2024 Biophysics Student Publications

2024 Publications:

Egemen D, Perkins RB, Cheung LC, Befano B, Rodriguez AC, Desai K, Lemay A, Ahmed SR, Antani S, Jeronimo J, Wentzensen N, Kalpathy-Cramer J, De Sanjose S, Schiffman M. Artificial intelligence-based image analysis in clinical testing: lessons from cervical cancer screening. J Natl Cancer Inst. 2024 Jan 10;116(1):26-33.

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. Abnormal vascular structure and function within brain metastases is linked to pembrolizumab resistance. Neuro Oncol. 2024 May 3;26(5):965-974.

Ahmed SR, Egemen D, Befano B, Rodriguez AC, Jeronimo J, Desai K, Teran C, Alfaro K, Fokom-Domgue J, Charoenkwan K, Mungo C, Luckett R, Saidu R, Raiol T, Ribeiro A, Gage JC, de Sanjose S, Kalpathy-Cramer J, Schiffman M. Assessing generalizability of an AI-based visual test for cervical cancer screening. PLOS Digit Health. 2024 Oct 2;3(10):e0000364.

de Sanjosé S, Perkins RB, Campos N, Inturrisi F, Egemen D, Befano B, Rodriguez AC, Jerónimo J, Cheung LC, Desai K, Han P, Novetsky AP, Ukwuani A, Marcus J, Ahmed SR, Wentzensen N, Kalpathy-Cramer J, Schiffman M; PAVE Study Group. Design of the HPV-automated visual evaluation (PAVE) study: Validating a novel cervical screening strategy. Elife. 2024 Jan 15;12:RP91469.

Lorenzo G, Ahmed SR, Hormuth DA, Vaughn B, Kalpathy-Cramer J, Solorio L, Yankeelov TE, Gomez H. Patient-Specific, Mechanistic Models of Tumor Growth Incorporating Artificial Intelligence and Big Data. Annu Rev Biomed Eng. 2024 Jul;26(1):529-560.

Abitua PB, Stump LM*, Aksel DC*, Schier AF. 2024. Axis formation in annual killifish: Nodal and β-catenin regulate morphogenesis without Huluwa prepatterning. Science. 384(6700):1105-1110. PMID: 38843334.  (*contributed equally).

Barabási DL*, Schuhknecht GFP*, Engert F. 2024. Functional neuronal circuits emerge in the absence of developmental activity. Nat Commun. 15(1):364. (*co-1st authors).

Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter JF, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. 2024. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nat Struct Mol Biol. 31(4):667-677.

Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. Structure. 2024 Sep 5;32(9):1528-1543.e3.

Marchant JK*, Ferris NG*, Grass D, Allen MS, Gopalakrishnan V, Olchanyi M, Sehgal D, Sheft M, Strom A, Bilgic B, Edlow B, Hillman EMC, Juttukonda MR, Lewis L, Nasr S, Nummenmaa A, Polimeni JR, Tootell RBH, Wald LL, Wang H, Yendiki A, Huang SY, Rosen BR, Gollub RL. Mesoscale Brain Mapping: Bridging Scales and Modalities in Neuroimaging - A Symposium Review. Neuroinformatics. 2024 Oct;22(4):679-706. (*co-1st authors).

Ferris NG, Klein V, Guerin B, Wald LL, Davids M. Influence of peripheral axon geometry and local anatomy on magnetostimulation chronaxie. J Neural Eng. 2024;21(3):10.1088/1741-2552/ad510a. Published 2024 Jun 11. PMID: 38806036 PMCID: PMC11228960 (available on 2025-06-11).

Souque C, González Ojeda I, Baym M. 2024. From Petri Dishes to Patients to Populations: Scales and Evolutionary Mechanisms Driving Antibiotic Resistance. Annu Rev Microbiol. 2024 Aug 14. doi: 10.1146/annurev-micro-041522-102707. Epub ahead of print. PMID: 39141706.

