CURRICULUM VITAE
Young-In Chi PhD
Young-In Chi PhD
Assistant Professor
Department of Surgery
Division of Administration
Department of Surgery
Division of Administration
OFFICE ADDRESS: |
Medical Education Building |
8701 Watertown Plank Rd |
Milwaukee, WI 53226 |
EDUCATION: |
08/30/1984 - 05/08/1988 BA, Central Methodist College, Fayette, MO |
08/25/1988 - 12/17/1994 PhD, Purdue University, West Lafayette, IN |
POSTGRADUATE TRAINING AND FELLOWSHIP APPOINTMENTS: |
10/01/1994 - 01/31/1998 Postdoctoral Fellow, Department of Chemistry, University of California, Berkeley, CA 94720 |
02/01/1998 - 08/30/2003 Research Fellow, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215 |
MILITARY SERVICE: |
09/1980 - 12/1983 Republic of Korea Army |
FACULTY APPOINTMENTS: |
09/2003 - 08/2011 Assistant Professor, Department of Molecular and Cellular Biochemistry, University of Kentucky School of Medicine, Lexington, KY |
09/2011 - 06/2017 Assistant Professor, Hormel Institute, University of Minnesota, Austin, MN |
07/2017 - 12/2018 Research Professor, Department of Internal Medicine, Kyungpook National University School of Medicine, Deagu, Republic of Korea |
02/2018 - Present Assistant Professor, Department of Surgery, Division of Research, The Medical College of Wisconsin, Milwaukee, WI |
CENTER/INSTITUTE AFFILIATIONS: |
02/11/2019 - Present Member, The Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, WI |
EDUCATIONAL ADMINISTRATIVE APPOINTMENTS: |
N/A |
HOSPITAL AND CLINICAL ADMINISTRATIVE APPOINTMENTS: |
N/A |
RESEARCH ADMINISTRATIVE APPOINTMENTS: |
01/01/2007 - 05/31/2011 SER-CAT alternative board member and institution representative, Advanced Photon Source, Argonne National Lab. |
HOSPITAL STAFF PRIVILEGES: |
N/A |
AWARDS AND HONORS: |
09/1985 - 05/1986 Bernice Fuller Connell Scholarship |
09/1986 - 05/1988 Kappa Mu Epsilon Honorary Mathematics Society |
05/1988 William L. Spencer Award |
05/1988 Sigma Epsilon Pi Academic Award |
05/1988 Magna cum laude graduate, Central Methodist College |
09/1990 - 12/1994 David Ross Research Fellowship |
01/1999 - 12/2000 Juvenile Diabetes Research Foundation Postdoc Fellowship |
01/2001 - 08/2003 Mary K. Iacocca Fellowship |
07/2001 American Diabetes Association Annual Meeting Travel Grant Award |
09/2004 - 08/2011 Charles T. Wethington Research Award |
07/2008 - 06/2013 American Diabetes Association Career Development Award |
MEMBERSHIPS IN HONORARY AND PROFESSIONAL SOCIETIES: |
American Society of Human Genetics |
American Crystallographic Association |
Korean-American Scientists and Engineers Association |
Biophysical Society |
American Diabetes Association |
Protein Society |
EDITORSHIPS/EDITORIAL BOARDS/JOURNAL REVIEWS: |
Ad-Hoc Reviewer |
Biophysical Chemistry |
Proceedings of the National Academy of Sciences |
Acta Crystallographica section D |
Diabetes |
Journal of Endocrinology and Diabetes |
Journal of Immune Research |
Nature Structural and Molecular Biology |
Oncotarget |
Cell Reports |
Journal of Drug Design and Research |
Nucleic Acid Research |
Computers in Biology and Medicine |
Acta Crystallographica section F |
European Journal of Medical Genetics |
