Selected Publications

• Vanpouille, C, Wells, A, DeGruttola, V, Lynch, ML, Zhang, X, Tu, X, Chaillon, A, Woodworth, B, Gaitan, N, Rawlings, ​SA, Landay, A, Weber, K, Scully, E, Karn, J, Gianella, S. (2025) Longitudinal T Cell Phenotypic Dynamics During Sustained
  ART in People with HIV. Open Forum Infectious Diseases (Dec), DOI: 10.1093/ofid/ofaf775

• Vanpouille, C, Wells, A, DeGruttola, V, Lynch, ML, Zhang, X, Fitzgerald M, Tu, X, Chaillon, A, Landay, A, Weber, K, Scully, E, Karn, J, Gianella, S. (2025) Cytokine trajectory over time in men and women with HIV on long-term ART. AIDS (Jan), 1(39): 1-10. doi:DOI: 10.1097/QAD.0000000000004033

• Acehan, D, Spoth, KA, Budziszewski, GR, Snell, ME, Campomizzi, CS, Lynch, ML, Bowman, SEJ. (2024) Reaching the potential of electron dffraction. Cell Reports Physical Science (May), 6(5) doi:10.1016/j.xcrp.2024.102007

• Babbitt GA, Rajendran M, Lynch ML, Asare-Bediako R, Mouli LT, Ryan CJ, Srivastava H, Rynkiewicz P, Phadke K, Reed ML, Moore N, Ferran MC, Fokoue EP. (2024) ATOMDANCE: Kernel-based denoising and choreographic analysis for protein dynamic comparison. Biophysical journal (Mar).

• Rajendran M, Ferran MC, Mouli L, Babbitt GA, Lynch ML. (2023) Evolution of drug resistance drives destabilization of flap region dynamics in HIV-1 protease. Biophysical reports (Sep), 3(3): 100121. doi:10.1016/j.bpr.2023.100121

• Budziszewski GR, Snell ME, Wright TR, Lynch ML, Bowman SEJ. (2023) High-Throughput Screening to Obtain Crystal Hits for Protein Crystallography. Journal of visualized experiments : JoVE (Mar)(193). doi:10.3791/65211

• Lynch ML, Snell ME, Potter SA, Snell EH, Bowman SEJ. (2023) 20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening. Acta crystallographica. Section D, Structural biology (Mar), 79(Pt 3): 198-205. doi:10.1107/S2059798323001274

• Martin JC, Sims JR, Gupta A, Hagoel TJ, Gao L, Lynch ML, Woloszynska A, Melendy T, Kane JF, Kuechle J, Ohm JE. (2022) CDC7 kinase (DDK) inhibition disrupts DNA replication leading to mitotic catastrophe in Ewing sarcoma. Cell death discovery (Feb), 8(1): 85. doi:10.1038/s41420-022-00877-x

• Hagoel TJ, Cortes Gomez E, Gupta A, Twist CJ, Kozielski R, Martin JC, Gao L, Kuechle J, Singh PK, Lynch M, Wei L, Liu S, Wang J, Ohm JE. (2022) Clinicopathologic and molecular analysis of a BCOR-CCNB3 undifferentiated sarcoma of the kidney reveals significant epigenetic alterations. Cold Spring Harbor molecular case studies (Jan), 8(1). doi:10.1101/mcs.a005942

• Rynkiewicz P, Lynch ML, Cui F, Hudson AO, Babbitt GA. (2022) Functional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains. Journal of biomolecular structure & dynamics (Jan), 40(21): 10978-10996. doi:10.1080/07391102.2021.1953604

• Lynch ML, DeGruttola V. (2022) Ensemble clustering of longitudinal bivariate HIV biomarker profiles to group patients by patterns of disease progression. International journal of data science and analytics (Jan), 14(3): 305-318. doi:10.1007/s41060-022-00323-2

• Babbitt GA, Lynch ML, McCoy M, Fokoue EP, Hudson AO. (2022) Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition. Journal of biomolecular structure & dynamics (Jan), 40(1): 468-483.

