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ACE2 expression in adipose tissue is associated with cardio-metabolic risk factors and cell type composition—implications for COVID-19
El-Sayed Moustafa, Julia S., Jackson, Anne U., Brotman, Sarah M., Guan, Li, Villicaña, Sergio, Roberts, Amy L., Zito, Antonino, Bonnycastle, Lori, Erdos, Michael R., Narisu, Narisu, Stringham, Heather M., Welch, Ryan, Yan, Tingfen, Lakka, Timo, Parker, Stephen, Tuomilehto, Jaakko, Seow, Jeffrey, Graham, Carl, Huettner, Isabella, Acors, Sam, Kouphou, Neophytos, Wadge, Samuel, Duncan, Emma L., Steves, Claire J., Doores, Katie J., Malim, Michael H., Collins, Francis S., Pajukanta, Päivi, Boehnke, Michael, Koistinen, Heikki A., Laakso, Markku, Falchi, Mario, Bell, Jordana T., Scott, Laura J., Mohlke, Karen L., Small, Kerrin S.
Published in International Journal of Obesity (01.08.2022)
Published in International Journal of Obesity (01.08.2022)
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sNucConv: A bulk RNA-seq deconvolution method trained on single-nucleus RNA-seq data to estimate cell-type composition of human adipose tissues
Sorek, Gil, Haim, Yulia, Chalifa-Caspi, Vered, Lazarescu, Or, Ziv-Agam, Maya, Hagemann, Tobias, Nono Nankam, Pamela Arielle, Blüher, Matthias, Liberty, Idit F., Dukhno, Oleg, Kukeev, Ivan, Yeger-Lotem, Esti, Rudich, Assaf, Levin, Liron
Published in iScience (19.07.2024)
Published in iScience (19.07.2024)
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Cryopreservation Preserves Cell-Type Composition and Gene Expression Profiles in Bone Marrow Aspirates From Multiple Myeloma Patients
Chen, Duojiao, Abu Zaid, Mohammad I., Reiter, Jill L., Czader, Magdalena, Wang, Lin, McGuire, Patrick, Xuei, Xiaoling, Gao, Hongyu, Huang, Kun, Abonour, Rafat, Walker, Brian A., Liu, Yunlong
Published in Frontiers in genetics (21.04.2021)
Published in Frontiers in genetics (21.04.2021)
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Seasonal changes in gene expression represent cell-type composition in whole blood
De Jong, Simone, Neeleman, Marjolein, Luykx, Jurjen J., Ten Berg, Maarten J., Strengman, Eric, Den Breeijen, Hanneke H., Stijvers, Leon C., Buizer-Voskamp, Jacobine E., Bakker, Steven C., Kahn, René S., Horvath, Steve, Van Solinge, Wouter W., Ophoff, Roel A.
Published in Human molecular genetics (15.05.2014)
Published in Human molecular genetics (15.05.2014)
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PATH-40. PROFILING PLEOMORPHIC XANTHROASTROCYTOMA WITH DNA METHYLATION AND EXPLORING THE TUMOR IMMUNE CELL-TYPE COMPOSITION WITH METHYLATION-BASED DECONVOLUTION
Tang, Karen, Kurland, David, Vasudevaraja, Varshini, Serrano, Jonathan, Radmanesh, Alireza, Snuderl, Matija
Published in Neuro-oncology (Charlottesville, Va.) (11.11.2019)
Published in Neuro-oncology (Charlottesville, Va.) (11.11.2019)
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Blood Transcriptomics Predicts Progression of Pulmonary Fibrosis and Associated Natural Killer Cells
Huang, Yong, Oldham, Justin M., Ma, Shwu-Fan, Unterman, Avraham, Liao, Shu-Yi, Barros, Andrew J., Bonham, Catherine A., Kim, John S., Vij, Rekha, Adegunsoye, Ayodeji, Strek, Mary E., Molyneaux, Philip L., Maher, Toby M., Herazo-Maya, Jose D., Kaminski, Naftali, Moore, Bethany B., Martinez, Fernando J., Noth, Imre
Published in American journal of respiratory and critical care medicine (15.07.2021)
Published in American journal of respiratory and critical care medicine (15.07.2021)
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Novel Insights into Post-Myocardial Infarction Cardiac Remodeling through Algorithmic Detection of Cell-Type Composition Shifts
Gural, Brian, Kirkland, Logan, Hockett, Abbey, Sandroni, Peyton, Zhang, Jiandong, Rosa-Garrido, Manuel, Swift, Samantha K, Chapski, Douglas, Flinn, Michael A, O'Meara, Caitlin C, Vondriska, Thomas M, Patterson, Michaela, Jensen, Brian C, Rau, Christoph D
Published in bioRxiv (10.08.2024)
Published in bioRxiv (10.08.2024)
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Biomolecular Data Science—in Honor of Professor Philip E. Bourne
Year of Publication 2023
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Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue
Kalafati, Marianthi, Lenz, Michael, Ertaylan, Gökhan, Arts, Ilja C. W., Evelo, Chris T., van Greevenbroek, Marleen M. J., Blaak, Ellen E., Adriaens, Michiel, Kutmon, Martina
Published in Frontiers in nutrition (Lausanne) (31.05.2021)
Published in Frontiers in nutrition (Lausanne) (31.05.2021)
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scDC: single cell differential composition analysis
Cao, Yue, Lin, Yingxin, Ormerod, John T., Yang, Pengyi, Yang, Jean Y.H., Lo, Kitty K.
