2022 Biophysics Student Publications

2022 Publications:

Li MD, Ahmed SR, Choy E, Lozano-Calderon SA, Kalpathy-Cramer J, Chang CY. Artificial intelligence applied to musculoskeletal oncology: a systematic review. Skeletal Radiol. 2022 Feb;51(2):245-256.

Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. 2022. Multiscale profiling of protease activity in cancer. Nat Commun. 13(1):5745.

Sankari S, Babu VMP, Bian K, Alhhazmi A, Andorfer MC, Avalos DM, Smith TA, Yoon K, Drennan CL, Yaffe MB, Lourido S, Walker GC. 2022. A haem-sequestering plant peptide promotes iron uptake in symbiotic bacteria. Nat Microbiol. 7(9):1453-1465.

Nicol PB, Barabási DL, Coombes KR, Asiaee A. 2022. SITH: An R package for visualizing and analyzing a spatial model of intratumor heterogeneity. Comput Syst Oncol. 2(2):e1033.

Bergal HT, Jiang Y, Yang D, Springer TA, Wong WP.  2022. Conformation of von Willebrand factor in shear flow revealed with stroboscopic single-molecule imaging. Blood. 140(23):2490-2499.

Gabriele M*, Brandão HB*, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh TS, Mirny L, Zechner C, Hansen AS. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. Science. 2022 Apr 29;376(6592):496-501. (*contributed equally).

Dequeker BJH, Scherr MJ, Brandão HB, Gassler J, Powell S, Gaspar I, Flyamer IM, Lalic A, Tang W, Stocsits R, Davidson IF, Peters JM, Duderstadt KE, Mirny LA, Tachibana K. MCM complexes are barriers that restrict cohesin-mediated loop extrusion. Nature. 2022 Jun;606(7912):197-203.

Tian F, Cheng Y, Zhou S, Wang Q, Monavarfeshani A, Gao K, Jiang W, Kawaguchi R, Wang Q, Tang M, Donahue R, Meng H, Zhang Y, Jacobi A, Yan W, Yin J, Cai X, Yang Z, Hegarty S, Stanicka J, Dmitriev P, Taub D, Zhu J, Woolf CJ, Sanes JR, Geschwind DH, He Z. Core transcription programs controlling injury-induced neurodegeneration of retinal ganglion cells. Neuron. 2022 Aug 17;110(16):2607-2624.e8.

Hauser BM, Sangesland M, St Denis KJ, Lam EC, Case JB, Windsor IW, Feldman J, Caradonna TM, Kannegieter T, Diamond MS, Balazs AB, Lingwood D, Schmidt AG. 2022. Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting. Cell Rep. 38(12):110561.

Nanishi E, Borriello F, O'Meara TR, McGrath ME, Saito Y, Haupt RE, Seo HS, van Haren SD, Cavazzoni CB, Brook B, Barman S, Chen J, Diray-Arce J, Doss-Gollin S, De Leon M, Prevost-Reilly A, Chew K, Menon M, Song K, Xu AZ, Caradonna TM, Feldman J, Hauser BM, Schmidt AG, Sherman AC, Baden LR, Ernst RK, Dillen C, Weston SM, Johnson RM, Hammond HL, Mayer R, Burke A, Bottazzi ME, Hotez PJ, Strych U, Chang A, Yu J, Sage PT, Barouch DH, Dhe-Paganon S, Zanoni I, Ozonoff A, Frieman MB, Levy O, Dowling DJ. 2022.  An aluminum hydroxide:CpG adjuvant enhances protection elicited by a SARS-CoV-2 receptor binding domain vaccine in aged mice. Sci Transl Med. 14(629):eabj5305.

Caradonna TM, Ronsard L, Yousif AS, Windsor IW, Hecht R, Bracamonte-Moreno T, Roffler AA, Maron MJ, Maurer DP, Feldman J, Marchiori E, Barnes RM, Rohrer D, Lonberg N, Oguin TH 3rd, Sempowski GD, Kepler TB, Kuraoka M, Lingwood D, Schmidt AG. 2022. An epitope-enriched immunogen expands responses to a conserved viral site. Cell Rep. 41(6):111628.

