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University of Pittsburgh
Molecular Pharmacology Graduate Program > Current Students > Student Publications

Current Students' Publications

Dennis Braden

Journal Articles

Zhu D, Dai W, Srinivasan P, McClellan H, Braden D, Allee-Munoz A, Hurtado PAG, Miller LH, Duffy PE. Characterization of AMA1-RON2L complex with native gel electrophoresis and capillary isoelectric focusing  Electrophoresis. 2021 Oct 22. doi: 10.1002/elps.202000365. Online ahead of print. PMID: 34679212

Caitlyn Chapman

Journal Articles

Garrudo FFF, Mikael PE, Xia K, Silva JC, Ouyang Y, Chapman CA, Hoffman PR, Yu Y, Han X, Rodrigues CAV, Cabral JMS, Morgado J, Ferreira FC, Linhardt RJ. The effect of electrospun scaffolds on the glycosaminoglycan profile of differentiating neural stem cells. Biochimie. 2021 Mar;182:61-72. doi: 10.1016/j.biochi.2021.01.001. Epub: 2021 Jan 7.
Garrudo FFF, Mikael PE, Rodrigues CAV, Udangawa RW, Paradiso P, Chapman CA, Hoffman P, Colaço R, Cabral JMS, Morgado J, Linhardt RJ, Ferreira FC. Polyaniline-polycaprolactone fibers for neural applications: Electroconductivity enhanced by pseudo-doping. Mater Sci Eng C Mater Biol Appl. 2021 Jan;120:111680. doi: 10.1016/j.msec.2020.111680. Epub: 2020 Nov 4
Bhattacharya S, Roy I, Tice A, Chapman C, Udangawa R, Chakrapani V, Plawsky JL, Linhardt RJ. High-Capacitance Electrospun Fibers for Supercapacitor Applications. ACS Appl Mater Interfaces. 2020 Apr 29;12(17):19369-19376. doi: 10.1021/acsami.9b21696. Epub: 2020 Apr 20.

Fabliha Chowdhury

Journal Articles

Wu L, Li X, Lin Q, Chowdhury F, Mazumder MH, Du W. (2020). FANCD2 and HES1suppress inflammation-induced PPAR? to prevent haematopoietic stem cell exhaustion. Br J Haematol. doi: 10.1111/bjh.17230. PMID: 33222180.
Lin, Q., Wu, L., Ma, Z., Chowdhury, F. A., Mazumder, H. H., & Du, W. (2020). Persistent DNA damage-induced NLRP12 improves hematopoietic stem cell function. JCI Insight, 5(10). https://doi.org/10.1172/jci.insight.133365. PMID: 32434992.
Wu, L., Lin, Q., Ma, Z., Chowdhury, F. A., Mazumder, M. H. H., & Du, W. (2020). Mesenchymal PGD2 activates an ILC2-Treg axis to promote proliferation of normal and malignant HSPCs. Leukemia. https://doi.org/10.1038/s41375-020-0843-8. PMID: 32366935
Ma, Z., Xu, J., Wu, L., Wang, J., Lin, Q., Chowdhury, F. A., Du, W. (2020). Hes1 deficiency causes hematopoietic stem cell exhaustion. Stem Cells. https://doi.org/10.1002/stem.3169. PMID: 32129527

Jaclyn Connelly

Journal Articles

Zhang X, Connelly J, Chao Y, Wang QJ. Multifaceted Functions of Protein Kinase D in Pathological Processes and Human Diseases.   Biomolecules. 2021 Mar 23;11(3):483. doi: 10.3390/biom11030483. PMID: 33807058  PMCID: PMC8005150
 
Zhang X, Connelly J, Levitan ES, Sun D, Wang JQ. Calcium/Calmodulin-Dependent Protein Kinase II in Cerebrovascular Diseases.  Transl Stroke Res. 2021 Aug;12(4):513-529. doi: 10.1007/s12975-021-00901-9. Epub 2021 Mar 13. PMID: 33713030
 

Kaylee Ermine

Journal Articles

Tong J, Tan X, Risnik D, Gao M, Song X, Ermine K, Shen L, Wang S, Yu J, Zhang L.  BET protein degradation triggers DR5-mediated immunogenic cell death to suppress colorectal cancer and potentiate immune checkpoint blockade. Oncogene. 2021 Oct 6. doi: 10.1038/s41388-021-02041-8. Online ahead of print. PMID: 34615996

Victoria Heinrich

Journal Articles

Manni ML, Heinrich VA, Buchan GJ, O’Brien JP, Uvalle C, Cechova V, Koudelka A, Ukani D, Rawas-Qalaji M, Oury TD, Hart R, Ellgass M, Mullet SJ, Fajt ML, Wenzel SE, Holguin F, Freeman BA, Wendell SG. Nitroalkene fatty acids modulate bile acid metabolism and lung function in obese asthma. Scientific Reports. 2021; 11(1): 17788.

