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Developing a ‘personalome’ for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes
Vitali, Francesca, Li, Qike, Schissler, A Grant, Berghout, Joanne, Kenost, Colleen, Lussier, Yves A
Published in Briefings in bioinformatics (21.05.2019)
Published in Briefings in bioinformatics (21.05.2019)
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Intracoronary Imaging, Cholesterol Efflux, and Transcriptomes after Intensive Statin Treatment: The YELLOW II study
Kini, Annapoorna S., MD, Vengrenyuk, Yuliya, PhD, Shameer, Khader, PhD, Maehara, Akiko, MD, Purushothaman, Meerarani, PhD, Yoshimura, Takahiro, MD, Matsumura, Mitsuaki, BS, Aquino, Melissa, MS, Haider, Nezam, PhD, Johnson, Kipp W., BS, Readhead, Ben, MBBS, Kidd, Brian A., PhD, Feig, Jonathan E., MD, PhD, Krishnan, Prakash, MD, Sweeny, Joseph, MD, Mahajan, Milind, PhD, Moreno, Pedro, MD, Mehran, Roxana, MD, Kovacic, Jason C., MD, PhD, Baber, Usman, MD, Dudley, Joel T., PhD, Narula, Jagat, MD, PhD, Sharma, Samin, MD
Published in Journal of the American College of Cardiology (14.02.2017)
Published in Journal of the American College of Cardiology (14.02.2017)
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RNA Sequencing Reveals Small and Variable Contributions of Infectious Agents to Transcriptomes of Postmortem Nervous Tissues From Amyotrophic Lateral Sclerosis, Alzheimer’s Disease and Parkinson’s Disease Subjects, and Increased Expression of Genes From Disease-Activated Microglia
Bennett, James P., Keeney, Paula M., Brohawn, David G.
Published in Frontiers in neuroscience (28.03.2019)
Published in Frontiers in neuroscience (28.03.2019)
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Endogenous retroviruses drive species-specific germline transcriptomes in mammals
Sakashita, Akihiko, Maezawa, So, Takahashi, Kazuki, Alavattam, Kris G., Yukawa, Masashi, Hu, Yueh-Chiang, Kojima, Shohei, Parrish, Nicholas F., Barski, Artem, Pavlicev, Mihaela, Namekawa, Satoshi H.
Published in Nature structural & molecular biology (01.10.2020)
Published in Nature structural & molecular biology (01.10.2020)
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Single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease
Wang, Qi, Antone, Jerry, Alsop, Eric, Reiman, Rebecca, Funk, Cory, Bendl, Jaroslav, Dudley, Joel T., Liang, Winnie S., Karr, Timothy L., Roussos, Panos, Bennett, David A., De Jager, Philip L., Serrano, Geidy E., Beach, Thomas G., Van Keuren-Jensen, Kendall, Mastroeni, Diego, Reiman, Eric M., Readhead, Benjamin P.
Published in Nature communications (10.07.2024)
Published in Nature communications (10.07.2024)
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Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas
Hulstaert, Eva, Morlion, Annelien, Avila Cobos, Francisco, Verniers, Kimberly, Nuytens, Justine, Vanden Eynde, Eveline, Yigit, Nurten, Anckaert, Jasper, Geerts, Anja, Hindryckx, Pieter, Jacques, Peggy, Brusselle, Guy, Bracke, Ken R., Maes, Tania, Malfait, Thomas, Derveaux, Thierry, Ninclaus, Virginie, Van Cauwenbergh, Caroline, Roelens, Kristien, Roets, Ellen, Hemelsoet, Dimitri, Tilleman, Kelly, Brochez, Lieve, Kuersten, Scott, Simon, Lukas M., Karg, Sebastian, Kautzky-Willers, Alexandra, Leutner, Michael, Nöhammer, Christa, Slaby, Ondrej, Prins, Roméo Willinge, Koster, Jan, Lefever, Steve, Schroth, Gary P., Vandesompele, Jo, Mestdagh, Pieter
Published in Cell reports (Cambridge) (29.12.2020)
Published in Cell reports (Cambridge) (29.12.2020)
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Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal
Lemay, Danielle G, Huang, Shurong, Huang, Liping, Alkan, Zeynep, Kirschke, Catherine, Burnett, Dustin J, Wang, Yining E, Hwang, Daniel H
Published in The Journal of nutritional biochemistry (01.10.2019)
Published in The Journal of nutritional biochemistry (01.10.2019)
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Interpretation of 'Omics dynamics in a single subject using local estimates of dispersion between two transcriptomes
Li, Qike, Zaim, Samir Rachid, Aberasturi, Dillon, Berghout, Joanne, Li, Haiquan, Vitali, Francesca, Kenost, Colleen, Zhang, Helen Hao, Lussier, Yves A
Published in AMIA ... Annual Symposium proceedings (2019)
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Published in AMIA ... Annual Symposium proceedings (2019)
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N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes
Li, Qike, Schissler, A. Grant, Gardeux, Vincent, Achour, Ikbel, Kenost, Colleen, Berghout, Joanne, Li, Haiquan, Zhang, Hao Helen, Lussier, Yves A.