Journal of Biological Chemistry |
Journal of Cellular and Molecular Medicine |
Journal of Molecular Biology |
RNA |
Scientific Reports (Nature Publishing Group) |
Biochemistry |
Genes and Development |
Nature Genetics |
Journal of Diabetes Research |
LOCAL/REGIONAL APPOINTED LEADERSHIP AND COMMITTEE POSITIONS: |
05/2006 Outside Examiner for Tao Liu's Final Examination Committee (College of Pharmacy, Univ. of Kentucky) |
06/2006 - 05/2008 Thesis Committee for Brandon Adkins (Department of Molecular and |
08/2006 - 08/2009 University of Kentucky Radiation Safety Committee |
02/2007 Outside Examiner for Paul Kiptoo's Final Examination Committee (College of Pharmacy, Univ. of Kentucky) |
03/2011 Outside Examiner for Lorenzo Federico's Final Examination Committee (College of Pharmacy, Univ. of Kentucky) |
09/2015 Outside Examiner for Carlos Ramirez-Mondragon's Preliminary Written Examination (BICB, Univ. of Minnesota) |
RESEARCH GRANTS/AWARDS/CONTRACTS/PROJECTS: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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INVITED LECTURES/WORKSHOPS/PRESENTATIONS: |
International |
Department of Molecular Cell Biology Seminar, Sungkyunkwan University School of Medicine, Suwon, Korea, 07/31/2007 |
XXI Congress and General Assembly of the International Union of Crystallography (IUCr), Osaka, Japan, 08/30/2008 |
Department of Life Sciences Seminar, Sogang University, Seoul, Korea, 05/19/2011 |
School of Life Sciences and Biotechnology Seminar, Korea University, Seoul, Korea, 05/20/2011 |
Department of Molecular Cell Biology Seminar, Sungkyunkwan University School of Medicine, Suwon, Korea, 05/24/2011 |
Department of Molecular Biology Seminar, Pusan National University, Pusan, Korea, 09/15/2017 |
National |
Dept. of Microbiology, Molecular Biology, and Biochemistry Seminar, University of Idaho, 01/14/2002 |
Department of Molecular and Cell Biology Seminar, University of Connecticut, 02/04/2002 |
Department of Cell Biology Seminar, Harvard Medical School, Boston, MA, 10/04/2002 |
Structural Biology Seminar, Purdue University, 01/21/2004 |
Structural Biology Seminar, Berkeley Structural Genomics Center, CA, USA, 10/14/2005 |
Graduate Center for Toxicology Seminar Series, University of Kentucky, 02/03/2006 |
Graduate Center for Nutritional Sciences Seminar Series, University of Kentucky, 10/31/2007 |
Meeting of the American Crystallographic Association (ACA), Knoxville, TN, USA, 06/01/2008 |
Department of Molecular Therapeutics, Scripps Florida, Jupiter, FL, 09/13/2010 |
Nanobiomedical Center Seminar, University of Cincinnati College of Medicine, 02/21/2011 |
International Conference of RNA Nanotechnology and Therapeutics, University of Kentucky, 04/13/2013 |
Regional |
Epigenetic and Chromatin Dynamics Lab, Mayo Clinic, Rochester, Minnesota, 12/14/2011 |
Biomedical Informatics and Computational Biology (BICB) program, University of Minnesota, 09/13/2012 |
Hormel Institute Research Seminar, University of Minnesota, 10/22/2015 |
Local |
GSPMC Faculty Seminar, Medical College of Wisconsin, 05/12/2021 |
GSPMC Faculty Seminar, Medical College of Wisconsin, 10/12/2022 |
Mellowes Center Faculty Seminar, Medical College of Wisconsin, 12/01/2023 |