Angela Hinchie

Journal Articles

Sullivan DI, Jiang M, Hinchie AM, Roth MG, Bahudhanapati H, Nouraie M, et al. Transcriptional and Proteomic Characterization of Telomere-Induced Senescence in a Human Alveolar Epithelial Cell Line. Front Med (Lausanne). 2021;8:600626.
 
Ren X, Hinchie A, Swomley A, Powell DK, Butterfield DA. Profiles of brain oxidative damage, ventricular alterations, and neurochemical metabolites in the striatum of PINK1 knockout rats as functions of age and gender: Relevance to Parkinson disease. Free Radic Biol Med. 2019 01;143:146–52.
 

Lisa Hong

Journal Articles

Lin CC, Mabe NW, Lin YT, Yang WH, Tang X, Hong L, Sun T, Force J, Marks JR, Yao TP, Alvarez JV, Chi JT.  RIPK3 upregulation confers robust proliferation and collateral cystine-dependence on breast cancer recurrence. Cell Death Differ. 2020 Jul;27(7):2234-2247. doi: 10.1038/s41418-020-0499-y. Epub 2020 Jan 27. PMID: 31988496

Mohd Azrin bin Jamalruddin

Journal Articles

Brunette GJ, Jamalruddin MA, Baldock RA, Clark NL, Bernstein KA.   Evolution-based screening enables genome-wide prioritization and discovery of DNA repair genes.  Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19593-19599. doi: 10.1073/pnas.1906559116. Epub 2019 Sep 9. PMID: 31501324  PMCID: PMC6765268
 

Aaron Johnson

Journal Articles

G. L. Seim, E. C. Britt, S. V. John, F. J. Yeo, A. R. Johnson, R. S. Eisenstein, D. J. Pagliarini, J. Fan. 2019. Two-stage metabolic remodeling in macrophages in response to LPS and interferon-γ stimulation. Nature Metabolism 2019, 1 (7) 731-742. Pubmed PMID: 322590

Nicole Kaminski

Journal Articles

Evgeniia Prokhorova, Thomas Agnew, Anne R Wondisford, Michael Tellier, Nicole Kaminski, Danique Beijer, James Holder, Josephine Groslambert, Marcin J Suskiewicz, Kang Zhu, Julia M Reber, Sarah C Krassnig, Luca Palazzo, Shona Murphy, Michael L Nielsen, Aswin Mangerich, Dragana Ahel, Jonathan Baets, Roderick J O'Sullivan, Ivan Ahel. Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease. Molecular Cell.2021 Jun 17;81(12):2640-2655.e8.
doi: 10.1016/j.molcel.2021.04.028. Epub 2021 May 20.
Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ.  Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol. 2020 Dec;27(12):1152-1164. doi: 10.1038/s41594-020-0512-7. Epub 2020 Oct 12. PMID: 33046907  PMCID: PMC7809635
 
Kaminski, N.A. and Wong, E.A. (2018) Differential mRNA expression of nutrient transporters in male and female chickens. Poultry Science, (97)1: 313–318, https://doi.org/10.3382/ps/pex262
 

Matthew Keeney

Journal Articles

Keeney, M. T., Hoffman, E. K., Greenamyre, J. T. and Di Maio, R. (2021). Measurement of LRRK2 Kinase Activity by Proximity Ligation Assay. Bio-protocol 11(17): e4140. DOI: 10.21769/BioProtoc.4140.
Keeney, M.T., Hoffman E.K., Farmer, K., Bodle, C.R., Fazzari, M., Zharikov, A., Castro, S., Kofler, J., Cifuentes-Pagano, E., Pagano, P.J, Burton, E.A, Hastings, T. G., Greenamyre, J. T, & Di Maio, R. (2021). Neuronal NADPH Oxidase 2 in Parkinson’s Disease Pathogenesis. bioRxiv doi: https://doi.org/10.1101/2021.05.13.443999.
Rocha EM, De Miranda BR, Castro S, Drolet R, Hatcher NG, Yao L, Smith SM, Keeney MT, Di Maio R, Kofler J, Hastings TG, Greenamyre JT.    LRRK2 inhibition prevents endolysosomal deficits seen in human Parkinson's disease.Neurobiol Dis. 2020 Feb;134:104626. doi: 10.1016/j.nbd.2019.104626. Epub 2019 Oct 13. PMID: 31618685 PMCID: PMC7345850
 

