Resources

DATASETS

Mammary Gland Aging

Brittany L. Angarola, Siddhartha Sharma, Neerja Katiyar, Hyeon Gu Kang, Djamel Nehar-Belaid, SungHee Park, Rachel Gott, Giray N. Eryilmaz, Mark A. LaBarge, Karolina Palucka, Jeffrey H. Chuang, Ron Korstanje, Duygu Ucar*, Olga Anczukόw*. Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. Nature Aging. 2024.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE216542

Human islet cell stress responses

Eishani Kumar Sokolowski, Romy Kursawe, Vijay Selvam, Redwan Bhuiyan, Asa Thibodeau, Chi Zhao, Cassandra Spracklen, Duygu Ucar*, Michael L. Stitzel*. Comparative Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Insights into Type 2 Diabetes Genetics. Cell Metabolism. 36 (11), 2468-2488. e7 PMID: 39383866 (Article, Co-senior)..

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE251913

Infant Immune Responses to Early Life Vaccinations

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002926.v1.p1

Genomics and Epigenomics of the Elderly Response to Pneumococcal Vaccines

Sathyabaarathi Ravichandran⁺, Fernando Erra-Diaz⁺, Emin Onur Karakaslar⁺, Radu Marches, Lisa Kenyon-Pesce, Robert Rossi, Damien Chaussabel, Djamel Nehar-Belaid, David C. LaFon, Virginia Pascual, Karolina Palucka, Silke Paust, Moon H Nahm, George A Kuchel, Jacques Banchereau, Duygu Ucar. Distinct baseline immune characteristics associated with responses to conjugated and unconjugated pneumococcal polysaccharide vaccines in older adults. Nature Immunology. 2024;25(2):316-29. PMID: 38182669 (Article) (Senior).

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002361.v2.p1

Epigenetic memory of COVID-19

Jin-Gyu Cheong, Arjun Ravishankar, Siddhartha Sharma, Christopher N Parkhurst, Simon A Grassmann, Claire K Wingert, Paoline Laurent, Sai Ma, Lucinda Paddock, Isabella C Miranda, Emin Onur Karakaslar, Djamel Nehar-Belaid, Asa Thibodeau, Michael J Bale, Vinay K Kartha, Jim K Yee, Minh Y Mays, Chenyang Jiang, Andrew W Daman, Alexia Martinez de Paz, Dughan Ahimovic, Victor Ramos, Alexander Lercher, Erik Nielsen, Sergio Alvarez-Mulett, Ling Zheng, Andrew Earl, Alisha Yallowitz, Lexi Robbins, Elyse LaFond, Karissa L Weidman, Sabrina Racine-Brzostek, He S Yang, David R Price, Louise Leyre, André F Rendeiro, Hiranmayi Ravichandran, Junbum Kim, Alain C Borczuk, Charles M Rice, R Brad Jones, Edward J Schenck, Robert J Kaner, Amy Chadburn, Zhen Zhao, Virginia Pascual, Olivier Elemento, Robert E Schwartz, Jason D Buenrostro, Rachel E Niec, Franck J Barrat, Lindsay Lief, Joseph C Sun, Duygu Ucar*, Steven Z Josefowicz*. Epigenetic memory of COVID-19 in innate immune cells and their progenitors. Cell. 2023 186(18). 3882-3902. PMID: 37597510 (Article) (Co-Senior).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196990

Sexual dimorphism in human immune system aging

Eladio J. Marquez, Djamel Nehar-belaid, Cheng-han Chung, Radu Marches, Robert Rossi, Karolina Palucka, Virginia Pascual, George A Kuchel^*, Jacques Banchereau^*, Duygu Ucar^*. Sexual dimorphism in human immune system aging. Nature Communications. February 2020. 11 (1), 1-17. (Article) (Co-Senior).

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001934.v1.p1

The chromatin accessibility signature of human immune aging stems from CD8+ T cells

Duygu Ucar*+, Eladio J. Marquez+, Cheng-han Chung+, Radu Marches, Robert Rossi, Asli Uyar, Te-Chia Wu, Joshy George, Michael Stitzel, Karolina Palucka, George A Kuchel*, and Jacques Banchereau*. (2017) The chromatin accessibility signature of aging in human blood leukocytes stems from CD8+ T cells. The Journal of Experimental Medicine (JEM), 214 (10), 3123-3144. (Article) (Co-Senior).

https://ega-archive.org/studies/EGAS00001002605

SOFTWARE

AMULET: A computational framework for detecting multiplets from single nucleus ATAC-seq (snATAC-seq) data.
Asa Thibodeau⁺, Alper Eroglu⁺, Christopher S McGinnis, Nathan Lawlor, Djamel Nehar-Belaid, Romy Kursawe, Radu Marches, Daniel N Conrad, George A Kuchel, Zev J Gartner, Jacques Banchereau, Michael L Stitzel, A Ercument Cicek, Duygu Ucar. AMULET: a novel read count-based method for effective multiplet detection from single nucleus ATAC-seq data. Genome Biology. December 2021. 1. 1-19. (Article) (Senior).
https://github.com/UcarLab/AMULET

Bias-Free Footprint Enrichment Test (BiFET): A probabilistic framework for effective analyses of TF footprints.
Ahrim Youn, Eladio J. Marquez, Nathan Lawlor, Michael L. Stitzel, Duygu Ucar. (2019) BiFET: A Bias-free Transcription Factor Footprint Enrichment Test. Nucleic Acids Research. January 2019, Vol. 47, No. 2 e11. (Article) (Senior).
R package: https://www.bioconductor.org/packages/devel/bioc/html/BiFET.html.

Prediction of Enhancers from ATAC-Seq (PEAS): A Neural Network based method to predict enhancers from ATAC-seq samples using Python scikit libraries.
Asa Thibodeau+, Asli Uyar+, Shubham Khetan, Michael Stitzel, Duygu Ucar. (2018) A neural network based model effectively predicts enhancers from clinical ATAC-seq samples. Scientific Reports, 8: 16048. (Article) (Senior).
https://github.com/UcarLab/PEAS.

QUIN: A software to build and interrogate chromatin interaction network.
Asa Thibodeau, Eladio J. Marquez, Dong-Guk Shin, Paola Vera-Licona*, Duygu Ucar*. (2017) Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin Scientific Reports, 7 (1), 14466. (Article) (Co-Senior).
https://github.com/UcarLab/QuIN

I-ATAC: A standalone software for the management and pre-processing of ATAC-seq samples, that combines pre-processing pipelines into a user-friendly software to enable non-computational scientists to process these samples.
Zeeshan Ahmed*, Duygu Ucar* (2017) I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples PeerJ, 5, e4040. (Article) (Co-Senior).
https://github.com/UcarLab/I-ATAC.

IA-SVA: A statistical framework to estimate hidden factors from scRNA-seq data.
Nathan Lawlor, Eladio J. Marquez, Donghyung Lee, and Duygu Ucar. V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data. Bioinformatics. March 2020, 10.1093/bioinformatics/btaa128. (Article) (Senior).
R package, https://bioconductor.org/packages/devel/bioc/html/iasva.html