Selected Publications by SCSB Faculty

Last Updated May 2022


  • Schein CH, Negi SS, Braun W. Still SDAPing Along: 20 Years of the Structural Database of Allergenic Proteins. Front Allergy. 2022 Mar 22;3:863172. doi: 10.3389/falgy.2022.863172.
  • Negi SS, Schein CH, Braun W. Regional and temporal coordinated mutation patterns in SARS-CoV-2 spike protein revealed by a clustering and network analysis. Sci Rep. 2022 Jan 21;12(1):1128. doi: 10.1038/s41598-022-04950-4.
  • Seely SM, Gagnon MG. Mechanisms of ribosome recycling in bacteria and mitochondria: a structural perspective. RNA Biol. 2022;19(1):662-677. doi: 10.1080/15476286.2022.2067712.
  • Yu B, Bien KG, Pletka CC, Iwahara J. Dynamics of Cations around DNA and Protein as Revealed by 23Na Diffusion NMR Spectroscopy. Anal Chem. 2022 Feb 8;94(5):2444-2452. doi: 10.1021/acs.analchem.1c04197.
  • Yu B, Pletka CC, Iwahara J. Protein Electrostatics Investigated through Paramagnetic NMR for Nonpolar Groups. J Phys Chem B. 2022 Mar 24;126(11):2196-2202. doi: 10.1021/acs.jpcb.1c10930.
  • Jacob H, Geng H, Shetty D, Halow N, Kenney LJ, Nakano MM. Distinct Interaction Mechanism of RNA Polymerase and ResD at Proximal and Distal Subsites for Transcription Activation of Nitrite Reductase in Bacillus subtilis. J Bacteriol. 2022 Feb 15;204(2):e0043221. doi: 10.1128/JB.00432-21.
  • Nussinov R, Jang H, Nir G, Tsai CJ, Cheng F. Open Structural Data in Precision Medicine. Annu Rev Biomed Data Sci. 2022 Apr 28. doi: 10.1146/annurev-biodatasci-122220-012951.
  • Nussinov R, Jang H, Nir G, Tsai CJ, Cheng F. A new precision medicine initiative at the dawn of exascale computing. Signal Transduct Target Ther. 2021 Jan 6;6(1):3. doi: 10.1038/s41392-020-00420-3.
  • Chen C, Yu B, Yousefi R, Iwahara J, Pettitt BM. Assessment of the Components of the Electrostatic Potential of Proteins in Solution: Comparing Experiment and Theory. J Phys Chem B. 2022 Jun 13. doi: 10.1021/acs.jpcb.2c01611.
  • Chen C, Pettitt BM. The Effects of Flexibility on dsDNA–dsDNA Interactions. Life. 2022;12(5):699; doi: 10.3390/life12050699.
  • Dutta AK, Sepuru KM, Rösgen J, Rajarathnam K. Characterizing Thermodynamics of Protein-Glycosaminoglycan Interactions Using Isothermal Titration Calorimetry. Methods Mol Biol. 2022;2303:307-317. doi: 10.1007/978-1-0716-1398-6_25.
  • Joseph PRB, Sepuru KM, Poluri KM, Rajarathnam K. Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions. Methods Mol Biol. 2022;2303:13-23. doi: 10.1007/978-1-0716-1398-6_2.
  • Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem. 2022 Apr 9;298(5):101924. doi: 10.1016/j.jbc.2022.101924.
  • Wang S, Sotcheff SL, Gallardo CM, Jaworski E, Torbett BE, Routh AL. Covariation of viral recombination with single nucleotide variants during virus evolution revealed by CoVaMa. Nucleic Acids Res. 2022 Jan 8:gkab1259. doi: 10.1093/nar/gkab1259.
  • Oh D, Chen Z, Biswas KH, Bai F, Ong HT, Sheetz MP, Groves JT. Competition for shared downstream signaling molecules establishes indirect negative feedback between EGFR and EphA2. Biophys J. 2022 May 17;121(10):1897-1908. doi: 10.1016/j.bpj.2022.04.015.
  • Wang YH, Ho TLF, Hariharan A, Goh HC, Wong YL, Verkaik NS, Lee MY, Tam WL, van Gent DC, Venkitaraman AR, Sheetz MP, Lane DP. Rapid recruitment of p53 to DNA damage sites directs DNA repair choice and integrity. Proc Natl Acad Sci U S A. 2022 Mar 8;119(10):e2113233119. doi: 10.1073/pnas.2113233119.
  • Yang YA, Nguyen E, Sankara Narayana GHN, Heuzé M, Fu C, Yu H, Mège RM, Ladoux B, Sheetz MP. Local contractions regulate E-cadherin rigidity sensing. Sci Adv. 2022 Jan 28;8(4):eabk0387. doi: 10.1126/sciadv.abk0387.
  • Fang FF, Shi PY. Omicron: a drug developer's perspective. Emerg Microbes Infect. 2022 Dec;11(1):208-211. doi: 10.1080/22221751.2021.2023330.
  • Liu Y, Liu J, Johnson BA, Xia H, Ku Z, Schindewolf C, Widen SG, An Z, Weaver SC, Menachery VD, Xie X, Shi PY. Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant. Cell Rep. 2022 May 17;39(7):110829. doi: 10.1016/j.celrep.2022.110829.
  • Xia H, Zou J, Kurhade C, Cai H, Yang Q, Cutler M, Cooper D, Muik A, Jansen KU, Xie X, Swanson KA, Shi PY. Neutralization and durability of 2 or 3 doses of the BNT162b2 vaccine against Omicron SARS-CoV-2. Cell Host Microbe. 2022 Apr 13;30(4):485-488.e3. doi: 10.1016/j.chom.2022.02.015.