Chapman AR, Lee DF, Cai W, Ma W, Li X, Sun W, Xie XS. 2022. Correlated gene modules uncovered by high-precision single-cell transcriptomics. Proc Natl Acad Sci USA. 119(51):e2206938119.

Klein V, Coll-Font J, Vendramini L, Straney D, Davids M, Ferris NG, Schad LR, Sosnovik DE, Nguyen CT, Wald LL, Guérin B. 2022. Measurement of magnetostimulation thresholds in the porcine heart. Magn Reson Med. 88(5):2242-2258.

Guo Y, Amir A. 2022. The effect of weak clonal interference on average fitness trajectories in the presence of macroscopic epistasis. Genetics. 220(4):iyac028.

Larson RC, Kann MC, Bailey SR, Haradhvala NJ, Llopis PM, Bouffard AA, Scarfó I, Leick MB, Grauwet K, Berger TR, Stewart K, Anekal PV, Jan M, Joung J, Schmidts A, Ouspenskaia T, Law T, Regev A, Getz G, Maus MV. 2022. CAR T cell killing requires the IFNγR pathway in solid but not liquid tumours. Nature. 604(7906):563-570.

Metsky HC, Welch NL, Pillai PP, Haradhvala NJ, Rumker L, Mantena S, Zhang YB, Yang DK, Ackerman CM, Weller J, Blainey PC, Myhrvold C, Mitzenmacher M, Sabeti PC. 2022. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol. 40(7):1123-1131.

Haradhvala NJ, Leick MB, Maurer K, Gohil SH, Larson RC, Yao N, Gallagher KME, Katsis K, Frigault MJ, Southard J, Li S, Kann MC, Silva H, Jan M, Rhrissorrakrai K, Utro F, Levovitz C, Jacobs RA, Slowik K, Danysh BP, Livak KJ, Parida L, Ferry J, Jacobson C, Wu CJ, Getz G, Maus MV. 2022. Distinct cellular dynamics associated with response to CAR-T therapy for refractory B cell lymphoma.  Nat Med. 28(9):1848-1859.

Sklavenitis-Pistofidis R, Aranha MP, Redd RA, Baginska J, Haradhvala NJ, Hallisey M, Dutta AK, Savell A, Varmeh S, Heilpern-Mallory D, Ujwary S, Zavidij O, Aguet F, Su NK, Lightbody ED, Bustoros M, Tahri S, Mouhieddine TH, Wu T, Flechon L, Anand S, Rosenblatt JM, Zonder J, Vredenburgh JJ, Boruchov A, Bhutani M, Usmani SZ, Matous J, Yee AJ, Jakubowiak A, Laubach J, Manier S, Nadeem O, Richardson P, Badros AZ, Mateos MV, Trippa L, Getz G, Ghobrial IM. 2022. Immune biomarkers of response to immunotherapy in patients with high-risk smoldering myeloma. Cancer Cell. 40(11):1358-1373.e8.

Boiarsky R, Haradhvala NJ, Alberge JB, Sklavenitis-Pistofidis R, Mouhieddine TH, Zavidij O, Shih MC, Firer D, Miller M, El-Khoury H, Anand SK, Aguet F, Sontag D, Ghobrial IM, Getz G. 2022. Single cell characterization of myeloma and its precursor conditions reveals transcriptional signatures of early tumorigenesis. Nat Commun. 13(1):7040.

Hager, E.R., Harringmeyer, O.S., Wooldridge, T.B., Theingi, S., Gable, J.T., McFadden, S., Neugeboren, B., Turner, K.M., Jensen, J.D., Hoekstra, H.E. 2022. A chromosomal inversion contributes to divergence in multiple traits between deer mouse ecotypes. Science 377(6604):399-405.

