Graduate School of Biomedical Sciences

Student Publications


Selected Publications 2016-2019


Our students and faculty frequently publish their research in prestigious, peer-reviewed journals. The selected listing below of publications from 2016-2019 provides a representative sampling of the depth and breadth of these publications.

Wilson SJ, Wilkins AD, Lin CH, Lua RC, Lichtarge O. 2017, DISCOVERY OF FUNCTIONAL AND DISEASE PATHWAYS BY COMMUNITY DETECTION IN PROTEIN-PROTEIN INTERACTION NETWORKS. Pac Symp Biocomput: 2017;22:336-347. doi: 10.1142/9789813207813_0032.

Young M, Dahoun T, Sokrat B, Arber C, Chen KM, Bouvier, Barth P. 2018. Computational design of orthogonal membrane receptor-effector switches for rewiring signaling pathways. Proc Natl Acad Sci U S A. 115(27):7051-7056. doi: 10.1073/pnas.1718489115. Epub 2018 Jun 18.

Wilson SJ, Wilkins AD, Lin CH, Lua RC, Lichtarge O. 2017, DISCOVERY OF FUNCTIONAL AND DISEASE PATHWAYS BY COMMUNITY DETECTION IN PROTEIN-PROTEIN INTERACTION NETWORKS. Pac Symp Biocomput: 2017;22:336-347. doi: 10.1142/9789813207813_0032.

Saltzman AB, Leng M, Bhatt B, Singh P, Chan DW, Dobrolecki L, Chandrasekaran H, Choi JM, Jain A, Jung SY, Lewis MT, Ellis MJ, Malovannaya A. 2018, gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data. Mol Cell Proteomics: 17(11):2270-2283. doi: 10.1074/mcp.TIR118.000850. Epub 2018 Aug 9.

Matsunuma R, Chan DW, Kim BJ, Singh P, Han A, Saltzman AB, Cheng C, Lei JT, Wang J, Roberto Da Silva L, Sahin E, Leng M, Fan C, Perou CM, Malovannaya A, Ellis MJ. 2018. DPYSL3 modulates mitosis, migration, and epithelial-to-mesenchymal transition in claudin-low breast cancer. Proc Natl Acad Sci U S A. 115(51):E11978-E11987. doi: 10.1073/pnas.1810598115. Epub 2018 Nov 29.

Bertolet G, Kongchan N, Miller R, Patel RK, Jain A, Choi JM, Saltzman AB, Christenson A, Jung SY, Malovannaya A, Grimson A, Neilson JR. 2019. MiR-146a wild-type 3' sequence identity is dispensable for proper innate immune function in vivo. Life Sci Alliance. 2(1). pii: e201800249. doi: 10.26508/lsa.201800249. Print 2019 Feb.

Farinhold T, Dinh C, Kuspa A. 2019. Social amoebae establish a protective interface with their bacterial associates by lectin agglutination. Sci Adv. 5(7):eaav4367. doi: 10.1126/sciadv.aav4367. eCollection 2019 Jul.

Timothy Farinhold, Christopher Dinh, Adam Kuspa. 2019. Social amoebae establish a protective interface with their bacterial associates by lectin agglutination. Science Advances 24 Jul 2019: Vol. 5, no. 7, eaav4367 DOI: 10.1126/sciadv.aav4367

Christopher Dinh, Timothy Farinholt, Sheigenori Hirose, Olga Zhuchenko, Adam Kuspa. 2018. Lectins modulate the microbiota of social amoebae. Science 27 Jul 2018: Vol. 361, Issue 6400, pp. 402-406 DOI: 10.1126/science.aat2058

Adamski, C. J., Cardenas, A. M., Brown, N. G., Horton, L. B., Sankaran, B., Prasad, B. V., . . . Palzkill, T. (2015). Molecular basis for the catalytic specificity of the CTX-M extended-spectrum beta-lactamases. Biochemistry, 54(2), 447-457. doi:10.1021/bi501195g

Adamski, C. J., & Palzkill, T. (2017). BLIP-II Employs Differential Hotspot Residues To Bind Structurally Similar Staphylococcus aureus PBP2a and Class A beta-Lactamases. Biochemistry, 56(8), 1075-1084. doi:10.1021/acs.biochem.6b00978

Adamski, C. J., & Palzkill, T. (2017). Systematic substitutions at BLIP position 50 result in changes in binding specificity for class A beta-lactamases. BMC Biochem, 18(1), 2. doi:10.1186/s12858-017-0077-1

Bodine, T. J., Evangelista, M. A., Chang, H. T., Ayoub, C. A., Samuel, B. S., Sucgang, R., & Zechiedrich, L. (2017). Escherichia coli DNA ligase B may mitigate damage from oxidative stress. PLoS One, 12(7), e0180800. doi:10.1371/journal.pone.0180800