  • Liu J, Liu Y, Xia H, Zou J, Weaver SC, Swanson KA, Cai H, Cutler M, Cooper D, Muik A, Jansen KU, Sahin U, Xie X, Dormitzer PR, Shi PY. BNT162b2-elicited neutralization of Delta plus, Lambda, Mu, B.1.1.519, and Theta SARS-CoV-2 variants. NPJ Vaccines. 2022 Apr 8;7(1):41. doi: 10.1038/s41541-022-00462-4.
  • Liu Y, Liu J, Shi PY. SARS-CoV-2 variants and vaccination. Zoonoses (Burlingt). 2022;2(1):6. doi: 10.15212/zoonoses-2022-0001.
  • Zou J, Xia H, Xie X, Kurhade C, Machado RRG, Weaver SC, Ren P, Shi PY. Neutralization against Omicron SARS-CoV-2 from previous non-Omicron infection. Nat Commun. 2022 Feb 9;13(1):852. doi: 10.1038/s41467-022-28544-w.
  • Fang FF, Shi PY. Omicron: a drug developer's perspective. Emerg Microbes Infect. 2022 Dec;11(1):208-211. doi: 10.1080/22221751.2021.2023330.
  • Hsu CW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Tang H, Zhang K, Sowers LC. Measurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase. J Biol Chem. 2022 Mar;298(3):101638. doi: 10.1016/j.jbc.2022.101638.
  • Wilson C, Mertens TC, Shivshankar P, Bi W, Collum SD, Wareing N, Ko J, Weng T, Naikawadi RP, Wolters PJ, Maire P, Jyothula SS, Thandavarayan RA, Ren D, Elrod ND, Wagner EJ, Huang HJ, Dickey BF, Ford HL, Karmouty-Quintana H. Sine oculis homeobox homolog 1 plays a critical role in pulmonary fibrosis. JCI Insight. 2022 May 23;7(10):e142984. doi:10.1172/jci.insight.142984.
  • LaForce GR, Farr JS, Liu J, Akesson C, Gumus E, Pinkard O, Miranda HC, Johnson K, Sweet TJ, Ji P, Lin A, Coller J, Philippidou P, Wagner EJ, Schaffer AE. Suppression of premature transcription termination leads to reduced mRNA isoform diversity and neurodegeneration. Neuron. 2022 Feb 4:S0896-6273(22)00057-5. doi: 10.1016/j.neuron.2022.01.018.
  • Dimet-Wiley A, Golovko G, Watowich SJ. One-Year Postfracture Mortality Rate in Older Adults With Hip Fractures Relative to Other Lower Extremity Fractures: Retrospective Cohort Study. JMIR Aging. 2022 Mar 16;5(1):e32683. doi: 10.2196/32683.
  • Murach KA, Dimet-Wiley AL, Wen Y, Brightwell CR, Latham CM, Dungan CM, Fry CS, Watowich SJ. Late-life exercise mitigates skeletal muscle epigenetic aging. Aging Cell. 2022 Jan;21(1):e13527. doi: 10.1111/acel.13527.
  • Azar SR, Campos RK, Yun R, Strange T, Rossi SL, Hanley KA, Vasilakis N, Weaver SC. Aedes aegypti Shows Increased Susceptibility to Zika Virus via Both In Vitro and In Vivo Models of Type II Diabetes. Viruses. 2022 Mar 23;14(4):665. doi: 10.3390/v14040665.
  • Liu Y, Liu J, Plante KS, Plante JA, Xie X, Zhang X, Ku Z, An Z, Scharton D, Schindewolf C, Widen SG, Menachery VD, Shi PY, Weaver SC. The N501Y spike substitution enhances SARS-CoV-2 infection and transmission. Nature. 2022 Feb;602(7896):294-299. doi: 10.1038/s41586-021-04245-0.
  • Nielsen MC, Machado RRG, Mitchell BM, McConnell AJ, Saada NI, Weaver SC, Ren P. A Comparison of Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV Assays with Spike Gene Sequencing for Detection of Known Severe Acute Respiratory Syndrome Coronavirus 2 Variants. J Mol Diagn. 2022 Feb 24:S1525-1578(22)00040-X. doi: 10.1016/j.jmoldx.2022.02.001.
  • Weldon CT, Weaver SC, Jacobsen KH. Impact of COVID-19 on the Vector-Borne Disease Research and Applied Public Health Workforce in the United States. Am J Trop Med Hyg. 2022 Feb 22:tpmd211340. doi: 10.4269/ajtmh.21-1340.
  • Clark LE, Clark SA, Lin C, Liu J, Coscia A, Nabel KG, Yang P, Neel DV, Lee H, Brusic V, Stryapunina I, Plante KS, Ahmed AA, Catteruccia F, Young-Pearse TL, Chiu IM, Llopis PM, Weaver SC, Abraham J. VLDLR and ApoER2 are receptors for multiple alphaviruses. Nature. 2022 Feb;602(7897):475-480. doi:10.1038/s41586-021-04326-0. 
  • Park J, Baruch-Torres N, Iwai S, Herrmann GK, Brieba LG, Yin YW. Human Mitochondrial DNA Polymerase Metal Dependent UV Lesion Bypassing Ability. Front Mol Biosci. 2022 Mar 9;9:808036. doi: 10.3389/fmolb.2022.808036.