Harringmeyer OS, Hoekstra HE. 2022. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat Ecol Evol. 6(12):1965-1979.

Tas JMJ, Koo JH, Lin YC, Xie Z, Steichen JM, Jackson AM, Hauser BM, Wang X, Cottrell CA, Torres JL, Warner JE, Kirsch KH, Weldon SR, Groschel B, Nogal B, Ozorowski G, Bangaru S, Phelps N, Adachi Y, Eskandarzadeh S, Kubitz M, Burton DR, Lingwood D, Schmidt AG, Nair U, Ward AB, Schief WR, Batista FD.  2022. Antibodies from primary humoral responses modulate the recruitment of naive B cells during secondary responses. Immunity. 55(10):1856-1871.e6.

Hauser BM, Feldman J, Sangesland M, Ronsard L, St Denis KJ, Sheehan ML, Cao Y, Boucau J, Windsor IW, Cheng AH, Vu ML, Cardoso MR, Kannegieter T, Balazs AB, Lingwood D, Garcia-Beltran WF, Schmidt AG. 2022. Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design. Cell Rep Med. 3(12):100834. Epub 2022 Nov 15.

Tan CS, Collier AY, Yu J, Liu J, Chandrashekar A, McMahan K, Jacob-Dolan C, He X, Roy V, Hauser BM, Munt JE, Mallory ML, Mattocks M, Powers JM, Meganck RM, Rowe M, Hemond R, Bondzie EA, Jaegle KH, Baric RS, Schmidt AG, Alter G, Le Gars M, Sadoff J, Barouch DH. 2022. Durability of Heterologous and Homologous COVID-19 Vaccine Boosts. JAMA Netw Open. 5(8):e2226335.

Amraei R, Xia C, Olejnik J, White MR, Napoleon MA, Lotfollahzadeh S, Hauser BM, Schmidt AG, Chitalia V, Mühlberger E, Costello CE, Rahimi N. 2022. Extracellular vimentin is an attachment factor that facilitates SARS-CoV-2 entry into human endothelial cells. Proc Natl Acad Sci USA. 119(6):e2113874119.

Hauser BM, Sangesland M, Lam EC, Feldman J, Balazs AB, Lingwood D, Schmidt AG. 2022. Humoral responses to the SARS-CoV-2 spike and receptor binding domain in context of pre-existing immunity confer broad sarbecovirus neutralization. Front Immunol. 13:902260.

Garcia-Beltran WF, St Denis KJ, Hoelzemer A, Lam EC, Nitido AD, Sheehan ML, Berrios C, Ofoman O, Chang CC, Hauser BM, Feldman J, Roederer AL, Gregory DJ, Poznansky MC, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. 2022. mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. Cell. 185(3):457-466.e4.

Hauser BM, Sangesland M, St Denis KJ, Lam EC, Case JB, Windsor IW, Feldman J, Caradonna TM, Kannegieter T, Diamond MS, Balazs AB, Lingwood D, Schmidt AG. 2022. Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting. Cell Rep. 38(12):110561.

Crowdis J, Balch S, Sterlin L, Thomas BS, Camp SY, Dunphy M, Anastasio E, Shah S, Damon AL, Ramos R, Sosa DM, Small IK, Tomson BN, Nguyen CM, McGillicuddy M, Chastain PS, He MX, Cheung ATM, Wankowicz S, Tewari AK, Kim D, AlDubayan SH, Dowdye A, Zola B, Nowak J, Manarite J, Gunn IH, Olson B, Lander ES, Painter CA, Wagle N, Van Allen EM. 2022. A patient-driven clinicogenomic partnership for metastatic prostate cancer. Cell Genom. 2(9):100169.

Ma F, Arai S, Wang K, Calagua C, Yuan AR, Poluben L, Gu Z, Russo JW, Einstein DJ, Ye H, He MX, Liu Y, Van Allen E, Sowalsky AG, Bhasin MK, Yuan X, Balk SP. 2022. Autocrine Canonical Wnt Signaling Primes Noncanonical Signaling through ROR1 in Metastatic Castration-Resistant Prostate Cancer. Cancer Res. 82(8):1518-1533.