Published in BMC bioinformatics (24.12.2019)
Published in BMC bioinformatics (24.12.2019)
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INFERENCE OF CELL TYPE COMPOSITION FROM HUMAN BRAIN TRANSCRIPTOMIC DATASETS ILLUMINATES THE EFFECTS OF AGE, MANNER OF DEATH, DISSECTION, AND PSYCHIATRIC DIAGNOSIS
Megan Hastings Hagenauer, Schulmann, Anton, Li, Jun Z, Vawter, Marquis P, Walsh, David M, Thompson, Robert C, Turner, Cortney A, Bunney, William E, Myers, Richard M, Barchas, Jack D, Schatzberg, Alan F, Watson, Stanley J, Akil, Huda
Published in bioRxiv (29.03.2018)
Published in bioRxiv (29.03.2018)
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Bulk tissue cell type deconvolution with multi-subject single-cell expression reference
Wang, Xuran, Park, Jihwan, Susztak, Katalin, Zhang, Nancy R., Li, Mingyao
Published in Nature communications (22.01.2019)
Published in Nature communications (22.01.2019)
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Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis
Fetahu, Irfete S., Esser-Skala, Wolfgang, Dnyansagar, Rohit, Sindelar, Samuel, Rifatbegovic, Fikret, Bileck, Andrea, Skos, Lukas, Bozsaky, Eva, Lazic, Daria, Shaw, Lisa, Tötzl, Marcus, Tarlungeanu, Dora, Bernkopf, Marie, Rados, Magdalena, Weninger, Wolfgang, Tomazou, Eleni M., Bock, Christoph, Gerner, Christopher, Ladenstein, Ruth, Farlik, Matthias, Fortelny, Nikolaus, Taschner-Mandl, Sabine
Published in Nature communications (26.06.2023)
Published in Nature communications (26.06.2023)
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Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney
Abedini, Amin, Zhu, Yuan O., Chatterjee, Shatakshee, Halasz, Gabor, Devalaraja-Narashimha, Kishor, Shrestha, Rojesh, S. Balzer, Michael, Park, Jihwan, Zhou, Tong, Ma, Ziyuan, Sullivan, Katie Marie, Hu, Hailong, Sheng, Xin, Liu, Hongbo, Wei, Yi, Boustany-Kari, Carine M., Patel, Uptal, Almaani, Salem, Palmer, Matthew, Townsend, Raymond, Blady, Shira, Hogan, Jonathan, Morton, Lori, Susztak, Katalin
Published in Journal of the American Society of Nephrology (01.03.2021)
Published in Journal of the American Society of Nephrology (01.03.2021)
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Cell type-aware analysis of RNA-seq data
Jin, Chong, Chen, Mengjie, Lin, Danyu, Sun, Wei
Published in Nature Computational Science (01.04.2021)
Published in Nature Computational Science (01.04.2021)
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Intraindividual Variation and Short-term Temporal Trend in DNA Methylation of Human Blood
Shvetsov, Yurii B., Song, Min-Ae, Cai, Qiuyin, Tiirikainen, Maarit, Xiang, Yong-Bing, Shu, Xiao-Ou, Yu, Herbert
Published in Cancer epidemiology, biomarkers & prevention (01.03.2015)
Published in Cancer epidemiology, biomarkers & prevention (01.03.2015)
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Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD
Li, Xiuying, Noell, Guillaume, Tabib, Tracy, Gregory, Alyssa D., Trejo Bittar, Humberto E., Vats, Ravi, Kaminski, Tomasz W., Sembrat, John, Snyder, Mark E., Chandra, Divay, Chen, Kong, Zou, Chunbin, Zhang, Yingze, Sundd, Prithu, McDyer, John F., Sciurba, Frank, Rojas, Mauricio, Lafyatis, Robert, Shapiro, Steve D., Faner, Rosa, Nyunoya, Toru
Published in Respiratory research (06.04.2021)
Published in Respiratory research (06.04.2021)
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Replicated methylation changes associated with eczema herpeticum and allergic response
Boorgula, Meher Preethi, Taub, Margaret A., Rafaels, Nicholas, Daya, Michelle, Campbell, Monica, Chavan, Sameer, Shetty, Aniket, Cheadle, Chris, Barkataki, Sangjucta, Fan, Jinshui, David, Gloria, Beaty, Terri H., Ruczinski, Ingo, Hanifin, Jon, Schneider, Lynda C., Gallo, Richard L., Paller, Amy S., Beck, Lisa A., Leung, Donald Y., Mathias, Rasika A., Barnes, Kathleen C.
Published in Clinical epigenetics (23.08.2019)
Published in Clinical epigenetics (23.08.2019)
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