Student Publications

Recent First Author Papers

(^indicates the student has defended)

2026

Andrew Montequin^ (LaBonne) Dynamic and non-uniform expression of key transcription factors provides insights into the emergence of neural crest cells at the neural plate border. Montequin A, LaBonne C. Development. 2026 Feb 15;153(4):dev2025254. doi: 10.1242/dev.205254. Epub 2026 Feb 20. PMID: 41718037

Alana Caldwell (X. Zhang) Emerging biologic modalities for targeted protein degradation. Caldwell AG, Parmar H, Zhang X. J Biol Chem. 2026 Feb 4;302(3):111248. doi: 10.1016/j.jbc.2026.111248. Online ahead of print. PMID: 41651431

Alana Caldwell (X. Zhang) Systematic Characterization of Cancer-Associated SPOP Mutants Reveals Novel and Reprogrammable Degradative Activities. Caldwell AG, Parmar H, Jin X, Zhou C, Zhang X. Chembiochem. 2026 Jan;27(1):e202500914. doi: 10.1002/cbic.202500914. PMID: 41532714. Free PMC article.

Bingxian Xu^ (Braun) VIST: variational inference for single cell time series. Xu B, Braun R. Genome Biol. 2026 Jan 15. doi: 10.1186/s13059-025-03874-2. Online ahead of print. PMID: 41535949. No abstract available.

2025

Daniel Kranz (Klein) Identification of a glia-associated amyloid β oligomer subtype and the rescue from reactive astrogliosis by inhibitor NU-9. Kranz DL, de Leon Velez O, Ulupinar E, Ozdinler PH, Silverman RB, Klein WL. Alzheimers Dement. 2025 Dec;21(12):e70968. doi: 10.1002/alz.70968. PMID: 41410237

Karlin Compton (LaBonne) WDR5 and Myc cooperate to regulate formation of neural crest stem cells. Compton K, Barter E, LaBonne C. Development. 2025 Dec 29:dev.205204. doi: 10.1242/dev.205204. Online ahead of print. PMID: 41459783 

Jack Sumner (Hartmann) Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression. Sumner JT, Huttelmaier S, Pickens CI, Moghadam AA, Abdala-Valencia H, Shen J; NU SCRIPT Study Investigators; Hauser AR, Seed PC, Wunderink RG, Hartmann EM. Cell Host Microbe. 2025 Dec 10;33(12):2148-2166.e8. doi: 10.1016/j.chom.2025.11.011. PMID: 41380668  

Jacob Miller (Tullman-Ercek) Self-Assembling Protein Materials with Genetically Programmable Morphology and Size. Miller JB, Abrahamson C, Lee MFS, Palmero BJ, Kennedy N, Mills CE, Tullman-Ercek D. ACS Nano. 2025 Nov 21. doi: 10.1021/acsnano.5c12294. Online ahead of print. PHID: 41268919.

Shiqi Liang (Tullman-Ercek) Synthetic Rewiring of Virus-like Particles via Circular Permutation Enables Modular Peptide Display and Protein Encapsulation. Liang S, Butaney K, de Castro Assumpção D, Jung J, Kennedy NW, Tullman-Ercek D. ACS Nano. 2025 Nov 18;19(45):39180. doi: 10.1021/acsnano.5c12293. Epub 2025 Oct 29. PMID: 41159643.

Xavier Anderson (Petersen) Planarian microtubules form a network within muscle and regulate injury-induced genes essential for regeneration patterning. Anderson XN, Petersen CP. Development. 2025 Oct 15;152(20):dev204669. doi: 10.1242/dev.204669. Epub 2025 Oct 16. PMID: 41099309.

Timothy (Young Jun) Kim (Mirkin) Inverse Design of DNA-Programmable Protein Colloidal Crystals. Han Z, Kim YJ, Mirkin CA. Journal of the American Chemical Society. Article ASAP DOI: 10.1021/jacs.5c15424.

