, no. 6 (April 2010): e90. https://doi.org/10.1093/nar/gkp1166.
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  - MacAlpine, Heather K., Raluca Gordân, Sara K. Powell, Alexander J. Hartemink, and David M. MacAlpine. “Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.” Genome Res 20, no. 2 (February 2010): 201–11. https://doi.org/10.1101/gr.097873.109.
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  - Gordân, R., L. Narlikar, and A. J. Hartemink. “Finding regulatory DNA motifs using alignment-free evolutionary conservation information.” Nucleic Acids Research 38, no. 6 (January 4, 2010). https://doi.org/10.1093/nar/gkp1166.
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  - Gordân, Raluca, Alexander J. Hartemink, and Martha L. Bulyk. “Distinguishing direct versus indirect transcription factor-DNA interactions.” Genome Res 19, no. 11 (November 2009): 2090–2100. https://doi.org/10.1101/gr.094144.109.
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  - Narlikar, Leelavati, Raluca Gordân, and Alexander J. Hartemink. “A nucleosome-guided map of transcription factor binding sites in yeast.” Plos Comput Biol 3, no. 11 (November 2007): e215. https://doi.org/10.1371/journal.pcbi.0030215.
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  - Narlikar, Leelavati, Raluca Gordân, Uwe Ohler, and Alexander J. Hartemink. “Informative priors based on transcription factor structural class improve de novo motif discovery.” Bioinformatics 22, no. 14 (July 15, 2006): e384–92. https://doi.org/10.1093/bioinformatics/btl251.
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- Conference Papers
  - Zhao, J., V. Martin, and R. Gordân. “Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13278 LNBI:36–51, 2022. https://doi.org/10.1007/978-3-031-04749-7_3.
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  - Afek, Ariel, Honglue Shi, Atul Rangadurai, Hashim M. Al-Hashimi, and Raluca M. Gordan. “Mismatched base pairs locally distort DNA structure, leading to increased DNA-binding by transcription factor proteins.” In Journal of Biomolecular Structure & Dynamics, 37:80–81. TAYLOR & FRANCIS INC, 2019.
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  - Zhao, Jingkang, Dongshunyi Li, Jungkyun Seo, Andrew S. Allen, and Raluca Gordân. “Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding.” In Res Comput Mol Biol, 10229:336–52, 2017. https://doi.org/10.1007/978-3-319-56970-3_21.
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  - Gordân, Raluca, and Alexander J. Hartemink. “Using DNA duplex stability information for transcription factor binding site discovery.” In Pac Symp Biocomput, 453–64, 2008.
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  - Gordân, Raluca, Leelavati Narlikar, and Alexander J. Hartemink. “A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery.” In Recomb, edited by Martin Vingron and Limsoon Wong, 4955:98–111. Springer, 2008.
  - Narlikar, Leelavati, Raluca Gordân, and Alexander J. Hartemink. “Nucleosome Occupancy Information Improves de novo Motif Discovery.” In Recomb, edited by Terence P. Speed and Haiyan Huang, 4453:107–21. Springer, 2007.
Teaching & Mentoring
Recent Courses

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Education, Training, & Certifications

Previous Appointments & Affiliations

In the News

Awards & Honors

Subject Headings

Selected Grants

External Relationships

Selected Publications

Academic Articles

Conference Papers

Recent Courses