Campbell, J. C., Kim, J. J., Li, K. Y., Huang, G. Y., Reger, A. S., Matsuda, S., . . . Kim, C. (2016). Structural Basis of Cyclic Nucleotide Selectivity in cGMP-dependent Protein Kinase II. J Biol Chem, 291(11), 5623-5633. doi:10.1074/jbc.M115.691303

Chen J, Zhao M, Jiang X, Sizovs A, Wang MC, Provost CR, Huang J, Wang J. Genetically anchored fluorescent probes for subcellular specific imaging of hydrogen sulfide.Analyst. (2016) Feb 21;141(4):1209-1213. doi: 10.1039/c5an02497h. PMID: 26806071

Chen J, Jiang X, Zhang C, MacKenzie KR, Stossi F, Palzkill T, Wang MC, Wang J. Reversible Reaction-Based Fluorescent Probe for Real-Time Imaging of Glutathione Dynamics in Mitochondria. ACS Sens. (2017) Sep 22;2(9):1257-1261. doi: 10.1021/acssensors.7b00425. Epub (2017) Aug 18. PMID: 28809477

Chou, A., Roa, M., Evangelista, M. A., Sulit, A. K., Lagamayo, E., Torres, B. C., . . . Zechiedrich, L. (2016). Emergence of Klebsiella pneumoniae ST273 Carrying blaNDM-7 and ST656 Carrying blaNDM-1 in Manila, Philippines. Microb Drug Resist, 22(7), 585-588. doi:10.1089/mdr.2015.0205

Feng X, Ambia J, Chen KM, Young M, Barth P. Computational design of ligand-binding membrane receptors with high selectivity. Nat Chem Biol. (2017) Jul;13(7):715-723. doi: 10.1038/nchembio.2371. Epub (2017) May 1.

Figard, L., Wang, M., Zheng, L., Golding, I., & Sokac, A. M. (2016). Membrane Supply and Demand Regulates F-Actin in a Cell Surface Reservoir. Dev Cell, 37(3), 267-278. doi:10.1016/j.devcel.2016.04.010

Galaz-Montoya, J. G., Hecksel, C. W., Baldwin, P. R., Wang, E., Weaver, S. C., Schmid, M. F., . . . Chiu, W. (2016). Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography. J Struct Biol, 194(3), 383-394. doi:10.1016/j.jsb.2016.03.018

Galaz-Montoya, M., Wright, S. J., Rodriguez, G. J., Lichtarge, O., & Wensel, T. G. (2017). beta2-Adrenergic receptor activation mobilizes intracellular calcium via a non-canonical cAMP-independent signaling pathway. J Biol Chem, 292(24), 9967-9974. doi:10.1074/jbc.M117.787119

Galvan DL, Green NH, Danesh FR. The hallmarks of mitochondrial dysfunction in chronic kidney disease. Kidney Int. (2017) Nov;92(5):1051-1057. doi: 10.1016/j.kint.(2017).05.034. PMID: 28893420

Hecksel, C. W., Darrow, M. C., Dai, W., Galaz-Montoya, J. G., Chin, J. A., Mitchell, P. G., . . . Chiu, W. (2016). Quantifying Variability of Manual Annotation in Cryo-Electron Tomograms. Microsc Microanal, 22(3), 487-496. doi:10.1017/S1431927616000799

Jiang X, Chen J, Bajic A, Zhang C, Song X, Carroll SL, Cai ZL, Tang M, Xue M, Cheng N, Schaaf CP, Li F, MacKenzie KR, Ferreon ACM, Xia F, Wang MC, Maletic-Savatic M, Wang J. Quantitative real-time imaging of glutathione. Nat Commun. (2017) Jul 13;8:16087. doi: 10.1038/ncomms16087.

Jiang X, Wang L, Carroll SL, Chen J, Wang MC, Wang J. Challenges and Opportunities for Small-Molecule Fluorescent Probes in Redox Biology Applications. Antioxid Redox Signal. (2018) Feb 16. doi: 10.1089/ars.(2017).7491. [Epub ahead of print] PMID: 29320869

Jin, F., Thaiparambil, J., Donepudi, S. R., Vantaku, V., Piyarathna, D. W. B., Maity, S., . . . Putluri, N. (2017). Tobacco-Specific Carcinogens Induce Hypermethylation, DNA Adducts, and DNA Damage in Bladder Cancer. Cancer Prev Res (Phila), 10(10), 588-597. doi:10.1158/1940-6207.capr-17-0198

Li, Z., Venegas, V., Nagaoka, Y., Morino, E., Raghavan, P., Audhya, A., . . . Zhou, Z. (2015). Correction: Necrotic Cells Actively Attract Phagocytes through the Collaborative Action of Two Distinct PS-Exposure Mechanisms. PLoS Genet, 11(7), e1005418. doi:10.1371/journal.pgen.1005418