Timothy (Young Jun) Kim (Mirkin) Cleavable Hydrophobic Anchors Optimize Immunomodulatory Effects of Oligonucleotides. Taokun Luo, Young Jun Kim, Alex Cushing, Yinglun Ma, Zhenyu Han, Ryan E. Johnson, Mia J. P. Pascall, and Chad A. Mirkin. Journal of the American Chemical Society. Article ASAP DOI: 10.1021/jacs.5c15110.

Omar Payán Parra^ (Yang) Cohesin regulation of genome organization in mature granule neurons in the mouse cerebellum. Payán Parra OA, Zhao Z, Yamada T, Yang Y. Epigenetics Chromatin. 2025 Sep 26;18(1):60. doi: 10.1186/s13072-025-00625-2. PMID: 41013693.

Brian Stevens (Petersen) Injury-induced Neuregulin-EGFR signaling from muscle mobilizes stem cells for whole-body regeneration in acoels. Stevens B, Popp R, Valera H, Krueger K, Petersen CP. Dev Biol. 2025 Sep 6;528:105-116. doi: 10.1016/j.ydbio.2025.08.024. Online ahead of print. PMID: 40921377.

Juhi Narula^ (Wignall) PLK-1 suppresses centrosome maturation and microtubule polymerization to ensure faithful oocyte meiosis. Narula JG, Wignall SM. J Cell Bio. 2025 Sep 1;224(9):e202503080.

Stephenie Droll^ (Bao) A dominant SRCAP truncating mutation promotes squamous cell carcinoma progression. Droll SH, Dewar EIO, Xue C, Levine MC, Zhang BJ, Bao X. Oncogenesis. 2025 Aug 26;14(1):33. doi: 10.1038/s41389-025-00576-z. PMID: 40858549; PMCID: PMC12381255.

Stephenie Droll^ (Bao) Skin Epidermal Progenitor Maintenance by the SRCAP-H2A.Z Axis Downstream to Extracellular Signal-Regulated Kinase and mTOR Signaling. Droll SH, Xue C, Dewar EIO, Chamberlain NK, Zhang BJ, Levine MC, Bao X. J Invest Dermatol. 2025 Aug 12:S0022-202X(25)02333-4. doi: 10.1016/j.jid.2025.07.022. Epub ahead of print. PMID: 40812470.

Eleanor Degen (Blythe) Bicoid-nucleosome competition sets a concentration threshold for transcription constrained by genome replication. Degen EA, Croslyn C, Mangan NM, Blythe SA. Cell Rep. 2025 Aug 26;44(8):116121. doi: 10.1016/j.celrep.2025.116121. Epub 2025 Aug 6. PMID: 40779393; PMCID: PMC12425142.

Citlayi Villaseñor (Kamat) Assessing Protein-Lipid Interactions with a Low-Cost, Accessible Centrifugation Assay. Villaseñor CG, Karagiaridi A, Dimitrova VS, Buyco DG, Candal I, Smirnova A, Pinkett HW, Kamat NP. Biophys Rep (NY). 2025 Jul 25:100224. doi: 10.1016/j.bpr.2025.100224. Online ahead of print. PMID: 40716612

Nicolas Scrutton Alvarado^ (Yang) Reorganization of the heterochromatin-associated gene-dense subcompartment in early neuronal development. Scrutton Alvarado NJ, Zhao Z, Yamada T, Yang Y. Biol Open. 2025 May 15;14(5):bio062005.

Sara Rigney^ (LaBonne) Krüppel-like factors play essential roles in regulating pluripotency and the formation of neural crest stem cells. Rigney S, York JR, LaBonne C. Development. 2025 May 1;152(9):dev204634. 

Taojunfeng Su (Kelleher) Proteoform-predictor: Increasing the Phylogenetic Reach of Top-Down Proteomics. Su T, Fellers RT, Greer JB, LeDuc RD, Thomas PM, Kelleher NL. Journal of Proteome Research. 2025 Apr 10. 24(4), 1861-1870.