Published in BMC medical genomics (24.05.2017)
Published in BMC medical genomics (24.05.2017)
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Sex-dependent neuro-deconvolution analysis of Alzheimer's disease brain transcriptomes according to CHI3L1 expression levels
Sanfilippo, Cristina, Castrogiovanni, Paola, Imbesi, Rosa, Musumeci, Giuseppe, Vecchio, Michele, Li Volti, Giovanni, Tibullo, Daniele, Broggi, Giuseppe, Caltabiano, Rosario, Ulivieri, Martina, Kazakova, Maria, Parenti, Rosalba, Vicario, Nunzio, Fazio, Francesco, Di Rosa, Michelino
Published in Journal of neuroimmunology (15.12.2022)
Published in Journal of neuroimmunology (15.12.2022)
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A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species
Hawkins, John A., Kaczmarek, Maria E., Müller, Marcel A., Drosten, Christian, Press, William H., Sawyer, Sara L.
Published in Proceedings of the National Academy of Sciences - PNAS (04.06.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (04.06.2019)
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Integration and transfer learning of single-cell transcriptomes via cFIT
Peng, Minshi, Li, Yue, Wamsley, Brie, Wei, Yuting, Roeder, Kathryn
Published in Proceedings of the National Academy of Sciences - PNAS (09.03.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (09.03.2021)
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Combining human platelet proteomes and transcriptomes: possibilities and challenges
Huang, Jingnan, Heemskerk, Johan W.M., Swieringa, Frauke
Published in Platelets (Edinburgh) (31.12.2023)
Published in Platelets (Edinburgh) (31.12.2023)
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Species delimitation in Amana (Liliaceae): transcriptomes battle with evolutionary complexity
Wang, Mei‐Zhen, Wu, Jing, Zhang, Sheng‐Lu, Mao, Li‐Mi, Ohi‐Toma, Tetsuo, Takano, Atsuko, Zhang, Yong‐Hua, Cameron, Kenneth M., Li, Pan
Published in Cladistics (01.04.2024)
Published in Cladistics (01.04.2024)
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Species-Specific Exon Loss in Human Transcriptomes
Wang, Jinkai, Lu, Zhi-xiang, Tokheim, Collin J., Miller, Sara E., Xing, Yi
Published in Molecular biology and evolution (01.02.2015)
Published in Molecular biology and evolution (01.02.2015)
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Matching of oligoclonal immunoglobulin transcriptomes and proteomes of cerebrospinal fluid in multiple sclerosis
Obermeier, Birgit, Mentele, Reinhard, Malotka, Joachim, Kellermann, Josef, Kümpfel, Tania, Wekerle, Hartmut, Lottspeich, Friedrich, Hohlfeld, Reinhard, Dornmair, Klaus
Published in Nature medicine (01.06.2008)
Published in Nature medicine (01.06.2008)
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A Gene Atlas of the Mouse and Human Protein-Encoding Transcriptomes
Su, Andrew I., Wiltshire, Tim, Batalov, Serge, Lapp, Hilmar, Ching, Keith A., Block, David, Zhang, Jie, Soden, Richard, Hayakawa, Mimi, Kreiman, Gabriel, Cooke, Michael P., Walker, John R., Hogenesch, John B., Vogt, Peter K.
Published in Proceedings of the National Academy of Sciences - PNAS (20.04.2004)
Published in Proceedings of the National Academy of Sciences - PNAS (20.04.2004)
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