Student Publications

Recent First Author Papers

(^indicates the student has defended)

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.

David Gittin^ (Petersen) A Wnt11 and Dishevelled signaling pathway acts prior to injury to control wound polarization for the onset of planarian regeneration. Gittin DI and Petersen CP. Current Biology. 2022 December 19;32(24):5262-5273.

Rebecca Rasmussen (O'Halloran/Lucks) Zur and zinc increase expression of E. coli ribosomal protein L31 through RNA-mediated repression of the repressor L31p. Rasmussen RA, Wang S, Camarillo JM, Sosnowski V, Cho B-K, Goo YA, Lucks JB, and O'Halloran TV. Nucleic Acids Research. 2022 December 9;50(22):12739-12753.

Hannah Horton (Wignall) Newfound features of meiotic chromosome organization that promote efficient congression and segregation in Caenorhabditis elegans oocytes. Horton HH, Divekar NS, and Wignall SM. Molecular Biology of the Cell. 2022 December 1;33(14):br25. 

Kristin Johnson^ (LaBonne) Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions. Johnson K, Freedman S, Braun R, and LaBonne C. BMC Genomics. 2022 October 23;23:723.

Antoineen White^ (Lackner) Loss of Num1-mediated cortical dynein anchoring negatively impacts respiratory growth. White AJ, Harper CS, Rosario EM, Dietz JV, Addis HG, Fox JL, Khalimonchuk O, and Lackner LL. Journal of Cell Science. 2022 October 3:jcs.259980.

David Bushhouse, Edric Choi, and Laura Hertz (Lucks) How does RNA fold dynamically? Bushhouse DZ, Choi EK, Hertz LM, and Lucks JB. Journal of Molecular Biology. 2022 September 30;434(18):167665.

Liyushang Chou^ (Mirkin) Disrupting the Interplay between Programmed Cell Death Protein 1 and Programmed Death Ligand 1 with Spherical Nucleic Acids in Treating Cancer. Chou L, Callmann CE, Dominguez D, Zhang B, and Mirkin CA.  ACS Central Science. 2022 September 28;8(9):1299-1305.  

Reese Richardson (Amaral) Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA. Richardson R, Jorgensen E, Arevalo P, Holden TM, Gostic KM, Pacilli M, Ghinai I, Lightner S, Cobey S, and Gerardin J. Nature Communications. 2022 September 22;13:5547.

Nolan Kennedy^ (Tullman-Ercek) Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB. Kennedy NW, Mills CE, Abrahamson CH, Archer AG, Shirman S, Jewett MC, Mangan NM, and Tullman-Ercek D. Journal of Bacteriology. 2022 September 20;204(9):e0057621. 

Sarah Lloyd^ (Bao) CDK9 activity switch associated with AFF1 and HEXIM1 controls differentiation initiation from epidermal progenitors. Lloyd SM, Leon DB, Brady MO, Rodriguez D, McReynolds MP, Kweon J, Neely AE, Blumensaadt LA, Ho PJ, and Bao X. Nature Communications. 2022 July 29;13:4408.

Nicolas Daffern^ (Radhakrishnan) A Novel Mechanism of Coactivator Recruitment by the Nurr1 Nuclear Receptor. Daffern N and Radhakrishnan I. Journal of Molecular Biology. 2022 August 30;434(16):167718.

Brandon Liauw^ (Vafabakhsh) Conformational fingerprinting of allosteric modulators in metabotropic glutamate receptor 2. Liauw BW, Foroutan A, Schamber MR, Lu W, Afsari HS, and Vafabakhsh R. eLife. 2022 July 1;11:e78982.

Aaron Sue^ (O'Halloran) Zinc transporters ZIPT-2.4 and ZIPT-15 are required for normal C. elegans fecundity. Sue AC, Wignall SM, Woodruff TK, and O'Halloran TV. Journal of Assisted Reproduction and Genetics. 2022 June;39(6):1261-1276.

