2023 Biophysics Student Publications

2023 Publications:

Gidwani M, Chang K, Patel JB, Hoebel KV, Ahmed SR, Singh P, Fuller CD, Kalpathy-Cramer J. Inconsistent Partitioning and Unproductive Feature Associations Yield Idealized Radiomic Models. Radiology. 2023 Apr;307(1):e220715.

Ahmed SR, Jenabi M, Gene M, Moreno R, Peck KK, Holodny A. Power spectral analysis can determine language laterality from resting-state functional MRI data in healthy controls. J Neuroimaging. 2023 Jul-Aug;33(4):661-670.

Ahmed SR, Befano B, Lemay A, Egemen D, Rodriguez AC, Angara S, Desai K, Jeronimo J, Antani S, Campos N, Inturrisi F, Perkins R, Kreimer A, Wentzensen N, Herrero R, Del Pino M, Quint W, de Sanjose S, Schiffman M, Kalpathy-Cramer J. Reproducible and clinically translatable deep neural networks for cervical screening. Sci Rep. 2023 Dec 8;13(1):21772.

Kim AE, Lou KW, Giobbie-Hurder A, Chang K, Gidwani M, Hoebel K, Patel JB, Cleveland MC, Singh P, Bridge CP, Ahmed SR, Bearce BA, Liu W, Fuster-Garcia E, Lee EQ, Lin NU, Overmoyer B, Wen PY, Nayak L, Cohen JV, Dietrich J, Eichler A, Heist R, Krop I, Lawrence D, Ligibel J, Tolaney S, Mayer E, Winer E, Perrino CM, Summers EJ, Mahar M, Oh K, Shih HA, Cahill DP, Rosen BR, Yen YF, Kalpathy-Cramer J, Martinez-Lage M, Sullivan RJ, Brastianos PK, Emblem KE, Gerstner ER. Structural and functional vascular dysfunction within brain metastases is linked to pembrolizumab inefficacy. bioRxiv [Preprint]. 2023 Aug 28:2023.08.25.554868.

Perkins RB, Smith DL, Jeronimo J, Campos NG, Gage JC, Hansen N, Rodriguez AC, Cheung LC, Egemen D, Befano B, Novetsky AP, Martins S, Kalpathy-Cramer J, Inturrisi F, Ahmed SR, Marcus J, Wentzensen N, de Sanjose S, Schiffman M. Use of risk-based cervical screening programs in resource-limited settings. Cancer Epidemiol. 2023 Jun;84:102369.

Aldama LA, Dalton KM, Hekstra DR. 2023. Correcting systematic errors in diffraction data with modern scaling algorithms. Acta Crystallogr D Struct Biol. 79(Pt 9):796-805.

Aung A, Cui A, Maiorino L, Amini (Soleimany) AP, Gregory JR, Bukenya M, Zhang Y, Lee H, Cottrell CA, Morgan DM, Silva M, Suh H, Kirkpatrick JD, Amlashi P, Remba T, Froehle LM, Xiao S, Abraham W, Adams J, Love JC, Huyett P, Kwon DS, Hacohen N, Schief WR, Bhatia SN, Irvine DJ. 2023. Low protease activity in B cell follicles promotes retention of intact antigens after immunization. Science. 379(6630):eabn8934.

Barabási DL, Beynon T, Katona Á, Perez-Nieves N. 2023. Complex computation from developmental priors. Nat Commun. 14(1):2226.

Barabási DL, Bianconi G, Bullmore E, Burgess M, Chung S, Eliassi-Rad T, George D, Kovács IA, Makse H, Nichols TE, Papadimitriou C, Sporns O, Stachenfeld K, Toroczkai Z, Towlson EK, Zador AM, Zeng H, Barabási AL, Bernard A, Buzsáki G. 2023. Neuroscience Needs Network Science. J Neurosci. 43(34):5989-5995.

Hummels KR, Berry SP, Li Z, Taguchi A, Min JK, Walker S, Marks DS, Bernhardt TG. 2023. Coordination of bacterial cell wall and outer membrane biosynthesis. Nature. 615(7951):300-304.

Ray S, Berry SP, Wilson EA, Zhang CH, Shekhar M, Singharoy A, Gaudet R. 2023. High-resolution structures with bound Mn²⁺ and Cd²⁺ map the metal import pathway in an Nramp transporter. Elife. 2023 Apr 11;12:e84006.

Bitran A, Park K, Serebryany E, Shakhnovich EI. 2023. Co-translational formation of disulfides guides folding of the SARS-CoV-2 receptor binding domain. Biophys J. 122(16):3238-3253.

Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. 2023. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Mol Cell. 83(11):1936-1952.e7.