EXTRAMURAL TEACHING: |
Graduate Student Education |
Fall, 2013 Computation and Biology (BICB 8510, Univ. of Minnesota) |
Fall, 2005 - spring, 2011 Fundamentals of Biochemistry (BCH401G, Univ. of Kentucky) |
Fall, 2007 - spring, 2008 Seminar in Biochemistry (BCH 618/619, Univ. of Kentucky) |
Fall, 2004 - spring, 2008 Biochemistry and Cell Biology of Nucleic Acids (BCH 611, Univ. of Kentucky) |
Fall, 2005 - spring, 2011 Structural Biology (BCH604, Univ. of Kentucky) |
EXTRAMURAL STUDENTS, FACULTY, RESIDENTS, AND CLINICAL/RESEARCH FELLOWS MENTORED: |
Undergraduate Students |
Bartley Morris; undergraduate (January 2005 - December 2005) |
Scott E. Collier; undergraduate (NSF-REU program; summer 2007) |
Eric Gilland; undergraduate (Chellgren Fellow; May, 2011), 2009 - August |
Tim Horn; undergraduate (SURE program; summer 2012) |
Graduate Students |
PhD Students Advised |
2006 - 2008 Brandon C. Adkins; graduate student, University of Kentucky |
2013 - 2014 Josh Lim; BICB graduate student, University of Minnesota |
PhD Committees |
2006 - 2008 Brandon C. Adkins; PhD candidate, University of Kentucky |
Postdoctoral Researchers |
Yun Li, Ph.D.; postdoc (June 2004 - December 2005) |
Jianguo Liu, Ph.D.; postdoc (August 2004 - February 2006) |
Peng Lu, Ph.D.; postdoc (January 2005 - February 2008) |
Guangteng Wu, Ph.D.; postdoc/research associate (January 2006 - December 2011) |
Gabriel J. Popa, Ph.D; postdoc (July 2008 - June 2009) |
Eun Hee Han, Ph.D.; postdoc (September 2011 - August 2013) |
Puja Singh, Ph.D.; postdoc (May 2012 - June 2017) |
Clinical/Research Fellows |
Eunkyung Yoo, MS; research assistant (July 2017 - December 2018) |
Jinhak Jeong, BS; lab technician (July 2017 – December 2018) |
James Endrizzi, PhD; research associate (March 2012 - August 2012) |
Geun Bae Rha, MS; research associate (July 2007 - March 2010) |
Seungmi Lee, BS; lab technician (July 2017 – December 2018) |
Amy Gorman, MS; research associate (February 2004 - January 2007) |
Faculty |
Shu-Ping Tung, MD/PhD; visiting Scholar (January 2014 - December 2014) |
PROGRAMMATIC DEVELOPMENTS: |
Research Programs |
3D Genomics |
Mellowes Center Molecular Modeling Group |
COMMUNITY SERVICE ACTIVITIES: |
04/01/2008 - 03/31/2016 Grant review:
American Association Peer Review Committees (the Region 1 Basic Cell Biol. 1 review group) |
BIBLIOGRAPHY |
Refereed Journal Publications/Original Papers |
1. Bohach, G.A., Chi, Y.-I. and Stauffacher, C.V. (1992) Crystallization and preliminary X-ray analysis of staphylococcal enterotoxin type C. Proteins 13:152-7. |
2. Hovde, C.J., Marr, J.C., Hoffmann, M.L., Hackett, S.P., Chi, Y.-I., Crum, K.K., Stevens, D.L., Stauffacher, C.V. and Bohach, G.A. (1994) Investigation of the role of the disulfide bond in activity and structure of staphylococcal enterotoxin C1. Mol. Micro. 13:897-909. |
3. Hoffmann, M.L., Jablonski, L.M., Crum, K.K., Chi, Y.-I., Stauffacher, C.V., Hackett, S.P., Stevens, D.L. and Bohach, G.A. (1994) Predictions of T-cell receptor and major histocompatibility complex binding sites on staphylococcal enterotoxin C1. Infect. Immun. 62:3396-407. |
