Student Publications

2024

Samantha Hayashi

Mohammed Hoque

The Cby3/ciBAR1 complex positions the annulus along the sperm flagellum during spermiogenesis https://pubmed.ncbi.nlm.nih.gov/38197861/

Eric Paulissen

A Chemically Inducible Muscle Ablation System for the Zebrafish https://pubmed.ncbi.nlm.nih.gov/38436568/

Live Imaging Transverse Sections of Zebrafish Embryo Explants https://pubmed.ncbi.nlm.nih.gov/38379824/

2023

Seamus Balinth

ΔNp63α in cancer: importance and therapeutic opportunities https://pubmed.ncbi.nlm.nih.gov/36115734/

Samantha Hayashi

Phosphorylation of Ack1 by the Receptor Tyrosine Kinase Mer https://doi.org/10.3390/kinasesphosphatases1030011

Ga-Ram Hwang

Analysis of MicroRNAs in Ferroptosis https://pubmed.ncbi.nlm.nih.gov/37578710/

Yixin Hu

Origins of DNA replication in eukaryotes https://pubmed.ncbi.nlm.nih.gov/36640769/

Jessica Imperato

Retinoic acid signaling during priming licenses intestinal CD103+ CD8 TRM cell differentiation https://pubmed.ncbi.nlm.nih.gov/36809399/

Yagmur Kan

Domain Architecture of the Nonreceptor Tyrosine Kinase Ack1 https://pubmed.ncbi.nlm.nih.gov/36980241/

Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk https://pubmed.ncbi.nlm.nih.gov/36854171/

Deborah Kim

Human uridine 5'-monophosphate synthase stores metabolic potential in inactive biomolecular condensates https://pubmed.ncbi.nlm.nih.gov/36708921/

Xinyuan Lei

1428-A Oral immunization with Listeria-based cancer vaccines elicits protective gastrointestinal focused immunity in an orthotopic transplantation model of colorectal cancer https://jitc.bmj.com/content/11/Suppl_2/A1853

Retinoic acid signaling during priming licenses intestinal CD103+ CD8 TRM cell differentiation https://doi.org/10.1084/jem.20210923

Victoria Mingione

Allosteric regulation and inhibition of protein kinases https://pubmed.ncbi.nlm.nih.gov/36794774/

Structural mechanism of a drug-binding process involving a large conformational change of the protein target https://pubmed.ncbi.nlm.nih.gov/37019905/

Megan Mladinich

Establishment of a CPER reverse genetics system for Powassan virus defines attenuating NS1 glycosylation sites and an infectious NS1-GFP11 reporter virus https://pubmed.ncbi.nlm.nih.gov/37489888/

ZIKV induction of tristetraprolin in endothelial and Sertoli cells post-transcriptionally inhibits IFNβ/λ expression and promotes ZIKV persistence https://pubmed.ncbi.nlm.nih.gov/37707056/

Greisly Nunez

Recruitment of the lipid kinase Mss4 to the meiotic spindle pole promotes prospore membrane formation in Saccharomyces cerevisiae https://pubmed.ncbi.nlm.nih.gov/36857169/

Zhe Qian

Manipulating PTPRD function with ectodomain antibodies https://pubmed.ncbi.nlm.nih.gov/37669874/

Padmina Shresha

Chd5 Regulates the Transcription Factor Six3 to Promote Neuronal Differentiation https://pubmed.ncbi.nlm.nih.gov/36636025/

Jialin Sun

Mutations in the transcriptional regulator MeCP2 severely impact key cellular and molecular signatures of human astrocytes during maturation https://pubmed.ncbi.nlm.nih.gov/36640327/

Yutong Xiao

An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation in Caenorhabditis elegans https://pubmed.ncbi.nlm.nih.gov/36722258/

2022

Seamus Balinth

EZH2 regulates a SETDB1/ΔNp63α axis via RUNX3 to drive a cancer stem cell phenotype in squamous cell carcinoma https://pubmed.ncbi.nlm.nih.gov/35864175/