Bethany Sump^ (Brickner) Mitotically heritable, RNA polymerase II-independent H3K4 dimethylation stimulates INO1 transcriptional memory.  Sump B, Brickner DG, D'Urso A, Kim SH, and Brickner JH. eLife. 2022 May 17;11:e77646.

Michael Schamber^ (Vafabakhsh) Mechanism of sensitivity modulation in the calcium-sensing receptor via electrostatic tuning. Schamber MR and Vafabakhsh R. Nature Communications. 2022 April 22;13:2194.

Grant Rybnicky^ (Jewett) Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences. Rybnicky GA, Fackler NA, Karim AS, Köpke M, and Jewett MC. Nucleic Acids Research. 2022 April 8;50(6):3523-3534.

Luyi Cheng^ (Lucks) Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Cheng L, White EN, Brandt NL, Yu AM, Chen AA, and Lucks JB. Nucleic Acids Research. 2022 March 28:gkac102.

Christopher Koo^ (Rosenzweig) Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer. Koo CW, Tucci FJ, He Y, and Rosenzweig AC. Science. 2022 March 18;375(6586):1287-1291.

Grant Rybnicky^ (Jewett) Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom. Rybnicky GA, Dixon RA, Kuhn RM, Karim AS, and Jewett MC. ACS Synthetic Biology. 2022 February 18;11(2):835-842.

Gabriel Cavin-Meza^ (Wignall) Multiple motors cooperate to establish and maintain acentrosomal spindle bipolarity in C. elegans oocyte meiosis. Cavin-Meza G, Kwan MM, and Wignall SM. eLife. 2022 February 11;11:e72872.

Heidi Anderson^ (Lackner) Hierarchical integration of mitochondrial and nuclear positioning pathways by the Num1 EF hand. Anderson HL, Casler JC, and Lackner LL. Molecular Biology of the Cell. 2022 February 1;33(2).

Alexander McFarland^ (Hartmann) Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper. McFarland AG, Kennedy NW, Mills CE, Tullman-Ercek D, Huttenhower C, and Hartmann EM. Bioinformatics. 2022 February 1;38(3):612-620.

Kevin Gallagher^ (Carthew) Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye. Gallagher KD, Mani M, and Carthew RW. eLife. 2022 January 17;11:e72806.

Jessica Lenoir^ (Horvath) Immune regulator LGP2 targets Ubc13/UBE2N to mediate widespread interference with K63 polyubiquitination and NF-κB activation. Lenoir JJ, Parisien J-P, and Horvath CM. Cell Reports. 2021 December 28;37(13):110175.

Ely Contreras (Schmidt) Melanopsin phototransduction: beyond canonical cascades. Contreras E, Nobleman AP, Robinson PR, and Schmidt TM. Journal of Experimental Biology. 2021 December;224(23):jeb226522.

Joy Nyaanga^ (Andersen) easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler. Nyaanga J, Crombie TA, Widmayer SJ, and Andersen EC. PLoS ONE. 2021 August 12;16(8):e0252000.

Vasin Dumrongprechachan^ (Kozorovitskiy) Cell-type and subcellular compartment-specific APEX2 proximity labeling reveals activity-dependent nuclear proteome dynamics in the striatum. Dumrongprechachan V, Salisbury RB, Soto G, Kumar M, MacDonald ML, and Kozorovitskiy Y. Nature Communications. 2021 August 11;12:4855.

Siyu Chen^ (He) Structural insights into the role of DNA-PK as a master regulator in NHEJ. Chen S, Lees-Miller JP, He Y, and Lees-Miller SP. Genome Instability & Disease. 2021 August;2(4):195-210.

Alexis Reyes^ (He) Structure and Function of Chromatin Remodelers. Reyes AA, Marcum RD, and He Y. Journal of Molecular Biology. 2021 July 9;433(14):166929.

