Discovering dominant tumor immune archetypes in a pan-cancer census

Authors: Spitzer, Matthew, Fong, Lawrence, Nelson, Amanda, Kumar, Raj, Lee, Justin, Burra, Arun, Hsu, Joy, Hackett, Caroline, Tolentino, Karen, Sjarif, Jasmine, Johnson, Peter, Shao, Evans, Abrau, Darrell, Lupin, Leonard, Shaw, Cole, Collins, Zachary, Lea, Tasha, Corvera, Carlos, Nakakura, Eric, Carnevale, Julia, Alvarado, Michael, Loo, Kimberley, Chen, Lawrence, Chow, Melissa, Grandis, Jennifer, Ryan, Will, El-Sayed, Ivan, Jablons, David, Woodard, Gavitt, Meng, Maxwell W., Porten, Sima P., Okada, Hideho, Tempero, Margaret, Ko, Andrew, Kirkwood, Kim, Vandenberg, Scott, Guevarra, Denise, Oropeza, Erica, Cyr, Chris, Glenn, Pat, Bolen, Jennifer, Morton, Amanda, Eckalbar, Walter, Combes, Alexis J., Samad, Bushra, Tsui, Jessica, Chew, Nayvin W., Yan, Peter, Reeder, Gabriella C., Kushnoor, Divyashree, Shen, Alan, Davidson, Brittany, Barczak, Andrea J., Adkisson, Michael, Edwards, Austin, Naser, Mohammad, Barry, Kevin C., Courau, Tristan, Hammoudi, Taymour, Argüello, Rafael J., Rao, Arjun Arkal, Olshen, Adam B., Cai, Cathy, Zhan, Jenny, Davis, Katelyn C., Kelley, Robin K., Chapman, Jocelyn S., Atreya, Chloe E., Patel, Amar, Daud, Adil I., Ha, Patrick, Diaz, Aaron A., Kratz, Johannes R., Collisson, Eric A., Fragiadakis, Gabriela K., Erle, David J., Boissonnas, Alexandre, Asthana, Saurabh, Chan, Vincent, Krummel, Matthew F.

Source: In Cell 6 January 2022 185(1):184-203

Mapping the 17q12—21.1 Locus for Variants Associated with Early-Onset Asthma in African Americans

Authors: Gui, Hongsheng, Levin, Albert M., Hu, Donglei, Sleiman, Patrick, Xiao, Shujie, Mak, Angel C. Y., Yang, Mao, Barczak, Andrea J., Huntsman, Scott, Eng, Celeste

Source: American journal of respiratory and critical care medicine. 203(4):424-436

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN625823308&indx=1&recIds=ETOCRN625823308

Comparison of Reproducibility, Accuracy, Sensitivity, and Specificity of miRNA Quantification Platforms

Authors: Godoy, Paula M., Barczak, Andrea J., DeHoff, Peter, Srinivasan, Srimeenakshi, Etheridge, Alton, Galas, David, Das, Saumya, Erle, David J., Laurent, Louise C.

Source: In Cell Reports 17 December 2019 29(12):4212-4222

Integrative approach identifies corticosteroid response variant in diverse populations with asthma

Authors: Levin, Albert M. ^∗, Gui, Hongsheng ^∗, Hernandez-Pacheco, Natalia, Yang, Mao, Xiao, Shujie, Yang, James J., Hochstadt, Samantha, Barczak, Andrea J., Eckalbar, Walter L., Rynkowski, Dean, Samedy, Lesly-Anne, Kwok, Pui-Yan, Pino-Yanes, Maria, Erle, David J., Lanfear, David E., Burchard, Esteban G., Williams, L. Keoki

Source: In The Journal of Allergy and Clinical Immunology May 2019 143(5):1791-1802

MiR‐199 family contributes to regulation of sonic hedgehog expression during craniofacial development

Authors: Richbourg, Heather A., Hu, Diane P., Xu, Yanhua, Barczak, Andrea J., Marcucio, Ralph S.