4. Jardetzky, T.S., Brown, J. H., Gorga, J.C., Stern, L.J., Urban, R.G., Chi, Y.-I., Stauffacher, C.V., Strominger, J.L. and Wiley, D.C. (1994) Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. Nature 368:711-8. |
5. Schlievert, P. M., Bohach, G. A., Olendorf, D. H., Stauffacher, C. V., Leung, D. Y. M., Murray, D. L., Prasad, S. P., Earhart, C. A., Jablonski, L. M., Hoffmann, M. L. and Chi, Y.-I. (1995) Molecular structure of staphylococcus and stteptococcus superantigens. J. Clinical Immun. 15:S4-10. |
6. Lawrence, C.M., Chi, Y.-I., Rodwell, V.W. and Stauffacher, C.V. (1995) Crystallization of 3-hydroxy-3-methylglutaryl coenzyme A reductase from Pseudomonas mevalonii. Acta Crystallographica D51:386-9. |
7. Bohach, G. A., Stauffacher, C. V., Ohlendorf, D. H., Chi, Y.-I., Vath, G. M. and Schlievert, P. M. (1996) The staphylococcal and streptococcal pyrogenic toxin family. Adv. Exp. Med. Biol. 391:131-54. |
8. Chi, Y.-I., Yokota, H. and Kim, S.-H. (1997) Apo structure of the Asp receptor ligand-binding domain from Escherichia coli and its structural comparison with ligand or pseudoligand-bound forms. FEBS Letters 414:327-32. |
9. Zhang, Z., Huang, L.-S., Schulmeister, V. M., Chi, Y.-I., Kim, K.-K., Hung, L.-W., Crofts, A. R., Berry, E. A. and Kim, S.-H. (1998) Electron transfer by domain movement in cytochrome bc1. Nature 392:677-84. |
10. Jang, S.-B., Hung, L. W., Chi, Y.-I., Holbrook, E. L., Carter, R. J. and Holbrook, S. R. (1998) Structure of an RNA internal loop consisting of tandem C-A base pairs. Biochemistry 37:11726-31. |
11. Chi, Y.-I., Martinez-Cruz, L. A., Jancarik, J., Swanson, R. V., Robertson, D. E. and Kim, S.-H. (1999) Crystal structure of the beta-glycosidase from the hyperthermophilic archeon Thermosphaera aggregans: insights into its activity and thermostability. FEBS Letters 445:375-83. |
12. Chi, Y.-I., Huang, L.-S., Zhang, Z., Fernandez-Velasco, J. G., Markin, R. and Berry, E. A. (2000) High resolution structure of a soluble domain of cytochrome f from Chlamydononas reinhardtii. Biochemistry 39:7689-701. |
13. Dhe-Paganon, S., Shigeta, R., Chi, Y.-I., Ristow, M. and Shoelson, S. E. (2000) Crystal structure of human frataxin. J. Biol. Chem. 275:30753-6. |
14. Dhe-Paganon, S., Werner, E. D., Chi, Y.-I. and Shoelson, S. E. (2002) Structure of the globular tail of nuclear lamin. J. Biol. Chem. 277:17381-4. |
15. Chi, Y.-I., Sadler, I., Jablonski, L. M., Callatine, S. D., Deobald, C. F., Stauffacher, C. V. and Bohach, G.A. (2002) Zinc-mediated dimerization and its effect on activity and stability of staphylococcal enterotoxin type C. J. Biol. Chem. 277:22839-46. |
16. Dhe-Paganon, S., Duda, K., Iwamoto, M., Chi, Y.-I. and Shoelson, S. E. (2002) Crystal structure of HNF4alpha ligand binding domain in complex with endogenous fatty acid ligand. J. Biol. Chem. 277:37973-6. |
17. Chi, Y.-I., Frantz, J. D., Oh, B.-C., Hansen, L. and Shoelson, S. E. (2002) Diabetes mutations delineate an atypical POU domain in HNF1alpha. Molecular Cell 10: 1129-37. |
18. Kim, K.-A., Kang, K., Chi, Y.-I., Chang, I., Lee, B.-W., Min, Y.-K., Lee, M.-K., Kim, K.-W., Shoelson, S. E. and Lee, M.-.S. (2003) Identification and functional characterization of a novel mutation of hepatocyte nuclear factor-1alpha gene in a Korean family with MODY3. Diabetologia. 46:721-7. |
