Training Grant Publications

2025

Courchesne-Krak NS, Chandrasekaran AR, Gonzalez J, Bianchi SB, Tran V, Johnson EO, Troiani V, Hettema JM, Stein MB, Coon H, Docherty AR, Berretini WH, MacKillop J, de Wit H, Marienfeld C, Palmer AA, Sanchez-Roige S. "Prescription Opioid Medication Survey: A Tool to Collect Deep Phenotypic Data on the Multifactorial Pathways to Opioid Use Disorder in Clinical and Population-Based Cohorts." Complex Psychiatry. 2025;11(1):72-93. PubMed PMC DOI
D'Antonio M, Arthur TD, Gonzalez Rivera WG, Wu X, Nguyen JP, Gymrek M, Woo-Yeong P, Frazer KA. "Genetic analysis of elevated levels of creatinine and cystatin C biomarkers reveals novel genetic loci associated with kidney function." Hum Mol Genet. 2025;34(9):751-764. PubMed PMC DOI
D'Antonio M, G Gonzalez Rivera W, Greenes RA, Gymrek M, Frazer KA. "A highly accurate risk factor-based XGBoost multiethnic model for identifying patients with skin cancer." Nat Commun. 2025;16(1):9542. PubMed PMC DOI
Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Godoy Magalhaes L, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean KJ, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. "Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining." NPJ Drug Discov. 2025;2(1):3. PubMed PMC DOI
Turner JL, Hinojosa-Gonzalez L, Sasaki T, Uchino S, Vouzas A, Soto MS, Chakraborty A, Alexander KE, Fitch CA, Brown AN, Ay F, Gilbert DM. "Master transcription-factor binding sites constitute the core of early replication control elements." EMBO J. 2025;44(16):4499-4524. PubMed PMC DOI

2024

Baghdassarian HM, Lewis NE. "Resource allocation in mammalian systems." Biotechnol Adv. 2024;71:108305. PubMed PMC DOI
Dolai A, Soltani S, Smarr B, Das A. "Divergent Circadian Foraging Strategies in Response to Diurnal Predation Versus Persistent Rain in Asian Weaver Ant, Oecophylla smaragdina, Suggest Possible Energetic Trade-offs." J Biol Rhythms. 2024;39(3):295-307. PubMed PMC DOI
Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Magalhaes LG, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean K, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. "Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining." Res Sq. 2024. PubMed PMC DOI
Luth MR, Godinez-Macias KP, Chen D, Okombo J, Thathy V, Cheng X, Daggupati S, Davies H, Dhingra SK, Economy JM, Edgar RCS, Gomez-Lorenzo MG, Istvan ES, Jado JC, LaMonte GM, Melillo B, Mok S, Narwal SK, Ndiaye T, Ottilie S, Palomo Diaz S, Park H, Peña S, Rocamora F, Sakata-Kato T, Small-Saunders JL, Summers RL, Tumwebaze PK, Vanaerschot M, Xia G, Yeo T, You A, Gamo FJ, Goldberg DE, Lee MCS, McNamara CW, Ndiaye D, Rosenthal PJ, Schreiber SL, Serra G, De Siqueira-Neto JL, Skinner-Adams TS, Uhlemann AC, Kato N, Lukens AK, Wirth DF, Fidock DA, Winzeler EA. "Systematic in vitro evolution in Plasmodium falciparum reveals key determinants of drug resistance." Science. 2024;386(6725):eadk9893. PubMed PMC DOI
Mah CK, Ahmed N, Lopez NA, Lam DC, Pong A, Monell A, Kern C, Han Y, Prasad G, Cesnik AJ, Lundberg E, Zhu Q, Carter H, Yeo GW. "Bento: a toolkit for subcellular analysis of spatial transcriptomics data." Genome Biol. 2024;25(1):82. PubMed PMC DOI
Mason AE, Kasl P, Soltani S, Green A, Hartogensis W, Dilchert S, Chowdhary A, Pandya LS, Siwik CJ, Foster SL, Nyer M, Lowry CA, Raison CL, Hecht FM, Smarr BL. "Elevated body temperature is associated with depressive symptoms: results from the TemPredict Study." Sci Rep. 2024;14(1):1884. PubMed PMC DOI
Pong A, Mah CK, Yeo GW, Lewis NE. "Computational cell-cell interaction technologies drive mechanistic and biomarker discovery in the tumor microenvironment." Curr Opin Biotechnol. 2024;85:103048. PubMed DOI
Zhang R, Fang J, Xie X, Carrico C, Meyer JG, Wei L, Bons J, Rose J, Riley R, Kwok R, Ashok Kumaar PV, Zhang Y, He W, Nishida Y, Liu X, Locasale JW, Schilling B, Verdin E. "Regulation of urea cycle by reversible high-stoichiometry lysine succinylation." Nat Metab. 2024;6(3):550-566. PubMed DOI