Source: Developmental dynamics. 249(9):1062-1076

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100108403377.0x000001&indx=1&recIds=ETOCvdc_100108403377.0x000001

Large Differences in Small RNA Composition Between Human Biofluids

Authors: Godoy, Paula M., Bhakta, Nirav R., Barczak, Andrea J., Cakmak, Hakan, Fisher, Susan, MacKenzie, Tippi C., Patel, Tushar, Price, Richard W., Smith, James F., Woodruff, Prescott G., Erle, David J.

Source: In Cell Reports 30 October 2018 25(5):1346-1358

Discovering dominant tumor immune archetypes in a pan-cancer census

Authors: Combes, Alexis J., Samad, Bushra, Tsui, Jessica, Chew, Nayvin W., Yan, Peter, Reeder, Gabriella C., Kushnoor, Divyashree, Shen, Alan, Davidson, Brittany, Barczak, Andrea J., Adkisson, Michael, Edwards, Austin, Naser, Mohammad, Barry, Kevin C., Courau, Tristan, Hammoudi, Taymour, Argüello, Rafael J., Rao, Arjun Arkal, Olshen, Adam B., Cai, Cathy, Zhan, Jenny, Davis, Katelyn C., Kelley, Robin K., Chapman, Jocelyn S., Atreya, Chloe E., Patel, Amar, Daud, Adil I., Ha, Patrick, Diaz, Aaron A., Kratz, Johannes R., Collisson, Eric A., Fragiadakis, Gabriela K., Erle, David J., Boissonnas, Alexandre, Asthana, Saurabh, Chan, Vincent, Krummel, Matthew F.

Source: Cell. 185(1):184-203.e19

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100154994879.0x000001&indx=1&recIds=ETOCvdc_100154994879.0x000001

CD40 Mediates Maturation of Thymic Dendritic Cells Driven by Self-Reactive CD4^+ Thymocytes and Supports Development of Natural Regulatory T Cells

Authors: Oh, Jaehak, Wu, Nan, Barczak, Andrea J., Barbeau, Rebecca, Erle, David J., Shin, Jeoung-Sook

Source: Journal of immunology. 200(4):1399-1412

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN614805429&indx=1&recIds=ETOCRN614805429

The mammalian target of rapamycin regulates cholesterol biosynthetic gene expression and exhibits a rapamycin-resistant transcriptional profile

Authors: Wang, Beatrice T., Ducker, Gregory S., Barczak, Andrea J., Barbeau, Rebecca, Erle, David J., Shokat, Kevan M.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2011 Sep . 108(37), 15201-15206.

Access URL: https://www.jstor.org/stable/41352070

The Protein Disulfide Isomerase AGR2 Is Essential for Production of Intestinal Mucus

Authors: Park, Sung-Woo, Zhen, Guohua, Verhaeghe, Catherine, Nakagami, Yasuhiro, Nguyenvu, Louis T., Barczak, Andrea J., Killeen, Nigel, Erle, David J., Parodi, Armando J.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2009 Apr . 106(17), 6950-6955.

Access URL: https://www.jstor.org/stable/40483355

Patients with abdominal aortic aneurysms have reduced levels of microRNA 122-5p in circulating exosomes.

Authors: Lopez, Jose L., Ramirez, Joel L., Phu, Tuan Anh, Duong, Phat, Bouchareychas, Laura, Kuhrau, Christina R., Lin, Pei-Yu, Eckalbar, Walter L., Barczak, Andrea J., Rudolph, Joshua D., Maliskova, Lenka, Conte, Michael S., Vartanian, Shant M., Raffai, Robert L., Oskowitz, Adam Z.

Source: PLoS ONE; 2/14/2023, Vol. 18 Issue 2, p1-18, 18p

Subject Terms: ABDOMINAL aortic aneurysms, NUCLEOTIDE sequencing, GENE expression, DUPLEX ultrasonography, CHRONIC obstructive pulmonary disease, EXOSOMES

Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling.