Mohammed Hoque

Essential Roles of Efferent Duct Multicilia in Male Fertility https://pubmed.ncbi.nlm.nih.gov/35159149/

Ga-Ram Hwang

Roles of microRNAs in Gastrointestinal Cancer Stem Cell Resistance and Therapeutic Development https://pubmed.ncbi.nlm.nih.gov/33562727/

Jessica Imperato

A blend of broadly-reactive and pathogen-selected Vγ4 Vδ1 T cell receptors confer broad bacterial reactivity of resident memory γδ T cells https://pubmed.ncbi.nlm.nih.gov/34462572/

The accumulation of Vγ4 T cells with aging is associated with an increased adaptive Vγ4 T cell response after foodborne Listeria monocytogenes infection of mice https://pubmed.ncbi.nlm.nih.gov/35501808/

Yagmur Kan

Activity of the nonreceptor tyrosine kinase Ack1 is regulated by tyrosine phosphorylation of its Mig6 homology region https://pubmed.ncbi.nlm.nih.gov/36178070/

Muyan Li

A Novel Role of SMG1 in Cholesterol Homeostasis That Depends Partially on p53 Alternative Splicing https://www.mdpi.com/2072-6694/14/13/3255

Victoria Mingione

Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome https://pubmed.ncbi.nlm.nih.gov/35625613/

Validation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations https://pubmed.ncbi.nlm.nih.gov/35595169/

Megan Mladinich

Measuring Transendothelial Electrical Resistance (TEER) for Dengue Infection Studies https://pubmed.ncbi.nlm.nih.gov/34709643/

Powassan Viruses Spread Cell to Cell during Direct Isolation from Ixodes Ticks and Persistently Infect Human Brain Endothelial Cells and Pericytes https://pubmed.ncbi.nlm.nih.gov/34643436/

Chun-Hao Pan

Dissecting the Oncogenic Roles of Keratin 17 in the Hallmarks of Cancer https://pubmed.ncbi.nlm.nih.gov/34921015/

Eric Paulissen

Somite morphogenesis is required for axial blood vessel formation during zebrafish embryogenesis https://pubmed.ncbi.nlm.nih.gov/35137687/

Aziz Rangwala

Discovery and molecular basis of subtype-selective cyclophilin inhibitors https://pubmed.ncbi.nlm.nih.gov/36163383/

Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome https://pubmed.ncbi.nlm.nih.gov/35625613/

Validation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations https://pubmed.ncbi.nlm.nih.gov/35595169/

Resistance to kinase inhibition through shortened target engagement https://pubmed.ncbi.nlm.nih.gov/35252553/

Sydney Snaider

Rb-E2F-HDAC Repressor Complexes Control Interferon-Induced Repression of Adenovirus To Promote Persistent Infection https://pubmed.ncbi.nlm.nih.gov/35546119/

2021

Seamus Balinth

BRD4 Regulates Transcription Factor ΔNp63α to Drive a Cancer Stem Cell Phenotype in Squamous Cell Carcinomas https://pubmed.ncbi.nlm.nih.gov/34697072/

Julie Bettke

Mutant p53 suppresses innate immune signaling to promote tumorigenesis https://pubmed.ncbi.nlm.nih.gov/33545063/

Inflammatory Monocytes Promote Granuloma-Mediated Control of Persistent Salmonella Infection https://pubmed.ncbi.nlm.nih.gov/35311578/

IKKα-Mediated Noncanonical NF-κB Signaling Is Required To Support Murine Gammaherpesvirus 68 Latency In Vivo https://pubmed.ncbi.nlm.nih.gov/35481781/

Samia Mohammed

Sublethal doxorubicin promotes migration and invasion of breast cancer cells: role of Src Family non-receptor tyrosine kinases https://pubmed.ncbi.nlm.nih.gov/34315513/

Robert Morabito

Cyclin-Dependent Kinase Sensor Transgenic Zebrafish Lines for Improved Cell Cycle State Visualization in Live Animals https://pubmed.ncbi.nlm.nih.gov/34669514/

Aziz Rangwala

Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance https://pubmed.ncbi.nlm.nih.gov/34750265/