Jeff (Yong Joon) Kim

Journal Articles

Xie, Y., Clarke, B. P., Kim, Y. J., Ivey, A. L., Hill, P. S., Shi, Y., & Ren, Y. (2021). Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2. Elife, 10, e65699.
 
Sun, D., Sang, Z., Kim, J., Xiang, Y., Cohen, T., Belford, A. K., ... & Shi, Y. (2021). Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes. bioRxiv. 2021 Mar 10;2021.03.09.434592.
doi: 10.1101/2021.03.09.434592. Preprint
 

Thong Luong

Journal Articles

Bonilla B, Brown AI, Hengel SR, Rapchak KS, Mitchell D, Pressimone CA, Fagunloye AA, Luong TT, Russell RA, Vyas RK, Mertz TM, Zaher HS, Mosammaparast N, Malc EP, Mieczkowski PA, Roberts S, Bernstein KA. The Shu complex prevents mutagenesis and cytotoxicity of single-strand specific alkylation lesions. Elife. 2021 Nov 1;10:e68080. doi: 10.7554/eLife.68080. Epub ahead of print. PMID: 34723799.

 
Grimley E, Cole AJ, Luong TT, McGonigal SC, Sinno S, Yang D, Bernstein KA, Buckanovich RJ. Aldehyde dehydrogenase inhibitors promote DNA damage in ovarian cancer and synergize with ATM/ATR inhibitors. Theranostics. 2021 Jan 20;11(8):3540-3551. doi: 10.7150/thno.51885. PMID: 33664846; PMCID: PMC7914353.
 
Baldock RA, Pressimone CA, Baird JM, Khodakov A, Luong TT, Grundy MK, Smith CM, Karpenshif Y, Bratton-Palmer DS, Prakash R, Jasin M, Garcin EB, Gon S, Modesti M, Bernstein KA.  RAD51D splice variants and cancer-associated mutations reveal XRCC2 interaction to be critical for homologous recombination.DNA Repair (Amst). 2019 Apr;76:99-107. doi: 10.1016/j.dnarep.2019.02.008. Epub 2019 Feb 23. PMID: 30836272  PMCID: PMC6508892
 

Egnatchik RA, Brittain EL, Shah AT, Fares WH, Ford HJ, Monahan K, Kang CJ, Kocurek EG, Zhu S, Luong T, Nguyen TT, Hysinger E, Austin ED, Skala MC, Young JD, Roberts LJ 2nd, Hemnes AR, West J, Fessel JP. Dysfunctional BMPR2 signaling drives an abnormal endothelial requirement for glutamine in pulmonary arterial hypertension. Pulm Circ. 2017 Feb 1;7(1):186-199. doi: 10.1086/690236. eCollection 2017 Mar. PubMed PMID: 28680578; PubMed Central PMCID: PMC5448547.

Hardeman KN, Peng C, Paudel BB, Meyer CT, Luong T, Tyson DR, Young JD, Quaranta V, Fessel JP. Dependence On Glycolysis Sensitizes BRAF-mutated Melanomas For Increased Response To Targeted BRAF Inhibition. Sci Rep. 2017 Feb 16;7:42604. doi: 10.1038/srep42604. PubMed PMID: 28205616; PubMed Central PMCID: PMC5311997.