Schiantarelli J, Pappa T, Conway J, Crowdis J, Reardon B, Dietlein F, Huang J, Stanizzi D, Carey E, Bosma-Moody A, Imamovic A, Han S, Camp S, Kofman E, Shannon E, Barletta JA, He MX, Liu D, Park J, Lorch JH, Van Allen EM. 2022. Mutational Footprint of Platinum Chemotherapy in a Secondary Thyroid Cancer. JCO Precis Oncol. 6:e2200183.

Liang J, Tran VN, Hemez C, Abel Zur Wiesch P. 2022. Current Approaches of Building Mechanistic Pharmacodynamic Drug-Target Binding Models. Methods Mol Biol. 2385:1-17.

Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel Zur Wiesch P. 2022. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J. 20:4688-4703.

Hodis E*, Torlai Triglia E*, Kwon JYH, Biancalani T, Zakka LR, Parkar S, Hütter JC, Buffoni L, Delorey TM, Phillips D, Dionne D, Nguyen LT, Schapiro D, Maliga Z, Jacobson CA, Hendel A, Rozenblatt-Rosen O, Mihm MC Jr, Garraway LA, Regev A. 2022. Stepwise-edited, human melanoma models reveal mutations' effect on tumor and microenvironment. Science. 376(6592):eabi8175. (* contributed equally)

Gillies JP, Reimer JM, Karasmanis EP, Lahiri I, Htet ZM, Leschziner AE, Reck-Peterson SL. 2022. Structural basis for cytoplasmic dynein-1 regulation by Lis1. Elife. 11:e71229.

Marsh SE, Walker AJ, Kamath T, Dissing-Olesen L, Hammond TR, de Soysa TY, Young AMH, Murphy S, Abdulraouf A, Nadaf N, Dufort C, Walker AC, Lucca LE, Kozareva V, Vanderburg C, Hong S, Bulstrode H, Hutchinson PJ, Gaffney DJ, Hafler DA, Franklin RJM, Macosko EZ, Stevens B. 2022. Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nat Neurosci. 25(3):306-316.

Kamath T*, Abdulraouf A*, Burris SJ, Langlieb J, Gazestani V, Nadaf NM, Balderrama K, Vanderburg C, Macosko EZ. 2022. Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson's disease. Nat Neurosci. 25(5):588-595. (*co-1st authors).

Levine MA, Mandeville JB, Calabro F, Izquierdo-Garcia D, Chonde DB, Chen KT, Hong I, Price JC, Luna B, Catana C. 2022.  Assessment of motion and model bias on the detection of dopamine response to behavioral challenge. J Cereb Blood Flow Metab. 42(7):1309-1321.

Liu, S.*, Iorgulescu, J.B.*, Li, S.*, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. 2022. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity. 55(10):1940-1952.e5. (*co-1st authors).

Lee SY, Parot VJ, Bouma BE, Villiger M. 2022. Confocal 3D reflectance imaging through multimode fiber without wavefront shaping. Optica. 9(1):112-120.

Peter JS, Schuemann J, Held K, McNamara AL. 2022. Nano-scale simulation of neuronal damage by galactic cosmic rays. Phys Med Biol. 67(23).

Odstrcil I, Petkova MD, Haesemeyer M, Boulanger-Weill J, Nikitchenko M, Gagnon JA, Oteiza P, Schalek R, Peleg A, Portugues R, Lichtman JW, Engert F. 2022. Functional and ultrastructural analysis of reafferent mechanosensation in larval zebrafish. Curr Biol. 32(1):176-189.e5.

Seyboldt R, Lavoie J, Henry A, Vanaret J, Petkova MD, Gregor T, François P. 2022. Latent space of a small genetic network: Geometry of dynamics and information. Proc Natl Acad Sci USA. 119(26):e2113651119.