Peidli S*, Green TD*, Shen C, Gross T, Min J, Garda S, Yuan B, Schumacher LJ, Taylor-King JP, Marks DS, Luna A, Blüthgen N, Sander C. 2024. scPerturb: harmonized single-cell perturbation data. Nat Methods. 21(3):531-540. (*co-1st authors).

Kingsley EP, Hager ER, Lassance JM, Turner KM, Harringmeyer OS, Kirby C, Neugeboren BI, Hoekstra HE. 2024. Adaptive tail-length evolution in deer mice is associated with differential Hoxd13 expression in early development. Nat Ecol Evol. 8(4):791-805.

Sousa AA, Hemez C, Lei L, Traore S, Kulhankova K, Newby GA, Doman JL, Oye K, Pandey S, Karp PH, McCray PB Jr, Liu DR. 2024. Systematic optimization of prime editing for the efficient functional correction of CFTR F508del in human airway epithelial cells. Nat Biomed Eng. 2024 Jul 10. doi: 10.1038/s41551-024-01233-3. Epub ahead of print. PMID: 38987629.

Kulhankova K, Cheng AX, Traore S, Auger M, Pelletier M, Hervault M, Wells KD, Green JA, Byrne A, Nelson B, Sponchiado M, Boosani C, Heffner CS, Snow KJ, Murray SA, Villacreses RA, Rector MV, Gansemer ND, Stoltz DA, Allamargot C, Couture F, Hemez C, Hallée S, Barbeau X, Harvey M, Lauvaux C, Gaillet B, Newby GA, Liu DR, McCray PB Jr, Guay D. 2024. Amphiphilic shuttle peptide delivers base editor ribonucleoprotein to correct the CFTR R553X mutation in well-differentiated airway epithelial cells. Nucleic Acids Res. 2024 Sep 24:gkae819. doi: 10.1093/nar/gkae819. Epub ahead of print. PMID: 39315713.

Kusakci E, Htet ZM, Zhao Y, Gillies JP, Reck-Peterson SL, Yildiz A. 2024. Lis1 slows force-induced detachment of cytoplasmic dynein from microtubules. Nat Chem Biol. 20(4):521-529.

Jackson JA, Denk-Lobnig M, Kitzinger KA, Martin AC. 2024. Change in RhoGAP and RhoGEF availability drives transitions in cortical patterning and excitability in Drosophila. Curr Biol. 2024 May 20;34(10):2132-2146.e5.

Brissette B, Ficaro L, Li C, Jones DR, Ramanathan S, Ringstad N. 2024. Chemosensory detection of polyamine metabolites guides C. elegans to nutritive microbes. Sci Adv. 10(12):eadj4387.

Cho SE, Li W, Beard AM, Jackson JA, Kiernan R, Hoshino K, Martin AC, Sun J. 2024. Actomyosin contraction in the follicular epithelium provides the major mechanical force for follicle rupture during Drosophila ovulation. Proc Natl Acad Sci USA. (39):e2407083121. PMID: 39292751; PMCID: PMC11441566.

Li Q, Sorscher B, Sompolinsky H. 2024. Representations and generalization in artificial and brain neural networks. Proc Natl Acad Sci USA. 121(27):e2311805121.

Russell AJC, Weir JA, Nadaf NM, Shabet M, Kumar V, Kambhampati S, Raichur R, Marrero GJ, Liu S, Balderrama KS, Vanderburg CR, Shanmugam V, Tian L, Iorgulescu JB, Yoon CH, Wu CJ, Macosko EZ, Chen F. 2024. Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. Nature. 625(7993):101-109. Erratum for: Nature. Publisher’s Correction. 2024 Jan;625(7993):101-109.

Wang S, Shin TW, Yoder HB 2nd, McMillan RB, Su H, Liu Y, Zhang C, Leung KS, Yin P, Kiessling LL, Boyden ES. 2024. Single-shot 20-fold expansion microscopy. Nat Methods. 2024 Oct 11. doi: 10.1038/s41592-024-02454-9. Epub ahead of print. PMID: 39394503.

Misra P, Shih Y-C, Yu H-Y, Weisholtz D, Madsen JR, Sceillig S, Kreiman G. 2024. Invariant neural representation of parts of speech in the human brain. bioRxiv 2024.01.15.575788.

