Student Projects

Each student will be analyzing either their own data, or data that I will provide (and will demo in class) and will complete a final project consisting of a publication quality figure, a project summary report written in Rmarkdown, and a web app built using Shiny that allows easy, web-based querying of your data.

Fall 2017

Student Lab Topic
Dan Beiting Beiting Transcriptional response of intestinal epithelium to Cryptosporidium infection
Tatyana Appelbaum Aguirre Canine RD (retina)
Leonardo Murgiano Aguirre Generation of a pipeline for retina data
Loic Dragin Alvarez Control of immune properties of microglia by hedgehog signaling
Pavan Vedula Kashina Mouse RNA-Seq data
Junling Wang Kashina tRNA Sequencing in mouse
Regina Turner Turner Equine testicular aging
Makoto Kurachi Wherry TF in CD8+ T cell differentiation
Jennifer Wu Wherry In vitro T cell exhaustion
Suchita Hodawadekar Atchison RNA-Seq of YY1 from mouse B cells
Sarmistha Banerjee Atchison RNA-Seq of T cell differentiation
Satabdi Nandi Atchison RNA-Seq in B cells under different activation conditions
Yue Zhang Atchison RNA-Seq in B cells under different activation conditions
Yifeng Wang Su Human RNA-Seq data
Elise English Striepen Crypto sexual development
Alexis Gibson Striepen Host response to Cryptosporidium
Adam Sateriale Striepen stage specific gene expression in Cryptosporidium
Isabel Sierra Anguera X-inactivation in neutrophils from a lupus mouse model
Anne Fosnocht NA (first year) RNA-Seq of NAc in rodents
Sabina Hlavaty Garden Canine MDSC transcriptomic characterization
Stephen Cole Rankin UTI transcriptome
Xinyuan Li Chen MDSC and cancer
Liz Kiernan Nathanson RNA-Seq from melanoma of different backgrounds
Jason Kennerdell Bonini Drosophila Brain Aging
Frances Taschuk Cherry Host response to DCV infection in Drosophila

Spring 2017

Student Lab Topic
Dan Beiting Beiting Transcriptional response of intestinal epithelium to Cryptosporidium infection
Liz Edgerton Michael Povelones Differences in the response of resistant and suseptible strains of Aedes agypti to infection with Dirofilaria
Kunal Hanagandi Igor Brodsky Role of Caspase-8 in the response of macrophages to TLR4 and TLR9 ligands
Sushil Kumar Rumela Chakrabarti TBD
Xin Liu Sunny Shin Role of GMCSF in the response of macrophages to Legionella infection
John Filosa Michael Povelones Identifying the Crythidia response to adherence
Lihua Shi Kate Sullivan Characterizing the T cell, B cell and macrophage profile in SLE patients
Mathieu Wimmer Chris Pierce Impact of nicotine on gene expression in the brain
Fatemeh Zare Serge Fuchs TBD
Vasiliki Pappa Steven Douglas Effect of NK1R signaling on monocyte differentiation
Paige Porrett Paige Porrett TBD
Vanessa Neal Jorge Henao-Mejia Role of Morrbid gene in basal gene expression in CD8 T cells
Kunal Patel John Wherry TBD
Laura McLane John Wherry TBD
Jan Pawlicki Jim Riley Role of RPM-ALK in transformation of primary human T cells
Yumi Ohtani Warren Pear Impact of drug treatment on human T-ALL cells
Bruce Freedman Bruce Freedman TBD
Nehal Solanki Steve Albelda TBD
Alexander Huang John Wherry tumor vs. perhperial blood profile of naive and effector CD8 T cells
Sarah Henrickson John Wherry TBD
Kayla Barekat Tracy Bale TBD
Jonathan DeLong Chris Hunter Effect of interleukin-27 on naive CD4 T cells with or without T cell receptor engagement
Annabel Torres Andrew Wells TBD
Megha Basavappa Sara Cherry LincRNA regulation during viral infection
Erin Doody Paul Schmidt Microbiota in natural populations of Drosophila melanogaster
Elaine De Martinis Dan Beiting Host-microbiome interactions in 3D intestinal cultures