2023

Baghdassarian H, Blackstone SA, Clay OS, Philips R, Matthiasardottir B, Nehrebecky M, Hua VK, McVicar R, Liu Y, Tucker SM, Randazzo D, Deuitch N, Rosenzweig S, Mark A, Sasik R, Fisch KM, Pimpale Chavan P, Eren E, Watts NR, Ma CA, Gadina M, Schwartz DM, Sanyal A, Werner G, Murdock DR, Horita N, Chowdhury S, Dimmock D, Jepsen K, Remmers EF, Goldbach-Mansky R, Gahl WA, O'Shea JJ, Milner JD, Lewis NE, Chang J, Kastner DL, Torok K, Oda H, Putnam CD, Broderick L. "Variant STAT4 and Response to Ruxolitinib in an Autoinflammatory Syndrome." N Engl J Med. 2023;388(24):2241-2252. PubMed PMC DOI
Horii M, To C, Morey R, Jacobs MB, Li Y, Nelson KK, Meads M, Siegel BA, Pizzo D, Adami R, Zhang-Rutledge K, Lamale-Smith L, Laurent LC, Parast MM. "Histopathologic and Transcriptomic Profiling Identifies Novel Trophoblast Defects in Patients With Preeclampsia and Maternal Vascular Malperfusion." Mod Pathol. 2023;36(2):100035. PubMed PMC DOI
Massarat AR, Lamkin M, Reeve C, Williams AL, D'Antonio M, Gymrek M. "Haptools: a toolkit for admixture and haplotype analysis." Bioinformatics. 2023;39(3). PubMed PMC DOI
Semaan A, Bernard V, Wong J, Makino Y, Swartzlander DB, Rajapakshe KI, Lee JJ, Officer A, Schmidt CM, Wu HH, Scaife CL, Affolter KE, Nachmanson D, Firpo MA, Yip-Schneider M, Lowy AM, Harismendy O, Sen S, Maitra A, Jakubek YA, Guerrero PA. "Integrated Molecular Characterization of Intraductal Papillary Mucinous Neoplasms: An NCI Cancer Moonshot Precancer Atlas Pilot Project." Cancer Res Commun. 2023;3(10):2062-2073. PubMed PMC DOI
Vo D, Ghosh P, Sahoo D. "Artificial intelligence-guided discovery of gastric cancer continuum." Gastric Cancer. 2023;26(2):286-297. PubMed PMC DOI

2022

Boeder S, Kobayashi E, Ramesh G, Serences B, Kulasa K, Majithia AR. "Accuracy and Glycemic Efficacy of Continuous Glucose Monitors in Critically Ill COVID-19 Patients: A Retrospective Study." J Diabetes Sci Technol. 2022:1.93E+16. PubMed DOI
Dekel C, Morey R, Hanna J, Laurent LC, Ben-Yosef D, Amir H. "Stabilization of hESCs in two distinct substates along the continuum of pluripotency." IScience. 2022;25(12):105469. PubMed PMC DOI
Hyun JC, Monk JM, Palsson BO. "Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity." BMC Genomics. 2022;23(1):7. PubMed PMC DOI
Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. "FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA." NAR Genom Bioinform. 2022;4(2):lqac032. PubMed PMC DOI
Li J, Pinto-Duarte A, Zander M, Cuoco MS, Lai CY, Osteen J, Fang L, Luo C, Lucero JD, Gomez-Castanon R, Nery JR, Silva-Garcia I, Pang Y, Sejnowski TJ, Powell SB, Ecker JR, Mukamel EA, Behrens MM. "Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3." Elife. 2022;11. PubMed PMC DOI
Nachmanson D, Officer A, Mori H, Gordon J, Evans MF, Steward J, Yao H, O'Keefe T, Hasteh F, Stein GS, Jepsen K, Weaver DL, Hirst GL, Sprague BL, Esserman LJ, Borowsky AD, Stein JL, Harismendy O. "The breast pre-cancer atlas illustrates the molecular and micro-environmental diversity of ductal carcinoma in situ." NPJ Breast Cancer. 2022;8(1):6. PubMed PMC DOI
Nachmanson D, Pagadala M, Steward J, Cheung C, Bruce LK, Lee NQ, O'Keefe TJ, Lin GY, Hasteh F, Morris GP, Carter H, Harismendy O. "Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes." J Transl Med. 2022;20(1):623. PubMed PMC DOI