Li, Z., & Zhou, Z. (2016). How are necrotic cells recognized by their predators? Worm, 5(1), e1120400. doi:10.1080/21624054.2015.1120400

Long J, Badal SS, Ye Z, Wang Y, Ayanga BA, Galvan DL, Green NH, Chang BH, Overbeek PA, Danesh FR. Long noncoding RNA Tug1 regulates mitochondrial bioenergetics in diabetic nephropathy. J Clin Invest. (2016) Nov 1;126(11):4205-4218. doi: 10.1172/JCI87927. Epub (2016) Oct 17. PMID: 27760051

Lua, R. C., Wilson, S. J., Konecki, D. M., Wilkins, A. D., Venner, E., Morgan, D. H., & Lichtarge, O. (2016). UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. Nucleic Acids Res, 44(D1), D308-312. doi:10.1093/nar/gkv1279

Moore, J. M., Correa, R., Rosenberg, S. M., & Hastings, P. J. (2017). Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli. PLoS Genet, 13(7), e1006733. doi:10.1371/journal.pgen.1006733

Nehring, R. B., Gu, F., Lin, H. Y., Gibson, J. L., Blythe, M. J., Wilson, R., . . . Rosenberg, S. M. (2015). An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic Acids Res. doi:10.1093/nar/gkv1131

Noonepalle, S. K., Gu, F., Lee, E. J., Choi, J. H., Han, Q., Kim, J., . . . Shi, H. (2017). Promoter Methylation Modulates Indoleamine 2,3-Dioxygenase 1 Induction by Activated T Cells in Human Breast Cancers. Cancer Immunol Res, 5(4), 330-344. doi:10.1158/2326-6066.cir-16-0182

Pham K, Dong J, Jiang X, Qu Y, Yu H, Yang Y, Olea W, Marini JC, Chan L, Wang J, Wehrens XH, Cui X, Li Y, Hadsell DL, Cheng N. Loss of glutaredoxin 3

impedes mammary lobuloalveolar development during pregnancy and lactation. Am J Physiol Endocrinol Metab. (2017) Mar 1;312(3):E136-E149. doi: 10.1152/ajpendo.00150.(2016). Epub (2016) Nov 15.PMID: 27894063

Pal, R., Bondar, V. V., Adamski, C. J., Rodney, G. G., & Sardiello, M. (2017). Inhibition of ERK1/2 Restores GSK3beta Activity and Protein Synthesis Levels in a Model of Tuberous Sclerosis. Sci Rep, 7(1), 4174. doi:10.1038/s41598-017-04528-5

Placzek, A. N., Molfese, D.L.*, Khatiwada, S.*, Di Prisco, G.V., Huang, W., Sidrauski, C., Krnjevic, K., Amos, C.L., Ray, R., Dani, J.A., Walter, P., Salas, R., & Costa-Mattioli, M. . (2016). Translational control of nicotine-evoked synaptic potentiation in mice and neuronal responses in human smokers by eIF2α. Elife.

Regenbogen S, Wilkins AD, Lichtarge O. Computing Therapy for Precision Medicine: Collaborative Filtering Integrates and Predicts Multi-Entity Interactions. Pac Symp Biocomput. (2016);21:21-32. PMID: 26776170

Rogers, E., Correa, R., Barreto, B., Bravo Núñez, M.A., Minnick, P.J., Vera Cruz, D., Xia, J., Hastings, P.J., and Rosenberg, S.M. (2016). Double-Strand-Break Repair, Mutagenesis and Stress. In Stress and Environmental Control of Gene Expression in Bacteria. Bruijn, ed. (Wiley-Blackwell Publishers).

Roh, S. H., Hryc, C. F., Jeong, H. H., Fei, X., Jakana, J., Lorimer, G. H., & Chiu, W. (2017). Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM. Proc Natl Acad Sci U S A, 114(31), 8259-8264. doi:10.1073/pnas.1704725114

Roh, S. H., Kasembeli, M., Bakthavatsalam, D., Chiu, W., & Tweardy, D. J. (2015). Contribution of the Type II Chaperonin, TRiC/CCT, to Oncogenesis. Int J Mol Sci, 16(11), 26706-26720. doi:10.3390/ijms161125975

Roh, S. H., Kasembeli, M., Galaz-Montoya, J. G., Trnka, M., Lau, W. C., Burlingame, A., . . . Tweardy, D. J. (2016). Chaperonin TRiC/CCT Modulates the

Folding and Activity of Leukemogenic Fusion Oncoprotein AML1-ETO. J Biol Chem, 291(9), 4732-4741. doi:10.1074/jbc.M115.684878

