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