John Seeler^ (O'Halloran) Metal ion fluxes controlling amphibian fertilization. Seeler JF, Sharma A, Zaluzec NJ, Bleher R, Lai B, Schultz EG, Hoffman BM, LaBonne C, Woodruff TK, and O'Halloran TV. Nature Chemistry. 2021 July;13(7):683-691.

Matthew Verosloff^ (Lucks) RNA Sequence and Structure Determinants of Pol III Transcriptional Termination in Human Cells. Verosloff MS, Corcoran WK, Dolberg TB, Bushhouse DZ, Leonard JN, and Lucks JB. Journal of Molecular Biology. 2021 June 25;433(13):166978.

Miranda Jacobs^ (Kamat) EPA and DHA differentially modulate membrane elasticity in the presence of cholesterol. Jacobs ML, Faizi HA, Peruzzi JA, Vlahovska PM, and Kamat NP. Biophysical Journal. 2021 June 1;120(11):P2317-2329.

Nikita Divekar^ (Wignall) A degron-based strategy reveals new insights into Aurora B function in C. elegans. Divekar NS, Davis-Roca AC, Zhang L, Dernburg AF, and Wignall SM. PLoS Genetics. 2021 May 20;17(5):e1009567.

Michael Chas Sumner^ (Brickner) Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates interchromosomal movement. Sumner MC, Torrisi SB, Brickner DG, and Brickner JH. eLife. 2021 May 18;10:e66238.

Siyu Chen^ (He) Structural basis of long-range to short-range synaptic transition in NHEJ. Chen S, Lee L, Naila T, Fishbain S, Wang A, Tomkinson AE, Lees-Miller SP, and He Y. Nature. 2021 May 13;593(7858):294-298.

Nolan Kennedy^ (Tullman-Ercek) Computational and Experimental Approaches to Controlling Bacterial Microcompartment Assembly. Li Y, Kennedy NW, Li S, Mills CE, Tullman-Ercek D, and Olvera de la Cruz M. ACS Central Science. 2021 April 28;7(4):658-670.  

Ryan Abdella^ and Anna Talyzina (He) Structure of the human Mediator-bound transcription preinitiation complex. Abdella R, Talyzina A, Chen S, Inouye CJ, Tjian R, and He Y. Science. 2021 April 2;372(6537):52-56.

Alexander McFarland^ (Hartmann) Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species. McFarland AG, Bertucci HK, Littman E, Shen J, Huttenhower C, and Hartmann EM. Applied and Environmental Microbiology. 2021 April;87(7):e02924-20. 

Emma Coughlin^ (Odom) Light-Mediated Directed Placement of Different DNA Sequences on Single Gold Nanoparticles. Coughlin EE, Hu J, Lee A, and Odom TW. Journal of the American Chemical Society. 2021 March 17;143(10):3671-3676.

Christopher Koo^ (Rosenzweig) Biochemistry of aerobic biological methane oxidation. Koo CW and Rosenzweig AC. Chemical Society Reviews. 2021 March 7;50(5):3424-3436.

Nikita Divekar^ (Wignall) Methods for Rapid Protein Depletion in C. elegans using Auxin-Inducible Degradation. Divekar NS, Horton HE, and Wignall SM. Current Protocols. 2021 February 1;1(2):e16.

Nolan Kennedy^ (Tullman-Ercek) Self-assembling Shell Proteins PduA and PduJ Have Essential and Redundant Roles in Bacterial Microcompartment Assembly. Kennedy NW, Ikonomova SP, Slininger Lee M, Raeder HW, and Tullman-Ercek D. Journal of Molecular Biology. 2021 January 22;433(2):166721.

Sarah Lloyd^ (Bao) Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration. Chen X, Lloyd SM, Kweon J, Gamalong GM, and Bao X. Nature Communications. 2021 January 19;12:448.

Brandon Liauw^ (Vafabakhsh) Conformational rearrangement during activation of a metabotropic glutamate receptor. Liauw BW, Afsari HS, and Vafabakhsh R. Nature Chemical Biology. 2021 January 4;17(3):291-297.