2020

Seamus Balinth

p63-related signaling at a glance https://pubmed.ncbi.nlm.nih.gov/32917730/

Jessica Imperato

Mucosal CD8 T Cell Responses Are Shaped by Batf3-DC After Foodborne Listeria monocytogenes Infection https://pubmed.ncbi.nlm.nih.gov/33042159/

Megan Mladinich

NS5 Sumoylation Directs Nuclear Responses That Permit Zika Virus To Persistently Infect Human Brain Microvascular Endothelial Cells https://pubmed.ncbi.nlm.nih.gov/32699085/

Robert Morabito

Visualizing the metazoan proliferation-quiescence decision in vivo https://pubmed.ncbi.nlm.nih.gov/33350383/

Jinelle Wint

Lrrk2 modulation of Wnt signaling during zebrafish development https://pubmed.ncbi.nlm.nih.gov/32623786/

2018

Deborah Kim

Viral FGARAT ORF75A promotes early events in lytic infection and gammaherpesvirus pathogenesis in mice https://pubmed.ncbi.nlm.nih.gov/29390024/

Chitra Mohan

VivosX, a disulfide crosslinking method to capture site-specific, protein-protein interactions in yeast and human cells. eLife 2018;7:e36654

Eric Paulissen

VivosX, a disulfide crosslinking method to capture site-specific, protein-protein interactions in yeast and human cells https://pubmed.ncbi.nlm.nih.gov/30091702/

Padmina Shrestha

Chromatin-mediated translational control is essential for neural cell fate specification https://pubmed.ncbi.nlm.nih.gov/30456361/

Jialin Sun

Activity-dependent aberrations in gene expression and alternative splicing in a mouse model of Rett syndrome https://pubmed.ncbi.nlm.nih.gov/29769330/

2017

Azeez Aranmolate

Myelination is delayed during postnatal brain development in the mdx mouse model of Duchenne muscular dystrophy https://www.ncbi.nlm.nih.gov/pubmed/28806929

Gregory Carbonetti

Fatty-acid-binding protein inhibition produces analgesic effects through peripheral and central mechanisms https://www.ncbi.nlm.nih.gov/pubmed/28326944

Sajjad Hossain

Discovery of Two Bacterial Nitric Oxide-Responsive Proteins and Their Roles in Bacterial Biofilm Regulation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654536/

Discovery of a Novel Nitric Oxide Binding Protein and Nitric-Oxide-Responsive Signaling Pathway in Pseudomonas aeruginosa https://www.ncbi.nlm.nih.gov/pubmed/28238256

Zhimin Liu

Bartender: a fast and accurate clustering algorithm to count barcode reads https://academic.oup.com/bioinformatics/article/34/5/739/4562326

A scalable double-barcode sequencing platform for characterization of dynamic protein-protein interactions https://www.nature.com/articles/ncomms15586

Debjani Pal

Rapid and tunable method to temporally control gene editing based on conditional Cas9 stabilization https://www.ncbi.nlm.nih.gov/pubmed/28224990

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells https://www.ncbi.nlm.nih.gov/pubmed/28092266

Eric Paulissen

The budding yeast Polo-like kinase localizes to distinct populations at centrosomes during mitosis https://www.molbiolcell.org/doi/10.1091/mbc.e16-05-0324

Anthony Rampello

Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing https://www.ncbi.nlm.nih.gov/pubmed/29097521

Identification of a Degradation Signal Sequence within Substrates of the Mitochondrial i-AAA Protease https://www.ncbi.nlm.nih.gov/pubmed/28214511

Danilo Segovia

Megan Mladinich

Zika Virus Persistently Infects and Is Basolaterally Released from Primary Human Brain Microvascular Endothelial Cells https://pubmed.ncbi.nlm.nih.gov/28698279/

Neha Puri

HspQ Functions as a Unique Specificity-Enhancing Factor for the AAA+ Lon Protease https://www.ncbi.nlm.nih.gov/pubmed/28575662

Lu Sun

Dual function of Swc5 in SWR remodeling ATPase activation and histone H2A eviction https://www.ncbi.nlm.nih.gov/pubmed/28973436