Vaccaro FA, Faber DA, Andree GA, Born DA, Kang G, Fonseca DR, Jost M, Drennan CL. 2023. Structural insight into G-protein chaperone-mediated maturation of a bacterial adenosylcobalamin-dependent mutase. J Biol Chem. 299(9):105109.

Vaccaro FA, Born DA, Drennan CL. 2023. Structure of metallochaperone in complex with the cobalamin-binding domain of its target mutase provides insight into cofactor delivery. Proc Natl Acad Sci USA. 120(8):e2214085120.

Polovnikov KE, Slavov B, Belan S, Imakaev M, Brandão HB, Mirny LA. Crumpled polymer with loops recapitulates key features of chromosome organization. Phys Rev X. 2023 Oct-Dec;13(4):041029.

Yang JH, Brandão HB, Hansen AS. DNA double-strand break end synapsis by DNA loop extrusion. Nat Commun. 2023 Apr 6;14(1):1913.

Banigan EJ, Tang W, van den Berg AA, Stocsits RR, Wutz G, Brandão HB, Busslinger GA, Peters JM, Mirny LA. Transcription shapes 3D chromatin organization by interacting with loop extrusion. Proc Natl Acad Sci USA. 2023 Mar 14;120(11):e2210480120.

Ronsard L, Yousif AS, Nait Mohamed FA, Feldman J, Okonkwo V, McCarthy C, Schnabel J, Caradonna T, Barnes RM, Rohrer D, Lonberg N, Schmidt A, Lingwood D. 2023. Engaging an HIV vaccine target through the acquisition of low B cell affinity. Nat Commun.14(1):5249.

Yang L, Caradonna TM, Schmidt AG, Chakraborty AK. 2023. Mechanisms that promote the evolution of cross-reactive antibodies upon vaccination with designed influenza immunogens. Cell Rep. 42(3):112160.

Nanishi E, Borriello F, Seo HS, O'Meara TR, McGrath ME, Saito Y, Chen J, Diray-Arce J, Song K, Xu AZ, Barman S, Menon M, Dong D, Caradonna TM, Feldman J, Hauser BM, Schmidt AG, Baden LR, Ernst RK, Dillen C, Yu J, Chang A, Hilgers L, Platenburg PP, Dhe-Paganon S, Barouch DH, Ozonoff A, Zanoni I, Frieman MB, Dowling DJ, Levy O. 2023. Carbohydrate fatty acid monosulphate: oil-in-water adjuvant enhances SARS-CoV-2 RBD nanoparticle-induced immunogenicity and protection in mice. NPJ Vaccines. 8(1):30. Erratum for: NPJ Vaccines. Publisher Correction: 2023 Feb 14;8(1):18.

Deng Z, Chen AY, Zakeri B, Zhong C, Lu TK. 2023. Full-colour Jabuticaba-like nanostructures via the multiplex and orthogonal self-assembly of protein-conjugated quantum dots with engineered biofilms. Mater Horiz. 10(4):1440-1445.

Klein V, Davids M, Vendramini L, Ferris NG, Schad LR, Sosnovik DE, Nguyen CT, Wald LL, Guérin B. 2023. Prediction of experimental cardiac magnetostimulation thresholds using pig-specific body models. Magn Reson Med. 90(4):1594-1609.

Greenfield DA, Feizpour A, Evans CL. 2023. Quantifying Inflammatory Response and Drug-Aided Resolution in an Atopic Dermatitis Model with Deep Learning. J Invest Dermatol. 143(8):1430-1438.e4.

Gopinathan KA, Mishra A, Mutlu BR, Edd JF, Toner M. 2023. A microfluidic transistor for automatic control of liquids. Nature. 622(7984):735-741.

Da Silveira Cavalcante L, Lopera Higuita M, González-Rosa JM, Marques B, To S, Pendexter CA, Cronin SEJ, Gopinathan K, de Vries RJ, Ellett F, Uygun K, Langenau DM, Toner M, Tessier SN. 2023. Zebrafish as a high throughput model for organ preservation and transplantation research. FASEB J. 37(10):e23187. Erratum in: PMID: 37718489; PMCID: PMC10754348.

Fok A, Brissette B, Hallacy T, Ahamed H, Ho E, Ramanathan S, Ringstad N. 2023. High-fidelity encoding of mechanostimuli by tactile food-sensing neurons requires an ensemble of ion channels. Cell Rep. 2023 May 30;42(5):112452.

Wuo MG, Dugan AE, Halim M, Hauser BM, Feldman J, Caradonna TM, Zhang S, Pepi LE, Atyeo C, Fischinger S, Alter G, Garcia-Beltran WF, Azadi P, Hung D, Schmidt AG, Kiessling LL. 2023. Lectin Fingerprinting Distinguishes Antibody Neutralization in SARS-CoV-2. ACS Cent Sci. 9(5):947-956.