Brett Palmero^ (Tullman-Ercek) Encapsulation of Select Violacein Pathway Enzymes in the 1,2-Propanediol Utilization Bacterial Microcompartment to Divert Pathway Flux. Palmero BJ, Gamero E, Mangan NM, Tullman-Ercek D. Metab Eng. 2025 Apr 3:S1096-7176(25)00053-9.

Tiffany Ge^ (Brickner) Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex. Ge T, Brickner DG, Zehr K, VanBelzen DJ, Zhang W, Caffalette C, Ungerleider S, Marcou N, Chait B, Rout MP, Brickner JH. Mol Cell. 2025 Mar 20;85(6):1101-1116.e8.

Caroline Bond (Meade) Gli pathway-targeted Co(lll) Schiff base complexes inhibit migration of basal cell carcinoma cells. Bond CE, Olson KD, Punar M, Friedman LB, Tang JH, Luo M, Bailey MD, Holmgren RA, Meade TJ. RSC Adv. 2025 Mar 19;15(11):8572-8579.

Katherine Lo^ (Petersen) map3k1 suppresses terminal differentiation of migratory eye progenitors in planarian regeneration. Lo KC, Petersen CP. PLoS Genet. 2025 Mar 17;21(3):e1011457.

Matthew Capek^ (Gallio) Evolution of temperature preference in flies of the genus Drosophila. Capek M, Arenas OM, Alpert MH, Zaharieva EE, Méndez-González ID, Simões JM, Gil H, Acosta A, Su Y, Para A, and Gallio M. Nature. 2025 Mar 5;Online ahead of print.

William Corcoran^ (Leonard) Exploring structure-function relationships in engineered receptor performance using computational structure prediction. Corcoran WK, Cosio A, Edelstein HI, Leonard JN. GEN Biotechnol. 2025 Feb;4(1):37-55. doi: 10.1089/genbio.2024.0057. Epub 2025 Feb 17. PMID: 40831913; PMCID: PMC12360184.

David Bushhouse (Lucks) RNA folding kinettcs control riboswitch sensitivity in vivo. Bushhouse DZ, Fu J, and Lucks JB. Nat. Commun. 2025 Jan 22;16(1):953.

Frank Tucci^ (Rosenzweig) Structures of methane and ammonia monooxygenases in native membranes. Tucci FJ, Rosenzweig AC. Proc. Natl. Acad. Sci. USA. 2025 Jan 7;122(1):e2417993121.

2024

Brett Wisniewski^ (Lackner) Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA. Wisniewski BT, Casler JC, and Lackner LL. Mol. Biol. Cell. 2024 Dec 1;35(12):br25.

Jake VanBelzen^ (Brickner) Chromatin endogenous cleavage provides a global view of yeast RNA polymerase II transcription kinetics. VanBelzen J, Sakelaris B, Brickner DG, Marcou N, Riecke H, Mangen NM, and Brickner JH. Elife. 2024 Nov 28:13:RP10076.

Feihong Xu (Amaral) Robust extraction of pneumonia-associated clinical states from electronic health records. Xu F, Morales FL, and Amaral LAN. Proc. Natl. Acad. Sci. USA. 2024 Nov 5;121(45):e24176889121.

Bingxian Xu^ (Braun) Detecting Rhythmic Gene Expression in Single-Cell Transcriptomics. Xu B, Ma D, Abruzzi K, and Braun R. J. Biol. Rhythms. 2024 Oct 8:7487304241273182.

Moneeza Agha (McLean) Cell-type-specific origins of locomotor rhythmicity at different speeds in larval zebrafish. Agha MA, Kishore S, and McLean DL. Elife. 2024 Sept 17;RP94349.

Emily Czajkowski^ (Wignall) The doublecortin-family kinase ZYG-8DCLK1 regulates microtubule dynamics and motor-driven forces to promote the stability of C. elegans acentrosomal spindles. Czajkowski ER, Zou Y, Divekar NS, and Wignall SM. PLoS Genet. 2024 Sept 3;20(9):e1011373.