Upasna Thapar

How Are Base Excision DNA Repair Pathways Deployed in vivo? https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357041/

Xiaoyu Zhao

A systematic evaluation of nucleotide properties for CRISPR sgRNA design https://doi.org/10.1186/s12859-017-1697-6

2016

Beth M. Harvey

Mapping Sites of O-Glycosylation and Fringe Elongation on Drosophila Notch http://www.jbc.org/content/291/31/16348.long

Jennifer L. DeLeon

Vps34 regulates Rab7 and late endocytic trafficking through recruitment of the GTPase-activating protein Armus https://journals.biologists.com/jcs/article/129/23/4424/55594/Vps34-regulates-Rab7-and-late-endocytic

Nadia Jaber

Megan Mladinich

Tackling Cancer Stem Cells via Inhibition of EMT Transcription Factors https://pubmed.ncbi.nlm.nih.gov/27840647/

Evelyn Prugar

Mek1 Down Regulates Rad51 Activity during Yeast Meiosis by Phosphorylation of Hed1 http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1006226

Michael Tramantano

Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex https://elifesciences.org/content/5/e14243

Jae Kyo Yi

Aging-related elevation of sphingoid bases shortens yeast chronological life span by compromising mitochondrial function https://pubmed.ncbi.nlm.nih.gov/27008706/

Deficiency of the alkaline ceramidase ACER3 manifests in early childhood by progressive leukodystrophy http://jmg.bmj.com/content/53/6/389.full

2015

Saadat U. Aleem

Constitutive Activity in an Ancestral Form of Abl Tyrosine Kinase http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131062

Protein-tyrosine Phosphatase and Kinase Specificity in Regulation of SRC and Breast Tumor Kinase http://www.jbc.org/content/290/26/15934.full

Azeez Aranmolate

Laminin promotes metalloproteinase-mediated dystroglycan processing to regulate oligodendrocyte progenitor cell proliferation http://onlinelibrary.wiley.com/doi/10.1111/jnc.13241/abstract

Anna Banach

miR-181a-5p Inhibits Cancer Cell Migration and Angiogenesis via Downregulation of Matrix Metalloproteinase-14 http://cancerres.aacrjournals.org/content/75/13/2674

Keratin-17 Promotes p27^KIP1 Nuclear Export and Degradation and Offers Potential Prognostic Utility http://cancerres.aacrjournals.org/content/75/17/3650

Brandon Cienewicz

Murine Gammaherpesvirus 68 Pathogenesis Is Independent of Caspase-1 and Caspase-11 in Mice and Impairs Interleukin-1β Production upon Extrinsic Stimulation in Culture http://jvi.asm.org/content/89/13/6562.full

Gregory Carbonetti

Defects in fatty acid amide hydrolase 2 in a male with neurologic and psychiatric symptoms http://ojrd.biomedcentral.com/articles/10.1186/s13023-015-0248-3

Janus kinase inhibition by ruxolitinib extends dasatinib- and dexamethasone-induced remissions in a mouse model of Ph+ ALL http://www.bloodjournal.org/content/125/9/1444?sso-checked=true

Qiwen Dong

Matthew W. Elmes

Fatty Acid-binding Proteins (FABPs) Are Intracellular Carriers for Δ⁹-Tetrahydrocannabinol (THC) and Cannabidiol (CBD) http://www.jbc.org/content/290/14/8711.full

Andrew Fesler

Inhibition of colorectal cancer stem cell survival and invasive potential by hsa-miR-140-5p mediated suppression of Smad2 and autophagy http://dx.doi.org/10.18632/oncotarget.3771

Identification of miR-215 mediated targets/pathways via translational immunoprecipitation expression analysis (TrIP-chip) http://dx.doi.org/10.18632/oncotarget.4425

Hana Goto

The zebrafish tailbud contains two independent populations of midline progenitor cells that maintain long-term germ layer plasticity and differentiate in response to local signaling cues http://dev.biologists.org/content/143/2/244