Clayton Dilks^ (Andersen) Quantitative benzimidazole resistance and fitness effects of parasitic nematode beta-tubulin alleles. Dilks CM, Hahnel SR, Sheng Q, Long L, McGrath PT, and Andersen EC. Intl Journal for Parasitology: Drugs & Drug Resistance. 2020 December;14:28-36.

Kaleigh Roberts^ (Meade) Cobalt(III) Schiff base complexes stabilize non-fibrillar amyloid-β aggregates with reduced toxicity. Roberts KF, Brue CR, Preston A, Baxter D, Herzog E, Varelas E, and Meade TJ. Journal of Inorganic Biochemistry. 2020 December;213:111265.

Ronald Biggs^ (Marko) Micromanipulation of prophase I chromosomes from mouse spermatocytes reveals high stiffness and gel-like chromatin organization. Biggs RJ, Liu N, Peng Y, Marko JF, and Qiao H. Communications Biology. 2020 September 30;3:542.

Ariel Thames (Jewett) Principles Learned from the International Race to Develop a Safe and Effective COVID-19 Vaccine. Thames AH, Wolniak KL, Stupp SI, and Jewett MC. ACS Central Science. 2020 August 26;6(8):1341-1347.

Clare Harper and Antoineen White^ (Lackner) The multifunctional nature of mitochondrial contact site proteins. Harper CS, White AJ, and Lackner LL. Current Opinion in Cell Biology. 2020 August;65:58-65.

Kathryn Evans^ (Andersen) The Gene scb-1 Underlies Variation in Caenorhabditis elegans Chemotherapeutic Responses. Evans KS and Andersen EC. G3: Genes, Genomes, Genetics. 2020 July 1;10(7):2353-2364.

Rachael Bakker^ (Carthew) The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. Bakker R, Mani M, and Carthew RW. eLife. 2020 June 22;9:e56076.

Molly Frey^ (Scott) Mapping the supramolecular assembly space of poly(sarcosine)-b-poly(propylene sulfide) using a combinatorial copolymer library. Frey M, Vincent M, Bobbala S, Burt R, and Scott E. Chemical Communications. 2020 June 21;56(49):6644-6647.

Isaac Larkin^ (Mirkin) Dual-Readout Sandwich Immunoassay for Device-Free and Highly Sensitive Anthrax Biomarker Detection. Larkin IN, Garimella V, Yamankurt G, Scott AW, Xing H, and Mirkin CA. Analytical Chemistry. 2020 June 2;92(11):7845-7851.

Daniel Shams^ (Schwab) Spatial gradient sensing and chemotaxis via excitability in $Dictyostelium$$discoideu\mathrm{m.\; Shams\; DP,\; Yang\; X,\; Mehta\; P,\; and\; Schwab\; DJ.\; Physical\; Review\; E.\; 2020\; June;101(6):062410.}$

Nolan Kennedy^ (Tullman-Ercek) Apparent size and morphology of bacterial microcompartments varies with technique. Kennedy NW, Hershewe JM, Nichols TM, Roth EW, Wilke CD, Mills CE, Jewett MC, and Tullman-Ercek D. PLoS ONE. 2020 March 9;15(3):e0226395.

Ryan Abdella^ (He) Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation. Abdella R, Aggarwal M, Okura T, Lamb RA, and He Y. PNAS. 2020 March 3;117(9):4931-4941.

Ritika Giri^ (Carthew) Ordered patterning of the sensory system is susceptible to stochastic features of gene expression. Giri R, Papadopoulos DK, Posadas DM, Potluri HK, Tomancak P, Mani M, and Carthew RW. eLife. 2020 February 26;9:e53638.

Joseph Muldoon^ (Leonard/Bagheri) Macrophages employ quorum licensing to regulate collective activation. Muldoon JJ, Chuang Y, Bagheri N, and Leonard JN. Nature Communications. 2020 February 13;11:878.

