Benchmarking of cell type deconvolution pipelines for transcriptomics data
Avila Cobos, Francisco, Alquicira-Hernandez, José, Powell, Joseph E, Mestdagh, Pieter, De Preter, Katleen
Published in Nature communications (06.11.2020)
Published in Nature communications (06.11.2020)
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Journal Article
No evidence that plasmablasts transdifferentiate into developing neutrophils in severe COVID‐19 disease
Alquicira‐Hernandez, José, Powell, Joseph E, Phan, Tri Giang
Published in Clinical & Translational Immunology (2021)
Published in Clinical & Translational Immunology (2021)
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Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Nellore, Abhinav, Jaffe, Andrew E, Fortin, Jean-Philippe, Alquicira-Hernández, José, Collado-Torres, Leonardo, Wang, Siruo, Phillips, III, Robert A, Karbhari, Nishika, Hansen, Kasper D, Langmead, Ben, Leek, Jeffrey T
Published in Genome Biology (30.12.2016)
Published in Genome Biology (30.12.2016)
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Journal Article
Nebulosa recovers single-cell gene expression signals by kernel density estimation
Alquicira-Hernandez, Jose, Powell, Joseph E
Published in Bioinformatics (Oxford, England) (25.08.2021)
Published in Bioinformatics (Oxford, England) (25.08.2021)
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Journal Article
scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data
Alquicira-Hernandez, Jose, Sathe, Anuja, Ji, Hanlee P, Nguyen, Quan, Powell, Joseph E
Published in Genome Biology (12.12.2019)
Published in Genome Biology (12.12.2019)
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Journal Article
Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease
Yazar, Seyhan, Alquicira-Hernandez, Jose, Wing, Kristof, Senabouth, Anne, Gordon, M Grace, Andersen, Stacey, Lu, Qinyi, Rowson, Antonia, Taylor, Thomas R P, Clarke, Linda, Maccora, Katia, Chen, Christine, Cook, Anthony L, Ye, Chun Jimmie, Fairfax, Kirsten A, Hewitt, Alex W, Powell, Joseph E
Published in Science (American Association for the Advancement of Science) (08.04.2022)
Published in Science (American Association for the Advancement of Science) (08.04.2022)
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Journal Article
Rail-RNA: scalable analysis of RNA-seq splicing and coverage
Nellore, Abhinav, Collado-Torres, Leonardo, Jaffe, Andrew E, Alquicira-Hernández, José, Wilks, Christopher, Pritt, Jacob, Morton, James, Leek, Jeffrey T, Langmead, Ben
Published in Bioinformatics (Oxford, England) (15.12.2017)
Published in Bioinformatics (Oxford, England) (15.12.2017)
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Journal Article
DevKidCC allows for robust classification and direct comparisons of kidney organoid datasets
Wilson, Sean B, Howden, Sara E, Vanslambrouck, Jessica M, Dorison, Aude, Alquicira-Hernandez, Jose, Powell, Joseph E, Little, Melissa H
Published in Genome medicine (22.02.2022)
Published in Genome medicine (22.02.2022)
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Journal Article
Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild/asymptomatic COVID-19
Khoo, Weng Hua, Jackson, Katherine, Phetsouphanh, Chansavath, Zaunders, John J., Alquicira-Hernandez, José, Yazar, Seyhan, Ruiz-Diaz, Stephanie, Singh, Mandeep, Dhenni, Rama, Kyaw, Wunna, Tea, Fiona, Merheb, Vera, Lee, Fiona X.Z., Burrell, Rebecca, Howard-Jones, Annaleise, Koirala, Archana, Zhou, Li, Yuksel, Aysen, Catchpoole, Daniel R., Lai, Catherine L., Vitagliano, Tennille L., Rouet, Romain, Christ, Daniel, Tang, Benjamin, West, Nicholas P., George, Shane, Gerrard, John, Croucher, Peter I., Kelleher, Anthony D., Goodnow, Christopher G., Sprent, Jonathan D., Powell, Joseph E., Brilot, Fabienne, Nanan, Ralph, Hsu, Peter S., Deenick, Elissa K., Britton, Philip N., Phan, Tri Giang
Published in Clinical immunology (Orlando, Fla.) (01.01.2023)
Published in Clinical immunology (Orlando, Fla.) (01.01.2023)
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Journal Article