Beth M. Harvey

Protein O-Glucosyltransferase 1 (POGLUT1) Promotes Mouse Gastrulation through Modification of the Apical Polarity Protein CRUMBS2 http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005551

Nadia Jaber

PTEN Functions by Recruitment to Cytoplasmic Vesicles http://www.cell.com/molecular-cell/fulltext/S1097-2765(15)00176-8

Post-transcriptional regulation in budding yeast meiosis http://link.springer.com/article/10.1007/s00294-015-0546-2#enumeration

JiHyun Kim

Using Sterol Substitution to Probe the Role of Membrane Domains in Membrane Functions http://link.springer.com/article/10.1007%2Fs11745-015-4007-y#enumeration

Samia Mohammed

P53-dependent upregulation of neutral sphingomyelinase-2: role in doxorubicin-induced growth arrest http://www.nature.com/cddis/journal/v6/n10/full/cddis2015268a.html

Benjamin Newcomb

A new twist to the emerging functions of ceramides in cancer: novel role for platelet acid sphingomyelinase in cancer metastasis http://embomolmed.embopress.org/content/7/6/692

Neha Puri

The effect of pyrite on Escherichia coli in water: proof-of-concept for the elimination of waterborne bacteria by reactive minerals http://jwh.iwaponline.com/content/13/1/42

Upasna Thapar

Enzyme mechanism-based, oxidative DNA–protein cross-links formed with DNA polymerase β in vivo http://www.pnas.org/content/112/28/8602

Fractionated Radiation Exposure of Rat Spinal Cords Leads to Latent Neuro-Inflammation in Brain, Cognitive Deficits, and Alterations in Apurinic Endonuclease 1 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0133016

Jae Kyo Yi

Tumor Necrosis Factor-α (TNFα)-induced Ceramide Generation via Ceramide Synthases Regulates Loss of Focal Adhesion Kinase (FAK) and Programmed Cell Death* http://www.jbc.org/content/290/42/25356.full

Alkaline Ceramidase 3 Deficiency Results in Purkinje Cell Degeneration and Cerebellar Ataxia Due to Dyshomeostasis of Sphingolipids in the Brain http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005591

Xiaoyu Zhao

An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis https://pubmed.ncbi.nlm.nih.gov/26516084/

2014

Ying Cai

Effects of the Yeast RNA-Binding Protein Whi3 on the Half-Life and Abundance of CLN3 mRNA and Other Targets http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0084630

Devin Camenares

Active and Accurate trans-Translation Requires Distinct Determinants in the C-terminal Tail of SmpB Protein and the mRNA-like Domain of Transfer Messenger RNA (tmRNA) http://www.jbc.org/content/288/42/30527.long

Nikki Evensen

Development of a High-Throughput Three-Dimensional Invasion Assay for Anti-Cancer Drug Discovery http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0082811

Unraveling the Role of KIAA1199, a Novel Endoplasmic Reticulum Protein, in Cancer Cell Migration http://jnci.oxfordjournals.org/content/105/18/1402.long

Wangzhi Li

Chd5 orchestrates chromatin remodelling during sperm development http://www.nature.com/ncomms/2014/140513/ncomms4812/full/ncomms4812.html?message-global=remove

Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromeshttp://www.futuremedicine.com/doi/abs/10.2217/epi.14.31

Mahalakshmi Ramadass

Generation of multiple fluid-phase C3b:plasma protein complexes during complement activation: possible implications in C3 glomerulopathies http://www.ncbi.nlm.nih.gov/pubmed/24367026

Enhanced recognition of plasma proteins in a non-native state by complement C3b. A possible clearance mechanism for damaged proteins in blood http://www.ncbi.nlm.nih.gov/pubmed/25466612

Krithika Venkataraman

Distinct tmRNA sequence elements facilitate RNase R engagement on rescued ribosomes for selective nonstop mRNA decay http://dx.doi.org/10.1093/nar/gku802

Nonstop mRNA Decay: a Special Attribute of Trans-Translation Mediated Ribosome Rescue http://dx.doi.org/10.3389/fmicb.2014.00093

Student Research