Chang S, Thrall ES, Laureti L, Piatt SC, Pagès V, Loparo JJ. 2022. Compartmentalization of the replication fork by single-stranded DNA-binding protein regulates translesion synthesis. Nat Struct Mol Biol. 29(9):932-941. 

Thrall ES, Piatt SC, Chang S, Loparo JJ. 2022. Replication stalling activates SSB for recruitment of DNA damage tolerance factors. Proc Natl Acad Sci USA. 119(41):e2208875119.

Jang A, Petrova B, Cheong TC, Zawadzki ME, Jones JK, Culhane AJ, Shipley FB, Chiarle R, Wong ET, Kanarek N, Lehtinen MK. 2022. Choroid plexus-CSF-targeted antioxidant therapy protects the brain from toxicity of cancer chemotherapy. Neuron. 110(20):3288-3301.e8.

Blaeser AS, Sugden AU, Zhao J, Carneiro-Nascimento S, Shipley FB, Carrié H, Andermann ML, Levy D. 2022. Trigeminal afferents sense locomotion-related meningeal deformations. Cell Rep. 41(7):111648.

Bergman DT, Jones TR, Liu V, Ray J, Jagoda E, Siraj L, Kang HY, Nasser J, Kane M, Rios A, Nguyen TH, 2022. Grossman SR, Fulco CP, Lander ES, Engreitz JM. Compatibility rules of human enhancer and promoter sequences. Nature. 607(7917):176-184.

Liu R, Paz M, Siraj L, Boyd T, Salamone S, Lite TV, Leung KM, Chirinos JD, Shang HH, Townsend MJ, Rho J, Ni P, Ranganath K, Violante AD, Zhao Z, Silvernale C, Ahmad I, Krasnow NA, Barnett ES, Harisinghani M, Kuo B, Black KE, Staller K.  2022. Feeding intolerance in critically ill patients with COVID-19. Clin Nutr. 41(12):3069-3076.

Gupta A, Martin-Rufino JD, Jones TR, Subramanian V, Qiu X, Grody EI, Bloemendal A, Weng C, Niu SY, Min KH, Mehta A, Zhang K, Siraj L, Al' Khafaji A, Sankaran VG, Raychaudhuri S, Cleary B, Grossman S, Lander ES. 2022. Inferring gene regulation from stochastic transcriptional variation across single cells at steady state. Proc Natl Acad Sci USA. 119(34):e2207392119.

Anahtar M, Chan LW, Ko H, Rao A, Soleimany AP, Khatri P, Bhatia SN. 2022. Host protease activity classifies pneumonia etiology. Proc Natl Acad Sci USA. 119(25):e2121778119.

Bekdemir A, Tanner EEL, Kirkpatrick J, Soleimany AP, Mitragotri S, Bhatia SN. 2022. Ionic Liquid-Mediated Transdermal Delivery of Thrombosis-Detecting Nanosensors. Adv Healthc Mater. 11(11):e2102685.

Soleimany AP, Martin-Alonso C, Anahtar M, Wang CS, Bhatia SN. 2022. Protease Activity Analysis: A Toolkit for Analyzing Enzyme Activity Data. ACS Omega. 7(28):24292-24301.

Kirkpatrick JD, Soleimany AP, Dudani JS, Liu HJ, Lam HC, Priolo C, Henske EP, Bhatia SN. 2022. Protease activity sensors enable real-time treatment response monitoring in lymphangioleiomyomatosis. Eur Respir J. 59(4):2100664.

Choi YS, Erlich TH, von Franque M, Rachmin I, Flesher JL, Schiferle EB, Zhang Y, Pereira da Silva M, Jiang A, Dobry AS, Su M, Germana S, Lacher S, Freund O, Feder E, Cortez JL, Ryu S, Babila Propp T, Samuels YL, Zakka LR, Azin M, Burd CE, Sharpless NE, Liu XS, Meyer C, Austen WG Jr, Bojovic B, Cetrulo CL Jr, Mihm MC, Hoon DS, Demehri S, Hawryluk EB, Fisher DE.  2022. Topical therapy for regression and melanoma prevention of congenital giant nevi. Cell. 185(12):2071-2085.e12.