Patrick Donahue^ (Leonard) The COMET toolkit for composing customizable genetic programs in mammalian cells. Donahue PS, Draut JW, Muldoon JJ, Edelstein HI, Bagheri N, and Leonard JN. Nature Communications. 2020 February 7;11:779.

Peter Doubleday^ (Kelleher) Elucidating Proteoform Dynamics Underlying the Senescence Associated Secretory Phenotype. Doubleday PF, Fornelli L, and Kelleher NL. Journal of Proteome Research. 2020 February 7;19(2):938-948.

Pamela Agbu^ (Carthew) MicroRNA miR-7 Regulates Secretion of Insulin-Like Peptides. Agbu P, Cassidy JJ, Braverman J, Jacobson A, and Carthew RW. Endocrinology. 2020 February;161(2):bqz040.

Gokay Yamankurt^ (Mirkin/Carthew) The effector mechanism of siRNA spherical nucleic acids. Yamankurt G, Stawicki RJ, Posadas DM, Nguyen JQ, Carthew RW, and Mirkin CA. PNAS. 2020 January 21;117(3):1312-1320.

Alexander Karge^ (Petersen) tec-1 kinase negatively regulates regenerative neurogenesis in planarians. Karge A, Bonar NA, Wood S, and Petersen CP. eLife. 2020 January 20;9:e47293.

Erik Schad^ (Petersen) STRIPAK Limits Stem Cell Differentiation of a WNT Signaling Center to Control Planarian Axis Scaling. Schad EG and Petersen CP. Current Biology. 2020 January 20;30(2):254-263.e2.

Nisan Hubbard^ (Mayo) Activation of Notch Signaling by Oocytes and Jag1 in Mouse Ovarian Granulosa Cells. Hubbard N, Prasasya RD, and Mayo KE. Endocrinology. 2019 December;160(12):2863-2876.

Justin Finkle^ (Bagheri) Hybrid analysis of gene dynamics predicts context specific expression and offers regulatory insights. Finkle JD and Bagheri N. Bioinformatics. 2019 November 15;35(22):4671-4678.

Kaleigh Roberts^ (Meade) Inhibition of Amyloid-β Aggregation by Cobalt(III) Schiff Base Complexes: A Computational and Experimental Approach. Iscen A, Brue CR, Roberts KF, Kim J, Schatz GC, and Meade TJ. Journal of the American Chemical Society. 2019 October 23;141(42):16685-16695.

Benjamin Parker^ (Weiss) Mapping low-affinity/high-specificity peptide–protein interactions using ligand-footprinting mass spectrometry. Parker BW, Goncz EJ, Krist DT, Statsyuk AV, Nesvizhskii AI, and Weiss EL. PNAS. 2019 October 15;116(42):21001-21011.

Patric Ho (Bao) Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Ho PJ, Lloyd SM, and Bao X. Development. 2019 September 30;146(19):178780.

Ryan Marcum^ (Radhakrishnan) Inositol phosphates and core subunits of the Sin3L/Rpd3L histone deacetylase (HDAC) complex up-regulate deacetylase activity. Marcum RD and Radhakrishnan I. Journal of Biological Chemistry. 2019 September 20;294(38):13928-13938.

Joseph Muldoon^ (Bagheri) Network inference performance complexity: a consequence of topological, experimental and algorithmic determinants. Muldoon JJ, Yu JS, Fassia M-K, and Bagheri N. Bioinformatics. 2019 September 15;35(18):3421-3432.

Sarah Lloyd^ (Bao) Pinpointing the Genomic Localizations of Chromatin‐Associated Proteins: The Yesterday, Today, and Tomorrow of ChIP‐seq. Lloyd SM and Bao X. Current Protocols in Cell Biology. 2019 September 3;84(1):e89.

Amy Neely (Bao) Nuclei Isolation Staining (NIS) Method for Imaging Chromatin‐Associated Proteins in Difficult Cell Types. Neely AE and Bao X. Current Protocols in Cell Biology. 2019 September 3;84(1):e94.