Kock KH, Kimes PK, Gisselbrecht SS, Inukai S, Phanor SK, Anderson JT, Ramakrishnan G, Lipper CH, Song D, Kurland JV, Rogers JM, Jeong R, Blacklow SC, Irizarry RA, Bulyk ML. 2024. DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nat Commun. 2024 15(1):3110.

Xu H, Lotfy P, Gelb S, Pragana A, Hehnly C, Byer LIJ, Shipley FB, Zawadzki ME, Cui J, Deng L, Taylor M, Webb M, Lidov HGW, Andermann ML, Chiu IM, Ordovas-Montanes J, Lehtinen MK. 2024. The choroid plexus synergizes with immune cells during neuroinflammation. Cell. 187(18):4946-4963.e17. PMID: 39089253; PMCID: PMC11458255.

Tringides CM, Mooney DJ. 2024. Conductive Hydrogel Scaffolds for the 3D Localization and Orientation of Fibroblasts. Macromol Biosci. 24(1):e2300044.

Najibi AJ, Lane RS, Sobral MC, Bovone G, Kang S, Freedman BR, Gutierrez Estupinan J, Elosegui-Artola A, Tringides CM, Dellacherie MO, Williams K, Ijaz H, Müller S, Turley SJ, Mooney DJ. 2024. Durable lymph-node expansion is associated with the efficacy of therapeutic vaccination. Nat Biomed Eng. 2024 Oct;8(10):1226-1242.

Tringides CM, Boulingre M, Mooney DJ. 2024. Metal-based porous hydrogels for highly conductive biomaterial scaffolds. Oxf Open Mater Sci. 3(1):itad002.

Li W, Plante JA, Lin C, Basu H, Plung JS, Fan X, Boeckers JM, Oros J, Buck TK, Anekal PV, Hanson WA, Varnum H, Wells A, Mann CJ, Tjang LV, Yang P, Reyna RA, Mitchell BM, Shinde DP, Walker JL, Choi SY, Brusic V, Llopis PM, Weaver SC, Umemori H, Chiu IM, Plante KS, Abraham J. 2024. Shifts in receptors during submergence of an encephalitic arbovirus. Nature. 632(8025):614-621. PMID: 39048821; PMCID: PMC11324528.

Yang P, Li W, Fan X, Pan J, Mann CJ, Varnum H, Clark LE, Clark SA, Coscia A, Basu H, Smith KN, Brusic V, Abraham J. 2024. Structural basis for VLDLR recognition by eastern equine encephalitis virus. Nat Commun. 15(1):6548. PMID: 39095394; PMCID: PMC11297306.

Hewitt RA, Dalton KM, Mendez DA, Wang HK, Klureza MA, Brookner DE, Greisman JB, McDonagh D, Šrajer V, Sauter NK, Brewster AS, Hekstra DR. 2024. Laue-DIALS: Open-source software for polychromatic x-ray diffraction data. Struct Dyn. 11(5):054701. PMID: 39386198; PMCID: PMC11462730.

Yang HY, Leahy BD, Jang WD, Wei D, Kalma Y, Rahav R, Carmon A, Kopel R, Azem F, Venturas M, Kelleher CP, Cam L, Pfister H, Needleman DJ, Ben-Yosef D. 2024. BlastAssist: a deep learning pipeline to measure interpretable features of human embryos. Hum Reprod. 39(4):698-708.

Ziegler CGK, Owings AH, Galeas-Pena M, Kazer SW, Miao VN, Navia AW, Tang Y, Bromley JD, Lotfy P, Sloan M, Laird H, Williams HB, George M, Drake RS, Pride Y, Abraham GE 3rd, Senitko M, Robinson TO, Diamond G, Lionakis MS, Shalek AK, Ordovas-Montanes J, Horwitz BH, Glover SC. 2024. An enhanced IL17 and muted type I interferon nasal epithelial cell state characterizes severe COVID-19 with fungal coinfection. Microbiol Spectr. 2024 Jun 4;12(6):e0351623.