19. Duda, K., Chi, Y.-I., and Shoelson, S. E. (2004) Structural basis for HNF-4alpha activation by ligand and coactivator binding. J. Biol. Chem. 279:23311-6. |
20. Dhe-Paganon, S., Werner, E. D., Masahiro, N., Hansen, L., Chi, Y.-I. and Shoelson, S. E. (2004) A phenylalanine zipper mediates APS dimerization. Nature Struct. Mol. Biol. 11:968-74. |
21. Lu, P., Li, Y., Gorman, A. and Chi, Y.-I. (2006) Crystallization of hepatocyte nuclear factor 1β in complex with DNA. Acta Crystallogr. F62:525-9. |
22. Lu, P., Rha, G. B. and Chi, Y.-I. (2007) Structural basis of disease-causing mutations in hepatocyte nuclear factor 1beta. Biochemistry 46:12071-80. |
23. Lu, P., Liu, J., Melikishvili, M., Fried, M. G. and Chi, Y.-I. (2008) Crystallization of hepatocyte nuclear factor 4α (HNF4α) in complex with the HNF1α promoter element. Acta Crystallogr. F64:313-7. |
24. Chi Y.-I., Martick, M., Lares, M., Kim, R., Scott, W. G. and Kim, S.-H. (2008) Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biology 6:e234. |
25. Lu, P., Rha, G., Melikishvili, M., Wu, G., Adkins, B. C., Fried, M. G. and Chi, Y.-I. (2008) Structural basis of natural promoter recognition by a unique nuclear receptor HNF4alpha: Diabetes gene product. J. Biol. Chem. 283:33685-97. |
26. Rha, G., Wu, G., Shoelson, S. E. and Chi, Y.-I. (2009) Multiple binding modes between HNF4alpha and the LXXLL motifs of PGC-1alpha lead to full activation. J. Biol. Chem. 284:35165-76. |
27. Yang, X., Lu, X., Lombes, M., Guerin, T. M., Rha, G., Chi, Y. -I., Smart, E. J. and Liu, J. (2010) The G0/G1 switch gene 2 regulates adipose lipolysis through association with adipose triglyceride lipase. Cell Metab. 11:194-205. |
28. Lin, Y., Wu, Y., Li, J., Dong, C., Ye, X., Chi, Y.-I., Evers, B. M. and Zhou, B. P. (2010) The SNAG domain of Snail1 functions as a molecular hook for recruiting lysine-specific demethylase 1. EMBO J. 29:1803-16. |
29. Robertson, M. P., Chi, Y.-I. and Scott, W. G. (2010) Solving novel RNA structures using only secondary structural fragments. Methods 52:168-72. |
30. Rha, G., Wu, G. and Chi, Y.-I. (2011) Probing the effect of MODY mutations near the coactivator binding pocket of HNF4alpha. Biosci. Rep. 31:411-9. |
31. Han, E. H., Rha, G. B. and Chi, Y.-I. (2012) MED25 is a Mediator component of HNF4alpha-driven transcription leading to insulin secretion in pancreatic beta-cells. PLoS One 7:e44007. |
32. Dong, C., Wu, Y., Wang Y., Wang C., Kang, T., Rychahou, P. G., Chi, Y.-I., Evers, B. M. and Zhou, B. P. (2013) Interaction with Suv39H1 is critical for snail-mediated E-cadherin repression in breast cancer. Oncogene 32:1351-62. |
33. Lancman, J. J., Zvenigorodsky, N., Gate, K. P., Zhang, D., Solomon, K., Humphrey, R. K., Kuo, T., Setiawan, L., Verkade, H., Chi, Y.-I., Jhala, U. S., Wright, C. V., Stainier, D. Y. and Dong, P. D. (2013) Specification of hepatopancreas progenitors in zebrafish by hnf1b and wnt2bb. Development 140:2669-79. |