• Halcrow PW, Lynch ML, Geiger JD, Ohm JE. (2021) Role of endolysosome function in iron metabolism and brain carcinogenesis. Seminars in cancer biology (Nov), 76: 74-85. doi:10.1016/j.semcancer.2021.06.013

• Martin JC, Hoegel TJ, Lynch ML, Woloszynska A, Melendy T, Ohm JE. (2021) Exploiting Replication Stress as a Novel Therapeutic Intervention. Molecular cancer research : MCR (Feb), 19(2): 192-206. doi:10.1158/1541-7786.MCR-20-0651

• Lynch ML, Dudek MF, Bowman SEJ. (2020) A Searchable Database of Crystallization Cocktails in the PDB: Analyzing the Chemical Condition Space. Patterns (New York, N.Y.) (Jul), 1(4). doi:10.1016/j.patter.2020.100024

• Konstorum A, Lynch ML, Torti SV, Torti FM, Laubenbacher RC. (2018) A Systems Biology Approach to Understanding the Pathophysiology of High-Grade Serous Ovarian Cancer: Focus on Iron and Fatty Acid Metabolism. Omics : a journal of integrative biology (Jul), 22(7): 502-513. doi:10.1089/omi.2018.0060

• Malcolm, KB, Dinwoodey, DL, Cundiff, MC, Regis, SM, Borondy-Kitts, AK, Wald, C, Lynch, ML, Al-Husami, W, McKee, AB & McKee, BJ (2018). Qualitative coronary artery calcium assessment on CT lung screening exam helps predict first cardiac events. Journal of Thoracic Disease, 10(5), 2740.

• Ghorani, E, Rosenthal, R, McGranahan, N, Reading, JL, Lynch, M, Peggs, KS, Swanton, C, & Quezada, SA (2018). Differential binding affinity of mutated peptides for MHC class I is a predictor of survival in advanced lung cancer and melanoma. Annals of Oncology, 29(1), 271.

• Lemler, DL, Lynch, ML, Tesfay, L, Deng, Z, Paul, BT, Wang, X, Hegde, P, Manz, DH, Torti, SV & Torti, FM (2017). DCYTB is a predictor of outcome in breast cancer that functions via iron-dependent mechanisms.  Breast Cancer Research 19 (25).

• Basuli, D, Tesfay, L, Deng, Z, Paul, B, Yamamoto, Y, Ning, G, Xian, N, McKeon, F, Lynch, ML, Crum, CP, Hedge, P, Brewer, M, Wang, X, Miller, LD, Dyment, N, Torti, FM, & Torti, SV (2017). Iron addiction: A novel therapeutic target in ovarian cancer. Oncogene, 36, 4089.

• Gerber, C, Harel, M, Lynch, ML, Herbst, KW, Ferrer, FA, & Shapiro, LH (2016). Proximal tubule proteins are significantly elevated in bladder urine of patients with ureteropelvic junction obstruction and may represent novel biomarkers. Journal of Pediatric Urology, 12 (2), 120.e1.

• Lynch, ML & DeGruttola, V (2015). Predicting time to threshold for initiating antiretroviral treatment to evaluate cost of treatment as HIV prevention. Journal of the Royal Statistical Society Series C, Applied Statistics, 64(2), 359.

• Lynch, ML & Clement, JM (2015). Bayesian Functional Data Methods in Copy Number Alteration Studies: Applications in Urothelial Bladder Carcinoma. In JSM Proceedings, Biometrics Section.  Alexandria, VA: American Statistical Association, 2129.

• Duda, JB, Lynch, ML, Bhatt, S, Dogra, VS (2012). Computed Tomography Mimics of Acute Appendicitis: Predictors of Appendiceal Disease Confirmed at Pathology. Journal of Clinical Imaging Science, 2, 73.

• Strain, JJ, Davidson, PW, Thurston, SW, Harrington, D, Mulhern, MS, McAfee, AJ, van Wijngaarden, E, Shamlaye, CF, Henderson, J, Watson, GE, Zareba, G, Cory-Slechta, DA, Lynch, M, Wallace, JM, McSorley, EM, Bonham, MP, Stokes-Riner, A, Sloane-Reeves, J, Janciuras, J, Wong, R, Clarkson, TW & Myers, GJ (2012). Maternal PUFA status but not prenatal methylmercury exposure is associated with children’s language functions at age five years in the Seychelles. Journal of Nutrition, 142(11), 1943.

• Lynch, ML, Huang, LS, Cox, C, Strain, JJ, Myers, GJ, Bonham, MP, Shamlaye, CF, Stokes-Riner, A, Wallace, JM, Duffy, EM, Clarkson, TW & Davidson, PW (2011). Varying coefficient function models to explore interactions between maternal nutritional status and prenatal methylmercury toxicity in the Seychelles Child Development Nutrition Study. Environmental Research, 111 (1), 75.

• Watson, GE, Lynch, M, Myers, GJ, Shamlaye, CF, Thurston, SW, Zareba, G, Clarkson, TW & Davidson, PW (2011). Prenatal exposure to dental amalgam: evidence from the Seychelles Child Development Study main cohort. Journal of the American Dental Association, 142(11), 1283.

• Hietala, KA, Lynch, ML, Allhouse, JC, Johns, CJ & Roane, TM (2006). A mathematical model of Saccharomyces cerevisiae growth in response to cadmium toxicity. Journal of Basic Microbiology, 46(3), 19.

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