Doe-Tetteh SA, Camp SY, Reales D, Crowdis J, Noronha AM, Wolff B, Alano T, Galle J, Selcuklu SD, Viale A, Socci ND, Liu YL, Tew WP, Aghajanian C, Ladanyi M, He MX, AlDubayan SH, Mazor RD, Shpilberg O, Hershkovitz-Rokah O, Riancho JA, Hernandez JL, Gonzalez-Vela MC, Buthorn JJ, Wilson M, Webber AE, Yabe M, Petrova-Drus K, Rosenblum M, Durham BH, Abdel-Wahab O, Berger MF, Donoghue MTA, Kung AL, Glade Bender J, Shukla NN, Funt SA, Dogan A, Soslow RA, Al-Ahmadie H, Feldman DR, Van Allen EM, Diamond EL, Solit DB. 2023. Overcoming Barriers to Tumor Genomic Profiling through Direct-to-Patient Outreach. Clin Cancer Res. 2023 29(13):2445-2455.

Martinecz A, Boeree MJ, Diacon AH, Dawson R, Hemez C, Aarnoutse RE, Abel Zur Wiesch P. 2023. High rifampicin peak plasma concentrations accelerate the slow phase of bacterial decline in tuberculosis patients: Evidence for heteroresistance. PLoS Comput Biol. 19(4):e1011000.

Jackson JA, Imran Alsous J, Martin AC. 2023. Live Imaging of Nurse Cell Behavior in Late Stages of Drosophila Oogenesis. Methods Mol Biol. 2626:219-232.

Jackson JA, Romeo N, Mietke A, Burns KJ, Totz JF, Martin AC, Dunkel J, Alsous JI. 2023. Scaling behaviour and control of nuclear wrinkling. Nat Phys. 19(12):1927-1935. PMID: 38831923; PMCID: PMC11146749.

Salazar-Martín AG*, Kalluri AS*, Villanueva MA, Hughes TK, Wadsworth MH 2nd, Dao TT, Balcells M, Nezami FR, Shalek AK, Edelman ER. 2023. Single-Cell RNA Sequencing Reveals That Adaptation of Human Aortic Endothelial Cells to Antiproliferative Therapies Is Modulated by Flow-Induced Shear Stress. Arterioscler Thromb Vasc Biol. 43(12):2265-2281. (*co-1st authors).

Gazestani V, Kamath T, Nadaf NM, Dougalis A, Burris SJ, Rooney B, Junkkari A, Vanderburg C, Pelkonen A, Gomez-Budia M, Välimäki NN, Rauramaa T, Therrien M, Koivisto AM, Tegtmeyer M, Herukka SK, Abdulraouf A, Marsh SE, Hiltunen M, Nehme R, Malm T, Stevens B, Leinonen V, Macosko EZ. 2023. Early Alzheimer's disease pathology in human cortex involves transient cell states. Cell. 186(20):4438-4453.e23.

Dolan MJ, Therrien M, Jereb S, Kamath T, Gazestani V, Atkeson T, Marsh SE, Goeva A, Lojek NM, Murphy S, White CM, Joung J, Liu B, Limone F, Eggan K, Hacohen N, Bernstein BE, Glass CK, Leinonen V, Blurton-Jones M, Zhang F, Epstein CB, Macosko EZ, Stevens B. 2023. Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat Immunol. 24(8):1382-1390.

Kamath T, Macosko EZ. 2023. Insights into Neurodegeneration in Parkinson's Disease from Single-Cell and Spatial Genomics. Mov Disord. 38(4):518-525.

Maury EA, Sherman MA, Genovese G, Gilgenast TG, Kamath T, Burris SJ, Rajarajan P, Flaherty E, Akbarian S, Chess A, McCarroll SA, Loh PR, Phillips-Cremins JE, Brennand KJ, Macosko EZ, Walters JTR, O'Donovan M, Sullivan P; Psychiatric Genomic Consortium Schizophrenia and CNV workgroup; Brain Somatic Mosaicism Network; Sebat J, Lee EA, Walsh CA. 2023. Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions. Cell Genom. 3(8):100356.

Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nat Commun. 14(1):8328.

Kimchi O, Brenner MP, Colwell LJ. 2023. Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User's Guide to the LandscapeFold Algorithm. Methods Mol Biol. 2586:49-77.

Kimchi O, King EM, Brenner MP. 2023. Uncovering the mechanism for aggregation in repeat expanded RNA reveals a reentrant transition. Nat Commun. 14(1):332.

Mizes KGC, Lindsey J, Escola GS, Ölveczky BP. 2023. Dissociating the contributions of sensorimotor striatum to automatic and visually guided motor sequences. Nat Neurosci. 26(10):1791-1804.