34. Zhang, H., Endrizzi, J. A., Shu, Y., Haque, F., Sauter, C., Shlyakhtenko, L. S., Lyubchenko, Y., Guo, P. and Chi, Y.-I. (2013) Crystal structure of 3WJ core revealing divalent ion promoted thermostability and assembly of the phi29 hexameric motor pRNA. RNA 19:1226-37. |
35. Jung, S. K., Lee, M. H., Lim, D. Y., Kim, J. E., Singh, P., Lee, S. Y., Jeong, C. H., Lim, T. G., Chen, H., Chi, Y.-I., Kunda, J. K., Lee, N. H., Lee, C. C., Cho, Y. Y., Bode, A. M., Lee, K. W. and Dong, Z. (2014) Isoliquiritigenin induces apoptosis and inhibits xenograft tumor growth of human lung cancer cells by targeting both wildtype and L858R/T790M mutant EGFR. J. Biol. Chem. 289:35839-48. |
36. Rao, E., Singh, P., Zhai, X., Li, Y., Zhu, G., Zhang, Y., Hao, J., Chi, Y.-I., Brown, R., Cleary, M. P. and Li, B. (2015) Inhibition of tumor growth by a newly-identified activator for epidermal fatty acid binding protein. Oncotarget 6:7815-27. |
37. Rao, E., Singh, P., Li. Y., Zhang, Y., Chi, Y.-I., Suttles, J. and Li, B. (2015) Targeting epidermal fatty acid binding protein for treatment of experimental autoimmune encephalomyelitis. BMC Immunol. 16:28. |
38. Han, E., Gorman, A., Singh, P. and Chi, Y.-I. (2015) Repression of HNF1alpha-mediated transcription by amino-terminal enhancer of split (AES). Biochem. Biophys. Res. Commun. 468:14-20. |
39. Wu, Y., Wang, Y., Lin, Y., Liu, Y., Wang, Y., Jia, J., Singh, P., Chi, Y.-I., Wang, C., Dong, D., Li, W., Tao, M., Napier, D., Shi, Q., Deng, J., Evers, B. M. and Zhou, B. P. (2017) Dub3 inhibition suppresses breast cancer invasion and metastasis by promoting snail1 degradation. Nature Commun. 8:14228. |
40. Singh, P., Han, E., Endrizzi, J. A., O’Brien, R. M. and Chi, Y.-I. (2017) Crystal structures reveal a new and novel FoxO1 binding site within the human glucose-6-phosphatase catalytic subunit 1 gene promoter. J. Struct. Biol. 198:54-64. |
41. Jardetzky, T. S., Brown, J. H., Gorga, J. C., Stern, L. J., Urban, R.G., Chi, Y.-I., Stauffacher, C. V., Strominger, J. L. and Wiley, D. C. (2018) Pillars article: Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. Nature 368: 711-718. J. Immunol. 201:1819-26. |
42. Singh, P., Tung, S.-P., Han, E. H., Lee, I.-K. and Chi, Y.-I. (2019) Dimerization defective MODY mutations of hepatocyte nuclear factor 4alpha. Mutat. Res. 814:1-6. |
43. Lee, D., Pagire, S., Pagire, H., Bae, E. J., Dighe, M., Kim, M., Lee, K. M., Jang, Y. K., Jaladi, A., Jung, K.-Y., Yoo, E. K., Gim, H. E., Lee, S. M., Choi, W.-I., Chi, Y.-I., Song, J.-S., Bae, M. A., Jeon, Y. H., Lee, G.-H., Liu, K.-H., Lee, T., Park, S., Jeon, J.-H., Lee, I. K. and Ahn, J. H. (2019) Discovery of novel pyruvate dehydrogenase kinase 4 inhibitors for potential oral treatment of metabolic diseases. J. Med. Chem. 62:575-88. |
44. Han, E., Singh, P., Lee, I.-K., Urrutia, R. and Chi, Y.-I. (2019) ErbB3-binding protein 1 (EBP1) represses HNF4alpha-mediated transcription and insulin secretion in pancreatic beta-cells. J. Biol. Chem. 294:13983-94. |
45. Dou, L., Yan, F., Pang, J., Zheng, D., Li, D., Gao, L., Wang, L., Xu, Y., Shi, J., Wang, Q., Zhou, L., Shen, N., Singh, P., Wang, L., Li, Y., Gao, Y., Liu, T., Chen, C., Al-Kali, A., Litzow, M. R., Chi, Y.-I., Bode, A. M., Liu, C., Huang, H., Liu, D., Marcucci, G., Liu, S. and Yu, L. (2019) Protein lysine 43 methylation by EZH1 promotes AML1-ETO transcriptional repression in leukemia. Nature Commun. 10:5051. |
