Student Publications

Recent First Author Papers

(^indicates the student has defended)

2024

Feihong Xu (Amaral) Robust extraction of pneumonia-associated clinical states from electronic health records. Xu F, Morales FL, 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, 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, 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, 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, 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.

2022

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.

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 November;135(21):jcs259980.

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.

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.

2021

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.