2020 Student and Postdoc Accomplishments
Papers and Reports (Accepted or Published in 2020)*Co first-author
CCIB graduate student
CCIB undergraduate student
CCIB postdoctoral researcher
1. Allred SR, McQuade ST, Merrill NJ, Piccoli B, Spielman D, Villacis C, Whiting R, Yadav A, Zacher, Ziminski D. Regional health system shortfalls with a novel COVID-19 model. 16 Mar 2020. https://rand.camden.rutgers.edu/files/CovidModelAllredMarch16th_technical.pdf
2. An Z, Merrill NJ, Lee K, Robin R, Hayat A, Zapfe O, Piccoli B. A two-step model of human entrainment: a quantitative study of circadian period and phase of entrainment. Bull Math Biol. 2021 Jan 7;83(2):12. doi: 10.1007/s11538-020-00829-5.
3. Bhadra-Lobo S, Kim MK, Lun DS. Assessment of transcriptomic constraint-based methods for central carbon flux inference. PLoS One. 2020 Sep 9;15(9):e0238689. doi: 10.1371/journal.pone.0238689.
4. Blessing B, Trout C, Morales A, Rybacki K, Love SA, Lamoureux G, O’Malley SM, Hu X, Salas-de la Cruz D. The impact of composition and morphology on ionic conductivity of silk/cellulose bio-composites fabricated from ionic liquid and varying percentages of coagulation agents. Int J Mol Sci. 2020 Jun 30;21(13):4695. doi: 10.3390/ijms21134695.
5. Böhm R, Amodeo GF, Murlidaran S, Chavali S, Wagner G, Winterhalter M, Brannigan G, Hiller S. The structural basis for low conductance in the membrane protein VDAC upon β-NADH binding and voltage gating. Structure. 2020 Feb 4;28(2):206-214.e4. doi: 10.1016/j.str.2019.11.015.
6. Borden EA*, Furey M*, Gattone NJ*, Hambardikar VD*, Liang XH*, Scoma ER*, Abou Samra A, D-Gary LR, Dennis DJ, Fricker D, Garcia C, Jiang Z, Khan SA, Kumarasamy D, Kuppala H, Ringrose S, Rosenheim EJ, Van Exel K, Vudhayagiri HS, Zhang J, Zhang Z, Guitart-Mampel M, Urquiza P, Solesio ME. Is there a link between inorganic polyphosphate (polyP), mitochondria, and neurodegeneration? Pharmacol Res. 2020 Oct 1;105211. doi: 10.1016/j.phrs.2020.105211.
7. Ciallella HL*, Russo DP*, Aleksunes LM, Grimm FA, Zhu H. Predictive modeling of estrogen receptor agonism, antagonism, and binding activities using machine- and deep-learning approaches. Lab Invest. 2020. doi: 10.1038/s41374-020-00477-2.
8. de Young KD, Stankeviciute G, Klein EA. Sugar-phosphate metabolism regulates stationary-phase entry and stalk elongation in Caulobacter crescentus. J Bacteriol. 2020 Jan 29;202(4):e00468-19. doi: 10.1128/JB.00468-19.
9. Fu J, Wang Z, Liang XH, Oh SW, St.Iago-McRae E, Zhang T. DNA-scaffolded proximity assembly and confinement of multienzyme reactions. Top Curr Chem (Cham). 2020 Apr 4;378(3):38. doi: 10.1007/s41061-020-0299-3.
10. Gong X, Piccoli B, Visconti G. Mean-field limit of a hybrid system for multi-lane multi-class traffic. arXiv. 2020 Jul 29:2007.14655v1.
11. Grgicak CM, Karkar S, Yearwood-Garcia X, Alfonse LE, Duffy KR, Lun DS. A large-scale validation of NOCIt's a posteriori probability of the number of contributors and its integration into forensic interpretation pipelines. Forensic Sci Int Genet. 2020 Jul;47:102296. doi: 10.1016/j.fsigen.2020.102296.
12. Guan L, Grigoriev A. Age-related Argonaute loading of ribosomal RNA fragments. Microrna. 2020;9(2):142-152. doi: 10.2174/2211536608666190920165705.
13. Guan L, Karaiskos S, Grigoriev A. Inferring targeting modes of Argonaute-loaded tRNA fragments. RNA Biol. 2020 Aug;17(8):1070-1080. doi: 10.1080/15476286.2019.1676633.
14. Gunter G, Gloudemans D, Stern RE, McQuade S, Bhadani R, Bunting M, Monache MLD, Lysecky R, Seibold B, Sprinkle J, Piccoli B, Work DB. Are commercially implemented adaptive cruise control systems string stable? IEEE T Intell Transp. doi: 10.1109/TITS.2020.3000682.
15. Koritala BSC, Wager C, Waters JC, Pachucki R, Piccoli B, Feng Y, Scheinfeldt LB, Shende SM, Park S, Hozier JI, Lalakia P, Kumar D, Lee K. Habitat-specific clock variation and its consequence on reproductive fitness. J Biol Rhythms. 2020 Apr;35(2):134-144. doi: 10.1177/0748730419896486.
16. Love SA, Popov E, Rybacki K, Hu X, Salas-de la Cruz D. Facile treatment to fine-tune cellulose crystals in cellulose-silk biocomposites through hydrogen peroxide. Int J Biol Macromol. 2020 Mar 15;147:569-575. doi: 10.1016/j.ijbiomac.2020.01.100.
17. Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alvarado LHA, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, de la Campa MO, Paredes I, Wheeler B, Rupert A, Sam A, See K, Zapata SS, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic. bioRxiv. 2020 Dec 4:2020.12.01.406637. doi: 10.1101/2020.12.01.406637.