Reyvin Reyes (Rosenzweig) Methanobactins: Structures, Biosynthesis, and Microbial Diversity. Reyvin RM and Rosenzweig AC. Annu. Rev. Microbiol. 2024 Aug 9;Online ahead of print.

Eduardo Campos Chavez (Mondragón) Translational T-box riboswitces bind tRNA by modulating conformational flexibility. Campos-Chavez E, Sneha P, Zhou Z, Alonso D, Verma AR, Fei J, and Mondragón A. Nat Commun. 2024 Aug 3;15(1):6592.

Reyvin Reyes (Rosenzweig) Purification and biochemical characterization of methanobactin biosynthetic enzymes. Reyes RM and Rosenzweig AC. Methods Enzymol. 2024 July 14;702:701-187.

Andrew Liu (Carthew) Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila. Liu A, O'Connell J, Wall F, and Carthew RW. eLife. 2024 June 06;RP91572

Bingxian Xu^ (Braun) Temperature-driven coordination of circadion transcriptional regulation. Xu B, Hwangbo DS, Saurabh S, Rosensweig C, Allada R, Kath WL, and Braun R. PLOS Computational Biology. 2024 April 22;online ahead of print.

Tiffany Ge^ (Brickner) Inheritance of epigenetic transcriptional memory. Ge T and Brickner JH. Current Opinion in Genetics & Development. 2024 April;(2024)85:102174

Laura Hertz (Lucks) The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch. Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, and Lucks JB. Nucleic Acids Research. 2024 April 1;gkae21

Reese Richardson^ (Amaral) Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results. Richardson R, Navarro HT, Amaral LA, and Stoeger T. eLife. 2024 March 28;online ahead of print.

Emily Pujadas^ (Backman) Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependant mechanism. Pujadas EM, Wei X, Acosta N, Carter L, Yang J, Almassalha LM, Jain S, Daneshkhah A, Rao SSR, Seker-Polat F,  MacQuarrie KL, Ibarra H, Agrawal V, Aiden EL, Kanemaki MT,  Backman V, and Adli M. Genome Biology. 2024 March 22;(2024)25:77

Stephenie Droll^ (Bao) CASZ1 Is Essential for Skin Epidermal Terminal Differentiation. Droll SH, Zhang BJ, Levine MC, Xue C, Ho PJ, and Bao X. Journal of Investigative Dermatology. 2024 March 6;online ahead of print.

Jake VanBelzen^ (Brickner) ChEC-seq2: an improved chromatin endogenoud cleavage sequencing method and bioinformatic analysis pipeline for mapping in vivo protein-DNA interactions. VanBelzen J, Duan C, Brickner DG, and Brickner JH. NAR Genom. Bioinform. 2024 Feb 7;6(1):lqae012.

Patric Ho^ (Bao) Multi-omics integration identifies cell-state-specific repression by PBRM1-PIAS1 cooperation. Ho PJ, Kweon J, Blumensaadt LA, Neely AE, Kalika E, Leon DB, Oh S, Stringer CWP, Lloyd SM, Ren Z, and Bao X. Cell Genomics. 2024 January 10;4(1):100471.

Kristen Rivera (Pinkett) Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae. Rivera KG, Tanaka KJ, Buechel ER, Origel O, Harrison A, Mason KM, and Pinkett HW. Biochemistry. 2024 January 8:online ahead of print.

2023

Ely Contreras (Schmidt) Melanopsin activates divergent phototransduction pathways in intrinsically photosensitive retinal ganglion cell subtypes. Contreras E, Bhoi JD, Sonoda T, Birnbaumer L, and Schmidt TM. eLife. 2023 November 8;12:e80749.

Jungsoo Park^ (Mirkin) Enhancing Endosomal Escape and Gene Regulation Activity for Spherical Nucleic Acids. Park J, Evangelopoulos M, Vasher MK, Kudruk S, Ramani N, Mayer V, Solivan AC, Lee A, and Mirkin CA. Small. 2023 November 6:online ahead of print.