46. Chi, Y.-I., Stodola, T. J., De Assuncao, T. M., Leverence, E. N., Tripathi, S., Dsouza, N. R., Mathison, A. J., Basel, D. G., Volkman, B. F., Smith, B. C., Lomberk, G., Zimmermann, M. T., Urrutia, R. (2021) Molecular mechanics and dynamic simulations of well-known Kabuki syndrome-associated KDM6A variants reveal putative mechanisms of dysfunction. Orphanet. J. Rare Dis. 16:66. |
47. Stodola, T. J., Chi, Y.-I., De Assuncao, T. M., Leverence, E. N., Tripathi, S., Dsouza, N. R., Mathison, A. J., Volkman, B. F., Smith, B. C., Lomberk, G., Zimmermann, M. T., Urrutia, R. (2022) Computational modeling reveals key molecular properties and dynamic behavior of Dot1L and partnering complexes involved in leukemogenesis. Proteins 90:282-298. |
48. Chi, Y.-I., Stodola, T. J., De Assuncao, T. M., Leverence, E. N., Smith, B. C., Volkman, B. F., Mathison, A. J., Lomberk, G., Zimmermann, M. T., Urrutia, R. (2022) Structural bioinformatics enhances the interpretation of somatic mutations in KDM6A found in human cancers. Comput. Struct. Biotechnol. J. 20:2200-2211. |
49. Pollin, G., De Assuncao, T. M., Jorge, S. D., Chi, Y.-I., Charlesworth, N. C., Madden, B., Iovanna, J. L., Zimmermann, M. T., Urrutia, R. and Lomberk, G. (2023) Writers and readers of H3K9me2 form distinct protein networks during the cell cycle, which include candidates for H3K9 mimicry. Biosci. Rep. 43:BSR20231093. |
50. Chi, Y.-I., Jorge, S. D., Jensen, D. R., Smith, B. C., Volkman, B. F., Mathison, A. J., Lomberk, G., Zimmermann, M. T. and Urrutia, R. (2023) A multi-layered computational structural geneomics approach enhances domain-specific interpretation of Kleefstra syndrome variants in EHMT1. Comput. Struct. Biotechnol. J. 21:5249-58. |
51. Jorge, S. D., Chi, Y.-I., Mazaba, J. L., Haque, N., Wegenknecht, J., Smith, B. C., Volkman, B. F., Mathison, A. J., Lomberk, G., Zimmermann, M. T. and Urrutia, R. (2023) Deep computational phenotyping of genomic variants impacting the SET domain of KMT2C reveal molecular mechanisms for their dysfunction. Front. Genet. 14:1291307. |
52. Singh, E., Chi, Y.-I., Kopesky, J., Zimmermann, M. T., Basel, D. G., Urrutia, R. and Schowerer, J. S. (2024) Computational structural genomics and biochemical evidence support the gain of function of a novel variant in Branched Chain Ketoacid Dehydrogenase (BCKDK) detected on newborn screening for Maple Syrup Urine Disease (MSUD). JIMD Rep. 65:144-155. |
Books, Chapters, and Reviews |
1. Bohach, G. A., Jablonski, L. M., Deobald, C. F., Chi, Y.-I. and Stauffacher, C. V. (1995) Functional domains of staphylococcal enterotoxins. In Molecular Approaches to Food Safety: Issues involving Toxic Microorganisms. Alakan, Inc., Fort Collins, CO. PP. 339-56. |
2. Chi, Y.-I. (2005) Homeodomain revisited: A lesson from disease-causing mutations. Human Genetics 116:433-44. |
3. Scott, W. G., Martick, M. and Chi, Y.-I. (2009) Structure and function of regulatory RNA elements: Ribozymes that regulate gene expression. Biochim. Biophys. Act (BBA) – Gene Regulatory Mechanism 1789:634-41. |