Michelle Lynskey

Journal Articles

Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ.  Regulation of ALT-associated homology-directed repair by polyADP-ribosylation.  Nat Struct Mol Biol. 2020 Dec;27(12):1152-1164. doi: 10.1038/s41594-020-0512-7. Epub 2020 Oct 12. PMID: 33046907  PMCID: PMC7809635
 
Barroso-González J, García-Expósito L, Hoang SM, Lynskey ML, Roncaioli JL, Ghosh A, Wallace CT, de Vitis M, Modesti M, Bernstein KA, Sarkar SN, Watkins SC, O'Sullivan RJ.  RAD51AP1 Is an Essential Mediator of Alternative Lengthening of Telomeres.   Mol Cell. 2019 Oct 3;76(1):11-26.e7. doi: 10.1016/j.molcel.2019.06.043. Epub 2019 Aug 7. PMID: 31400850  PMCID: PMC6778027
 

Bellina Mushala

Journal Articles

Mushala, B., & Scott, I. (2021). Adropin: a hepatokine modulator of vascular function and cardiac fuel metabolism. American journal of physiology. Heart and circulatory physiology, 320(1), H238–H244.
Thapa, D., Manning, J.R., Mushala, B., Stoner, M.W., Zhang, M. & Scott, I. (2020). Increased fatty acid oxidation enzyme activity in the hearts of mice fed a high fat diet does not correlate with improved cardiac contractile function. Current Research in Physiology. 3. 44-49

Sonja Plasil

Journal Articles

Plasil SL, Seth A, Homanics GE.  CRISPR Turbo Accelerated KnockOut (CRISPy TAKO) for Rapid in vivo Screening of Gene Function.  Front Genome Ed. 2020 Oct;2:598522. doi: 10.3389/fgeed.2020.598522. Epub 2020 Oct 21. PMID: 33604589 PMCID: PMC7889042
 
Baratta AM, Rathod RS, Plasil SL, Seth A, Homanics GE.  Exposure to drugs of abuse induce effects that persist across generations.  Int Rev Neurobiol. 2021;156:217-277. doi: 10.1016/bs.irn.2020.08.003. Epub 2020 Sep 30. PMID: 33461664  PMCID: PMC8167819
 
Rathod RS, Ferguson C, Seth A, Baratta AM, Plasil SL, Homanics GE.  Effects of Paternal Preconception Vapor Alcohol Exposure Paradigms on Behavioral Responses in Offspring.   Brain Sci. 2020 Sep 22;10(9):658. doi: 10.3390/brainsci10090658. PMID: 32971974 PMCID: PMC7564629
 

Sripriya Raja

Journal Articles

Raja, S., & Van Houten, B. (2021). The Multiple Cellular Roles of SMUG1 in Genome Maintenance and Cancer.
International journal of molecular sciences, 22(4), 1981. https://doi.org/10.3390/ijms22041981
Kumar N*, Raja S*, Van Houten B. The involvement of nucleotide excision repair proteins in the removal of oxidative DNA damage [published online ahead of print, 2020 Oct 3]. Nucleic Acids Res. 2020;gkaa777. doi:10.1093/nar/gkaa777

Hayley Rein

Journal Articles

Rein, H.L., Bernstein, K.A., and Baldock, R.A. (2021) RAD51 paralog function in replicative DNA damage and tolerance. Current Opinions in Genetics and Development, 71:86-91
Prakash, R., Sandoval, T., Morati, F., Zagelbaum, J.A., Taylor, B., Wang, R., Desclos, E.C.B., Sullivan, M.R., Rein, H.L., Bernstein, K.A., Krawczyk, P.M., Gautier, J., Modesti, M., Vanoli, F., Jasin, M. (2021) Distinct pathways homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex, Nature Communications, 12(1):4255
Jiang, Z., Lai, Y., Beaver, J., Tsegay, P., Zhao, M., Horton, J., Zamora,M., Rein, H., Mirales, F., Shaver, M., Hutcheson, J., Agoulnik I., Wilson, S. and Liu, Y. 2020. Oxidative DNA Damage Modulates DNA Methylation Pattern in Human Breast Cancer 1 (BRCA1) Gene via the Crosstalk between DNA Polymerase β and a de novo DNA Methyltransferase. Cells. 9(1):225

Anne Wondisford

Journal Articles

Prokhorova E, Agnew T, Wondisford AR, Tellier M, Kaminski N, Beijer D, Holder J, Groslambert J, Suskiewicz MJ, Zhu K, Reber JM, Krassnig SC, Palazzo L, Murphy S, Nielsen ML, Mangerich A, Ahel D, Baets J, O'Sullivan RJ, Ahel I. Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease. Mol Cell. 2021 Jun 17;81(12):2640-2655.e8. doi: 10.1016/j.molcel.2021.04.028. PMID: 34019811; PMCID: PMC8221567.
Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli
JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga
Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ.
Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol.
2020 Oct 12. doi: 10.1038/s41594-020-0512-7. PMID: 33046907 PMCID: PMC7809635