Özkale B, Lou J, Özelçi E, Elosegui-Artola A, Tringides CM, Mao AS, Sakar MS, Mooney DJ.  2022. Actuated 3D microgels for single cell mechanobiology. Lab Chip. 22(10):1962-1970. (Erratum 2022. 22(18):3565-3566.)

Tringides CM, Mooney DJ. 2022. Materials for Implantable Surface Electrode Arrays: Current Status and Future Directions. Adv Mater. 34(20):e2107207.

Vining KH, Marneth AE, Adu-Berchie K, Grolman JM, Tringides CM, Liu Y, Wong WJ, Pozdnyakova O, Severgnini M, Stafford A, Duda GN, Hodi FS, Mullally A, Wucherpfennig KW, Mooney DJ. 2022. Mechanical checkpoint regulates monocyte differentiation in fibrotic niches. Nat Mater. 21(8):939-950.

Nabel KG, Clark SA, Shankar S, Pan J, Clark LE, Yang P, Coscia A, McKay LGA, Varnum HH, Brusic V, Tolan NV, Zhou G, Desjardins M, Turbett SE, Kanjilal S, Sherman AC, Dighe A, LaRocque RC, Ryan ET, Tylek C, Cohen-Solal JF, Darcy AT, Tavella D, Clabbers A, Fan Y, Griffiths A, Correia IR, Seagal J, Baden LR, Charles RC, Abraham J.  2022. Structural basis for continued antibody evasion by the SARS-CoV-2 receptor binding domain. Science. 375(6578):eabl6251. Erratum in: Science. 2024 Feb 9;383(6683):eado3845.

Gaglia G, Kabraji S, Rammos D, Dai Y, Verma A, Wang S, Mills CE, Chung M, Bergholz JS, Coy S, Lin JR, Jeselsohn R, Metzger O, Winer EP, Dillon DA, Zhao JJ, Sorger PK, Santagata S. 2022. Temporal and spatial topography of cell proliferation in cancer. Nat Cell Biol. 24(3):316-326.

Coy S, Wang S, Stopka SA, Lin JR, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G, Regan M, Khadka P, Cole KA, Hwang J, Wen PY, Bandopadhayay P, Santi M, De Raedt T, Ligon KL, Agar NYR, Sorger PK, Touat M, Santagata S. 2022. Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Nat Commun. 13(1):4814.

Ding D, Green AG, Wang B, Lite TV, Weinstein EN, Marks DS, Laub MT. 2022. Co-evolution of interacting proteins through non-contacting and non-specific mutations. Nat Ecol Evol. 6(5):590-603.

Weinstein EN, Amin AN, Grathwohl WS, Kassler D, Disset J, Marks DS. 2022. Optimal design of stochastic DNA synthesis protocols based on generative sequence models. Proceedings of The 25th International Conference on Artificial Intelligence and Statistics, PMLR 151:7450-7482.

Weinstein EN*, Amin AN*, Frazer J, Marks DS. 2022. Non-identifiability and the blessings of misspecification in models of molecular fitness and phylogeny. Advances in Neural Information Processing Systems (NeurIPS). Proceedings of the 36th Conference on Neural Information Processing Systems 2022. (*Equal contribution)

Weisman CM, Murray AW, Eddy SR. 2022. Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes. Curr Biol. 32(12):2632-2639.e2.

Gordon KS, Kyung T, Perez CR, Holec PV, Ramos A, Zhang AQ, Agarwal Y, Liu Y, Koch CE, Starchenko A, Joughin BA, Lauffenburger DA, Irvine DJ, Hemann MT, Birnbaum ME. 2022. Screening for CD19-specific chimaeric antigen receptors with enhanced signaling via a barcoded library of intracellular domains. Nat Biomed Eng. 6(7):855-866.