Summer 2016

Student Lab Topic
Dan Beiting Beiting Role of Ripk3 in regulating inflammatory gene expression
Kavitha Sarma Wistar Inst Role of RNA binding by ATRX in gene expression
Ryan Staupe Wherry TBD
Nilam Sinha Brinster TBD
Rachel Blomberg Pure Impact of genotype and diet on mammary fat
Li-Yin Hung Herbert Role of TFF2 in macrophage response to epithelial wounding
Sutopa Dwivedi Povelones TBD
Shin Foong Ngiow Wherry TBD
Stephen Goldstein Weiss Response of airway epithelial cells to MERS-CoV
Nagaraju Indugu Pitta TBD
Caleb Radens rotating TBD
Jacob Paiano Brodsky* TBD
Laura Vella Wherry Comparison of naive, memory, and T follicular helper cells in response to stimulation
Josephine Giles Wherry Impact of anti-PD1 therapy on T cell phenotype and function
Alexandra DeLaney Brodsky Role of Caspase 8 in regulating inflammatory gene expression
Roy Wade Forrest TBD

Fall/Winter 2015

Student Lab Topic
Dan Beiting Beiting Role of Caspase-8 in regulating inflammatory gene expression
John Chojnowski Pure Role of tissue microenvironment in restriction of tumor growth
Jeffrey Thompson Albelda Transcriptional fate of engineered T cells
Bertram Bengsch Wherry Role of microRNAs on exhaustion of LCMV-specific CD8 T cells
Omar Khan Wherry Role of PD-1 in exhaustion of LCMV-specific CD8 T cells
Jonathan Kotzin Henao-Mejia Comparison of naive, memory, and T follicular helper cells in response to stimulation
Laura Cheslow Alvarez Cell-type specific inflammatory responses in human brain endothelia
Longfei Chen Hunter Transcriptional reprogramming during stage-switching of Toxoplasma gondii
Raghavi Sudharsan Beltran Identification of early pathways activated in canine retina by light exposure
Yan Sun Lopez Impact of DVGs on gene expression in the human nasal mucosa
Jennifer Grier Lopez Impact of DVGs on gene expression in the human nasal mucosa
Kanstantsin Katlinski Fuchs Role of Type I interferon and p53 in colorectal cancer
Christine Sansone Cherry Role of aging on the Drophsophila antiviral response
Jen Chan Bale Impact of paternal stress on the developing hypothalamus
Lou Taylor Anguera Role of BMP signaling and topoisomerases in cell differentiation
Elisa Cruz Morales Laufer Role of Ror-gamma in Treg function in the colon
Helene Leger Luca Role of NDR1/2 genes in retinal degeneration
Daniela Gomez Atria Allman TBD

Summer 2015

Student Lab Topic
Dan Beiting Beiting Role of TLX in macrophage phenotype and function (Figure, summary report, Web app)
Arindam Basu Atchison Role of YY1 in B cell fate
Corbett Berry Freedman Role of CRAC channels in T cell biology
Gautami Das Aguire Genetic basis for retinal cone dysfunction in the dog
Gretchen Harms Hunter Tbet-dependent effects of TCR signaling in T cells
Yulyia Katlinskaya Fuchs Role of Type I interferon signaling in the colon
Kelly McCorkell May non-canonical NFkB signaling
Katie Morrison Bale Role of pre-pubertal stress on the aging brain
Fernanda Novais Scott Healing vs. non-healing L. braziliensis skin lesions
Naomi Philip Brodsky Regulation of TLR signaling by Casp8
Sarah Sneed Povelones Mosquito transcriptional response to hormone
Raghavi Sudharsan Beltran Biomarkers of canine retinal degeneration
Camille Syrett Anguera LincRNA regulation of HSC gene expression (Figure, summary report)
Brain Gaudette Allman central vs peripheral plasma cell programs