ascend: R package for analysis of single-cell RNA-seq data
Senabouth, Anne, Lukowski, Samuel W, Hernandez, Jose Alquicira, Andersen, Stacey B, Mei, Xin, Nguyen, Quan H, Powell, Joseph E
Published in Gigascience (01.08.2019)
Published in Gigascience (01.08.2019)
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Journal Article
Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
Võsa, Urmo, Claringbould, Annique, Bonder, Marc Jan, Deelen, Patrick, Zeng, Biao, Kirsten, Holger, Saha, Ashis, Yazar, Seyhan, Brugge, Harm, Oelen, Roy, van der Wijst, Monique G P, Kasela, Silva, Pervjakova, Natalia, Alves, Isabel, Favé, Marie-Julie, Agbessi, Mawussé, Christiansen, Mark W, Jansen, Rick, Seppälä, Ilkka, Tong, Lin, Teumer, Alexander, Schramm, Katharina, Verlouw, Joost, Yaghootkar, Hanieh, Sönmez Flitman, Reyhan, Brown, Andrew, Kukushkina, Viktorija, Kalnapenkis, Anette, Rüeger, Sina, Porcu, Eleonora, Kronberg, Jaanika, Kettunen, Johannes, Lee, Bernett, Zhang, Futao, Qi, Ting, Hernandez, Jose Alquicira, Arindrarto, Wibowo, Beutner, Frank, Dmitrieva, Julia, Elansary, Mahmoud, Fairfax, Benjamin P, Georges, Michel, Heijmans, Bastiaan T, Hewitt, Alex W, Kähönen, Mika, Kim, Yungil, Knight, Julian C, Kovacs, Peter, Krohn, Knut, Li, Shuang, Loeffler, Markus, Marigorta, Urko M, Mei, Hailang, Momozawa, Yukihide, Müller-Nurasyid, Martina, Nauck, Matthias, Nivard, Michel G, Penninx, Brenda W J H, Pritchard, Jonathan K, Raitakari, Olli T, Rotzschke, Olaf, Slagboom, Eline P, Stehouwer, Coen D A, Stumvoll, Michael, Sullivan, Patrick, 't Hoen, Peter A C, Thiery, Joachim, Tönjes, Anke, van Dongen, Jenny, van Iterson, Maarten, Völker, Uwe, Warmerdam, Robert, Wijmenga, Cisca, Swertz, Morris, Andiappan, Anand, Montgomery, Grant W, Ripatti, Samuli, Perola, Markus, Kutalik, Zoltan, Dermitzakis, Emmanouil, Bergmann, Sven, Frayling, Timothy, van Meurs, Joyce, Prokisch, Holger, Ahsan, Habibul, Pierce, Brandon L, Lehtimäki, Terho, Psaty, Bruce M, Gharib, Sina A, Awadalla, Philip, Milani, Lili, Ouwehand, Willem H, Downes, Kate, Battle, Alexis, Yang, Jian, Scholz, Markus, Powell, Joseph, Gibson, Greg, Esko, Tõnu, Franke, Lude
Published in Nature genetics (01.09.2021)
Published in Nature genetics (01.09.2021)
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Identifying genetic variants that influence the abundance of cell states in single-cell data
Rumker, Laurie, Sakaue, Saori, Reshef, Yakir, Kang, Joyce B, Yazar, Seyhan, Alquicira-Hernandez, Jose, Valencia, Cristian, Lagattuta, Kaitlyn A, Mah-Som, Annelise, Nathan, Aparna, Powell, Joseph E, Loh, Po-Ru, Raychaudhuri, Soumya
Published in bioRxiv : the preprint server for biology (15.11.2023)
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Published in bioRxiv : the preprint server for biology (15.11.2023)
Journal Article
Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution
Kang, Joyce B, Shen, Amber Z, Sakaue, Saori, Luo, Yang, Gurajala, Saisriram, Nathan, Aparna, Rumker, Laurie, Aguiar, Vitor R C, Valencia, Cristian, Lagattuta, Kaitlyn, Zhang, Fan, Jonsson, Anna Helena, Yazar, Seyhan, Alquicira-Hernandez, Jose, Khalili, Hamed, Ananthakrishnan, Ashwin N, Jagadeesh, Karthik, Dey, Kushal, Daly, Mark J, Xavier, Ramnik J, Donlin, Laura T, Anolik, Jennifer H, Powell, Joseph E, Rao, Deepak A, Brenner, Michael B, Gutierrez-Arcelus, Maria, Raychaudhuri, Soumya
Published in medRxiv : the preprint server for health sciences (20.03.2023)
Published in medRxiv : the preprint server for health sciences (20.03.2023)
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Journal Article
Identifying genetic variants that influence the abundance of cell states in single-cell data
Rumker, Laurie, Sakaue, Saori, Reshef, Yakir, Kang, Joyce B, Yazar, Seyhan, Alquicira-Hernandez, Jose, Valencia, Cristian, Lagattuta, Kaitlyn A, Mah-Som, Annelise, Nathan, Aparna, Powell, Joseph E, Po-Ru Loh, Raychaudhuri, Soumya
Published in bioRxiv (15.11.2023)
Published in bioRxiv (15.11.2023)
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