Authors: Giraldez, Maria D, Spengler, Ryan M, Etheridge, Alton, Godoy, Paula M, Barczak, Andrea J, Srinivasan, Srimeenakshi, De Hoff, Peter L, Tanriverdi, Kahraman, Courtright, Amanda, Lu, Shulin, Khoory, Joseph, Rubio, Renee, Baxter, David, Driedonks, Tom A P, Buermans, Henk P J, Nolte-'t Hoen, Esther N M, Jiang, Hui, Wang, Kai, Ghiran, Ionita, Wang, Yaoyu E

Source: Nature Biotechnology; Aug2022, Vol. 40 Issue 8, p746-757, 12p

5-fluoroindole resistance identifies tryptophan synthase beta subunit mutants in Arabidopsis thaliana.

Authors: Barczak, Andrea J., Zhao, Jianmin, Pruitt, Kim D.

Source: Genetics; May 1995, Vol. 140, p303-313, 11p

Mapping the 17q12-21.1 Locus for Variants Associated with Early-Onset Asthma in African Americans.

Authors: Hongsheng Gui, Levin, Albert M., Donglei Hu, Sleiman, Patrick, Shujie Xiao, Mak, Angel C. Y., Mao Yang, Barczak, Andrea J., Huntsman, Scott, Eng, Celeste, Hochstadt, Samantha, Zhang, Ellen, Whitehouse, Kyle, Simons, Samantha, Cabral, Whitney, Takriti, Sami, Abecasis, Gonçalo, Blackwell, Thomas W., Hyun Min Kang, Nickerson, Deborah A.

Source: American Journal of Respiratory & Critical Care Medicine; 2/15/2021, Vol. 203 Issue 4, p424-436, 13p

Subject Terms: ASTHMA, HEALTH of African Americans, CHROMOSOMES, LINKAGE disequilibrium, GENETIC polymorphisms, RESEARCH funding

Asthma and its relationship to mitochondrial copy number: Results from the Asthma Translational Genomics Collaborative (ATGC) of the Trans-Omics for Precision Medicine (TOPMed) program.

Authors: Cocco, Maxwell P., White, Evan, Xiao, Shujie, Hu, Donglei, Mak, Angel, Sleiman, Patrick, Yang, Mao, Bobbitt, Kevin R., Gui, Hongsheng, Levin, Albert M., Hochstadt, Samantha, Whitehouse, Kyle, Rynkowski, Dean, Barczak, Andrea J., Abecasis, Gonçalo, Blackwell, Thomas W., Kang, Hyun Min, Nickerson, Deborah A., Germer, Soren, Ding, Jun

Source: PLoS ONE; 11/25/2020, Vol. 16 Issue 11, p1-24, 24p

Subject Terms: MITOCHONDRIAL DNA, REACTIVE oxygen species, INDIVIDUALIZED medicine, ASTHMA, GENOMICS, DNA copy number variations, LEUKOCYTE count, ETHNICITY

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Erratum: Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling

Authors: Giraldez, Maria D, Spengler, Ryan M, Etheridge, Alton, Godoy, Paula M, Barczak, Andrea J, Srinivasan, Srimeenakshi, Hoff, Peter L De, Tanriverdi, Kahraman, Courtright, Amanda, Lu, Shulin, Khoory, Joseph, Rubio, Renee, Baxter, David, Driedonks, Tom A P, Buermans, Henk P J, Hoen, Esther N M Nolte-'t, Jiang, Hui, Wang, Kai, Ghiran, Ionita, Wang, Yaoyu E, Keuren-Jensen, Kendall Van, Freedman, Jane E, Woodruff, Prescott G, Laurent, Louise C, Erle, David J, Galas, David J, Tewari, Muneesh

Source: Nature biotechnology. 36(9):899-899

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100191101110.0x000001&indx=1&recIds=ETOCvdc_100191101110.0x000001

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