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](http://DIYtranscriptomics.github.io/lectures/Figure.pdf), [summary report](http://DIYtranscriptomics.github.io/R_scripts/Supplementary_code.pdf), [Web app](https://hostmicrobe.shinyapps.io/RNAseqWeb-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](http://DIYtranscriptomics.github.io/studentProjects/camille_fig.pdf), [summary report](http://DIYtranscriptomics.github.io/studentProjects/camille.html))
Brain Gaudette | Allman | central vs peripheral plasma cell programs