Genevieve Jouandet^ (Gallio) Rapid threat assessment in the Drosophila thermosensory system. Jouandet GC, Alpert MH, Simões JM, Suhendra R, Frank DD, Levy JI, Para A, Kath WL, and Gallio M. Nature Communications. 2023 November 3;14:7067.

Katherine Berman^ (Lucks) A transient intermediate RNA structure underlies the regulatory function of the E. coli thiB TPP translational riboswitch. Berman KE, Steans R, Hertz LM, and Lucks JB. RNA. 2023 November;29(11):1658-1672.

Evan Buechel^ (Pinkett) Activity of the pleiotropic drug resistance transcription factors Pdr1p and Pdr3p is modulated by binding site flanking sequences. Buechel ER and Pinkett HW. FEBS Letters. 2023 October 24:online ahead of print.

Krishna Paranandi (Mirkin) Cellular Export Fate of Liposomal Spherical Nucleic Acids. Paranandi KS, Lee A, Stanic N, and Mirkin CA. ACS Nano. 2023 October 10;17(19):19000-19010.

Clare Harper^ (Lackner) Temporal control of contact site formation reveals a relationship between mitochondrial division and Num1-mediated mitochondrial tethering. Harper CS, Casler JC, and Lackner LL. Molecular Biology of the Cell. 2023 October 1;34(11):ar108.

Alex Vogt (He) Structure and mechanism in non-homologous end joining. Vogt A and He Y. DNA Repair. 2023 October;130:103547.

Eleanor Clark (Petersen) BMP suppresses WNT to integrate patterning of orthogonal body axes in adult planarians. Clark EG and Petersen CP. PLoS Genetics. 2023 September 20;19(9):e1010608.

Anna Talyzina^ (He) Structural basis of TFIIIC-dependent RNA polymerase III transcription initiation. Talyzina A, Han Y, Banerjee C, Fishbain S, Reyes A, Vafabakhsh R, and He Y. Molecular Cell. 2023 August 3;83(15):2641-2652.e7.

Taojunfeng Su (Kelleher) Identification of Splice Variants and Isoforms in Transcriptomics and Proteomics. Su T, Hollas MAR, Fellers RT, and Kelleher NL. Annual Review of Biomedical Data Science. 2023 August;6:357-376.

Amy Neely^ (Bao) NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization. Neely AE, Blumensaadt LA, Ho PJ, Lloyd SM, Kweon J, Ren Z, and Bao X. Communications Biology. 2023 June 23;6:664.

Simrita Deol^ (Leonard) Comparative Evaluation of Synthetic Cytokines for Enhancing Production and Performance of NK92 Cell-Based Therapies. Deol S, Donahue PS, Mitrut RE, Hammitt-Kess IJ, Ahn J, Zhang B, and Leonard JN. GEN Biotechnology. 2023 June;2(3):228-246.

Ariel Thames^ (Jewett) GlycoCAP: A Cell-Free, Bacterial Glycosylation Platform for Building Clickable Azido-Sialoglycoproteins. Thames AH, Moons SJ, Wong DA, Boltje TJ, Bochner BS, and Jewett MC. ACS Synthetic Biology. 2023 April 21;12(4):1264-1274.

David Bushhouse (Lucks) Tuning strand displacement kinetics enables programmable ZTP riboswitch dynamic range in vivo. Bushhouse DZ and Lucks JB. Nucleic Acids Research. 2023 April 11;51(6):2891-2903.

Julie Liang^ (Tullman-Ercek) Construction of a constitutively active type III secretion system for heterologous protein secretion. Liang JM, Burdette LA, Wong HT, and Tullman-Ercek D. Applied Microbiology and Biotechnology. 2023 March;107(5-6):1785-1800.

Lauren Adams^ (Kelleher) Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling. Adams LM, DeHart CJ, Drown BS, Anderson LC, Bocik W, Boja ES, Hiltke TM, Hendrickson CL, Rodriguez H, Caldwell M, Vafabakhsh R, and Kelleher NL. Journal of Biological Chemistry. 2023 January;299(1):102768.