18. McQuade S, Merrill NJ, Piccoli B. Metabolic graphs, LIFE method and the modeling of drug action on Mycobacterium tuberculosis. arXiv. 2020 Mar 26:2003.12400v1.
19. Moorthy S, Byfield FJ, Janmey PA, Klein EA. Matrix stiffness regulates endosomal escape of uropathogenic E. coli. Cell Microbiol. 2020 May;22(5):e13196. doi: 10.1111/cmi.13196.
20. Revaitis NT, Niepielko MG, Marmion RA, Klein EA, Piccoli B, Yakoby N. Quantitative analyses of EGFR localization and trafficking dynamics in the follicular epithelium. Development. 2020 Aug 14;147(15):dev183210. doi: 10.1242/dev.183210. (Featured as Development cover paper)
21. Russo DP, Yan X, Shende S, Huang H, Yan B, Zhu H. Virtual molecular projections and convolutional neural networks for the end-to-end modeling of nanoparticle activities and properties. Anal Chem. 2020 Oct 20;92(20):13971-13979. doi: 10.1021/acs.analchem.0c02878.
22. Sheth N, Swaminathan H, Gonzalez AJ, Duffy KR, Grgicak CM. Towards developing forensically relevant single cell pipelines by incorporating Direct-to-PCR extraction: effects on signal quality and allele dropout. Int J Leg Med. In press.
23. Stevens CA, Revaitis NT, Caur R, Yakoby N. The ETS-transcription factor Pointed is sufficient to regulate the posterior fate of the follicular epithelium. Development. 2020 Nov 15;147(22):dev189787. doi: 10.1242/dev.189787.
24. Wang YT*, Russo DP\*, Liu C, Zhou Q, Zhu H, Zhang YH. Predictive modeling of angiotensin l-converting enzyme inhibitory peptides using various machine learning approaches. J Agric Food Chem. 2020 Oct 28;68(43):12132-12140. doi: 10.1021/acs.jafc.0c04624.
25. Waters JC, Jhaveri D, Biffinger JC, Lee K. Quantitative trait loci (QTL) underlying phenotypic variation in bioethanol-related processes in Neurospora crassa. PLoS One. 2020 Feb 4;15(2):e0221737. doi: 10.1371/journal.pone.0221737.
26. Yan X, Sedykh A, Wang W, Yan B, Zhu H. Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations. Nat Commun. 2020 May 20;11(1):2519. doi: 10.1038/s41467-020-16413-3.
27. Yan X, Zhang J, Russo DP, Zhu H, Yan B. Prediction of nano-bio interactions through convolutional neural network analysis of nanostructure images. ACS Sustainable Chem Eng. 2020. doi: 10.1021/acssuschemeng.0c07453.
28. Zhao L, Ciallella HL, Aleksunes LM, Zhu H. Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. Drug Discov Today. 2020;25(9):1624-1638. doi: 10.1016/j.drudis.2020.07.005.
29. Zhao L, Russo DP, Wang W, Aleksunes LM, Zhu H. Mechanism-driven read-across of chemical hepatotoxicants based on chemical structures and biological data. Toxicol Sci. 2020 Apr 1;174(2):178-188. doi: 10.1093/toxsci/kfaa005.
Meeting Abstracts
*Co first-author
CCIB graduate student
CCIB undergraduate student
CCIB postdoctoral researcher
1. Baenziger JE, Henault CM, Govaerts C, Estrada A, Lynch J, Bertrand D, Pardo E, Evans G, Woods KN, Elberson BW, Cuello LG, Brannigan GH, Nury H, Steyaert J, Ulens C. A lipid recognition site at a transmembrane helix kink shapes the agonist response of a pentameric ligand-gated ion channel. 64th Annual Meeting of the Biophysical Society. San Diego, CA. February 2020.
2. Lohia R, Bassi K, Hansen M, Brannigan G. Disease associated mutations in intrinsically disordered proteins show evidence of enrichment in hydrophobic blobs. 64th Annual Meeting of the Biophysical Society. San Diego, CA. February 2020.
3. Morales A, Blessing B, Rybacki K, Love S, O’Malley S, Hu X, Salas-de la Cruz D. Characterization of silk/cellulose biocomposites infused with rGO. American Physical Society Mid-Atlantic Section Fall Meeting 2020. Virtual. December 2020.
4. Ruzmetov T, Bhadra-Lobo S, Chakravarty D, Lamoureux G. Predicting physical properties of proteins using 3D convolutional neural networks. American Physical Society Mid-Atlantic Section Fall Meeting 2020. Virtual. December 2020.
5. Rybacki K, Bhadra-Lobo S, Lamoureux G, Salas-de la Cruz D. The use of molecular dynamics to understand ion mobility in protein and polysaccharide composites. American Chemical Society Online National Meeting and Expo. Virtual August 2020.
6. Rybacki K, Bhadra-Lobo S, Lamoureux G, Salas-de la Cruz D. The use of molecular dynamics to understand ion mobility in protein and polysaccharide composites. TAFDV Online Poster Competition at the University of Pennsylvania. Virtual. December 2020.
7. Sandberg J, Brannigan G. Coronavirus envelope protein: lipid sensitivity and membrane bending. American Physical Society Mid-Atlantic Section Fall Meeting 2020. Virtual. December 2020.
8. Sharp LM, Woods KN, Brannigan GH. Nicotinic acetylcholine receptors lipid preferences within complex quasi-native membranes. 64th Annual Meeting of the Biophysical Society. San Diego, CA. February 2020.
9. Sheth N, Swaminathan H, Gonzalez AJ, Duffy KR, Grgicak CM. Deconvolution of mixture samples using single-cell techniques for forensic human identification. PITTCON Conference & Expo. Chicago, IL. March 2020.