Roh, S. H., Kasembeli, M. M., Galaz-Montoya, J. G., Chiu, W., & Tweardy, D. J. (2016). Chaperonin TRiC/CCT Recognizes Fusion Oncoprotein AML1-ETO through Subunit-Specific Interactions. Biophys J, 110(11), 2377-2385. doi:10.1016/j.bpj.2016.04.045

Rothmiller S, Schröder S, Strobelt R, Wolf M, Wang J, Jiang X, Worek F, Steinritz D, Thiermann H, Schmidt A. Sulfur mustard resistant keratinocytes obtained elevated glutathione levels and other changes in the antioxidative defense mechanism. Toxicol Lett. (2017) Nov 26. pii: S0378-4274(17)31483-2. doi: 10.1016/j.toxlet.(2017).11.024. [Epub ahead of print] PMID: 29183814

Shafi, A. A., Putluri, V., Arnold, J. M., Tsouko, E., Maity, S., Roberts, J. M., . . . Weigel, N. L. (2015). Differential regulation of metabolic pathways by androgen receptor (AR) and its constitutively active splice variant, AR-V7, in prostate cancer cells. Oncotarget, 6(31), 31997-32012. doi:10.18632/oncotarget.5585

Shen, K., Calamini, B., Fauerbach, J. A., Ma, B., Shahmoradian, S. H., Serrano Lachapel, I. L., . . . Frydman, J. (2016). Control of the structural landscape and neuronal proteotoxicity of mutant Huntingtin by domains flanking the polyQ tract. Elife, 5. doi:10.7554/eLife.18065

Sun Z, Mehta SC, Adamski CJ, Gibbs RA, Palzkill T. Deep Sequencing of Random Mutant Libraries Reveals the Active Site of the Narrow Specificity CphA Metallo-β-Lactamase is Fragile to Mutations. Sci Rep. (2016) Sep 12;6:33195. doi: 10.1038/srep33195.

Stojanoski, V., Adamski, C. J., Hu, L., Mehta, S. C., Sankaran, B., Zwart, P., . . . Palzkill, T. (2016). Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine beta-Lactamases by Relieving Steric Strain. Biochemistry, 55(17), 2479-2490. doi:10.1021/acs.biochem.6b00056

Sung, Y. M., Wilkins, A. D., Rodriguez, G. J., Wensel, T. G., & Lichtarge, O. (2016). Intramolecular allosteric communication in dopamine D2 receptor revealed by evolutionary amino acid covariation. Proc Natl Acad Sci U S A, 113(13), 3539-3544. doi:10.1073/pnas.1516579113

Tian, L., Goldstein, A., Wang, H., Ching Lo, H., Sun Kim, I., Welte, T., . . . Zhang, X. H. (2017). Mutual regulation of tumour vessel normalization and immunostimulatory reprogramming. Nature, 544(7649), 250-254. doi:10.1038/nature21724

Tsoi PS, Choi KJ, Leonard PG, Sizovs A, Moosa MM, MacKenzie KR, Ferreon JC, Ferreon ACM. The N-Terminal Domain of ALS-Linked TDP-43 Assembles without Misfolding. Angew Chem Int Ed Engl. (2017) Aug 21. doi: 10.1002/anie.(2017)06769. [Epub ahead of print]

von Rundstedt, F. C., Rajapakshe, K., Ma, J., Arnold, J. M., Gohlke, J., Putluri, V., . . . Putluri, N. (2016). Integrative Pathway Analysis of Metabolic Signature in Bladder Cancer: A Linkage to The Cancer Genome Atlas Project and Prediction of Survival. J Urol, 195(6), 1911-1919. doi:10.1016/j.juro.2016.01.039

Wang, H., Tian, L., Goldstein, A., Liu, J., Lo, H. C., Sheng, K., . . . Zhang, X. H. (2017). Bone-in-culture array as a platform to model early-stage bone metastases and discover anti-metastasis therapies. Nat Commun, 8, 15045. doi:10.1038/ncomms15045

Welte, T., Kim, I. S., Tian, L., Gao, X., Wang, H., Li, J., . . . Zhang, X. H. (2016). Oncogenic mTOR signalling recruits myeloid-derived suppressor cells to promote tumour initiation. Nat Cell Biol, 18(6), 632-644. doi:10.1038/ncb3355

Xu, X., De Angelis, C., Burke, K. A., Nardone, A., Hu, H., Qin, L., . . . Schiff, R. (2017). HER2 Reactivation through Acquisition of the HER2 L755S Mutation as a Mechanism of Acquired Resistance to HER2-targeted Therapy in HER2+ Breast Cancer. Clin Cancer Res, 23(17), 5123-5134. doi:10.1158/1078-0432.CCR-16-2191

Xue, Z., & Sokac, A. M. (2016). -Back-to-back mechanisms drive actomyosin ring closure during Drosophila embryo cleavage. J