Tian H, Davis HC, Wong-Campos JD, Park P, Fan LZ, Gmeiner B, Begum S, Werley CA, Borja GB, Upadhyay H, Shah H, Jacques J, Qi Y, Parot V, Deisseroth K, Cohen AE. 2023. Video-based pooled screening yields improved far-red genetically encoded voltage indicators. Nat Methods. 20(7):1082-1094Erratum in: Nat Methods. 20(3):469.

Nikolić M, Antonetti V, Liu F, Muhaxheri G, Petkova MD, Scheeler M, Smith EM, Bialek W, Gregor T. 2023. Scale invariance in early embryonic development. Natl Acad Sci USA. 121(46):e2403265121.

Ruben BS, Brahmachari S, Contessoto VG, Cheng RR, Oliveira Junior AB, Di Pierro M, Onuchic JN. 2023. Structural reorganization and relaxation dynamics of axially stressed chromosomes. Biophys J. 122(9):1633-1645.

Sedlak JC, Yilmaz ÖH, Roper J. 2023.  Metabolism and Colorectal Cancer. Annu Rev Pathol. 18:467-492.

Sadegh C, Xu H, Sutin J, Fatou B, Gupta S, Pragana A, Taylor M, Kalugin PN, Zawadzki ME, Alturkistani O, Shipley FB, Dani N, Fame RM, Wurie Z, Talati P, Schleicher RL, Klein EM, Zhang Y, Holtzman MJ, Moore CI, Lin PY, Patel AB, Warf BC, Kimberly WT, Steen H, Andermann ML, Lehtinen MK. 2023. Choroid plexus-targeted NKCC1 overexpression to treat post-hemorrhagic hydrocephalus. Neuron. 111(10):1591-1608.e4.

Fame RM, Kalugin PN, Petrova B, Xu H, Soden PA, Shipley FB, Dani N, Grant B, Pragana A, Head JP, Gupta S, Shannon ML, Chifamba FF, Hawks-Mayer H, Vernon A, Gao F, Zhang Y, Holtzman MJ, Heiman M, Andermann ML, Kanarek N, Lipton JO, Lehtinen MK. 2023. Defining diurnal fluctuations in mouse choroid plexus and CSF at high molecular, spatial, and temporal resolution. Nat Commun. 14(1):3720.

Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. 2023. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun. 14(1):3439.

Midonet C, Bisset S, Shlosman I, Cava F, Rudner DZ, Bernhardt TG. 2023. MacP bypass variants of Streptococcus pneumoniae PBP2a suggest a conserved mechanism for the activation of bifunctional cell wall synthases. mBio. 14(6):e0239023.

Duvall JB, Massaad E, Siraj L, Kiapour A, Connolly I, Hadzipasic M, Elsamadicy AA, Williamson T, Shankar GM, Schoenfeld AJ, Fourman MS, Shin JH. 2023. Assessment of Spinal Metastases Surgery Risk Stratification Tools in Breast Cancer by Molecular Subtype. Neurosurgery. 92(1):83-91.

Fourman MS, Siraj L, Duvall J, Ramsey DC, De La Garza Ramos R, Hadzipasic M, Connolly I, Williamson T, Shankar GM, Schoenfeld A, Yassari R, Massaad E, Shin JH. 2023. Can We Use Artificial Intelligence Cluster Analysis to Identify Patients with Metastatic Breast Cancer to the Spine at Highest Risk of Postoperative Adverse Events? World Neurosurg. 174:e26-e34.

McNulty R, Sritharan D, Pahng SH, Meisch JP, Liu S, Brennan MA, Saxer G, Hormoz S, Rosenthal AZ. 2023. Probe-based bacterial single-cell RNA sequencing predicts toxin regulation. Nat Microbiol. 8(5):934-945.

Elosegui-Artola A, Gupta A, Najibi AJ, Seo BR, Garry R, Tringides CM, de Lázaro I, Darnell M, Gu W, Zhou Q, Weitz DA, Mahadevan L, Mooney DJ. 2023. Matrix viscoelasticity controls spatiotemporal tissue organization. Nat Mater. 22(1):117-127.

Tringides CM, Boulingre M, Khalil A, Lungjangwa T, Jaenisch R, Mooney DJ. 2023. Tunable Conductive Hydrogel Scaffolds for Neural Cell Differentiation. Adv Healthc Mater. Adv Healthc Mater. 12(7):e2202221.

Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK. 2023. Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Cell. 186(2):363-381.e19.

Weinstein EN, Miller. JW. 2023. Bayesian data selection. Journal of Machine Learning Research. 24(23):1−72.

Zhang AQ, Hostetler A, Chen LE, Mukkamala V, Abraham W, Padilla LT, Wolff AN, Maiorino L, Backlund CM, Aung A, Melo M, Li N, Wu S, Irvine DJ. 2023. Universal redirection of CAR T cells against solid tumours via membrane-inserted ligands for the CAR. Nat Biomed Eng. 7(9):1113-1128.