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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 transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis
He, Helen, Suryawanshi, Hemant, Morozov, Pavel, Gay-Mimbrera, Jesús, Del Duca, Ester, Kim, Hyun Je, Kameyama, Naoya, Estrada, Yeriel, Der, Evan, Krueger, James G., Ruano, Juan, Tuschl, Thomas, Guttman-Yassky, Emma
Published in Journal of allergy and clinical immunology (01.06.2020)
Published in Journal of allergy and clinical immunology (01.06.2020)
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A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response
Adamson, Britt, Norman, Thomas M., Jost, Marco, Cho, Min Y., Nuñez, James K., Chen, Yuwen, Villalta, Jacqueline E., Gilbert, Luke A., Horlbeck, Max A., Hein, Marco Y., Pak, Ryan A., Gray, Andrew N., Gross, Carol A., Dixit, Atray, Parnas, Oren, Regev, Aviv, Weissman, Jonathan S.
Published in Cell (15.12.2016)
Published in Cell (15.12.2016)
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Machine learning based analysis of single-cell data reveals evidence of subject-specific single-cell gene expression profiles in acute myeloid leukaemia patients and healthy controls
Chrysostomou, Andreas, Furlan, Cristina, Saccenti, Edoardo
Published in Biochimica et biophysica acta. Gene regulatory mechanisms (01.12.2024)
Published in Biochimica et biophysica acta. Gene regulatory mechanisms (01.12.2024)
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High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity
Setliff, Ian, Shiakolas, Andrea R., Pilewski, Kelsey A., Murji, Amyn A., Mapengo, Rutendo E., Janowska, Katarzyna, Richardson, Simone, Oosthuysen, Charissa, Raju, Nagarajan, Ronsard, Larance, Kanekiyo, Masaru, Qin, Juliana S., Kramer, Kevin J., Greenplate, Allison R., McDonnell, Wyatt J., Graham, Barney S., Connors, Mark, Lingwood, Daniel, Acharya, Priyamvada, Morris, Lynn, Georgiev, Ivelin S.
Published in Cell (12.12.2019)
Published in Cell (12.12.2019)
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High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome
Zheng, Wenshan, Zhao, Shijie, Yin, Yehang, Zhang, Huidan, Needham, David M., Evans, Ethan D., Dai, Chengzhen L., Lu, Peter J., Alm, Eric J., Weitz, David A.
Published in Science (American Association for the Advancement of Science) (03.06.2022)
Published in Science (American Association for the Advancement of Science) (03.06.2022)
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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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Single-Cell Profiling Reveals Immune Aberrations in Progressive Idiopathic Pulmonary Fibrosis
Unterman, Avraham, Zhao, Amy Y., Neumark, Nir, Schupp, Jonas C., Ahangari, Farida, Cosme, Carlos, Sharma, Prapti, Flint, Jasper, Stein, Yan, Ryu, Changwan, Ishikawa, Genta, Sumida, Tomokazu S., Gomez, Jose L., Herazo-Maya, Jose D., Dela Cruz, Charles S., Herzog, Erica L., Kaminski, Naftali
Published in American journal of respiratory and critical care medicine (15.08.2024)
Published in American journal of respiratory and critical care medicine (15.08.2024)
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Characterization of the COPD alveolar niche using single-cell RNA sequencing
Sauler, Maor, McDonough, John E., Adams, Taylor S., Kothapalli, Neeharika, Barnthaler, Thomas, Werder, Rhiannon B., Schupp, Jonas C., Nouws, Jessica, Robertson, Matthew J., Coarfa, Cristian, Yang, Tao, Chioccioli, Maurizio, Omote, Norihito, Cosme, Carlos, Poli, Sergio, Ayaub, Ehab A., Chu, Sarah G., Jensen, Klaus H., Gomez, Jose L., Britto, Clemente J., Raredon, Micha Sam B., Niklason, Laura E., Wilson, Andrew A., Timshel, Pascal N., Kaminski, Naftali, Rosas, Ivan O.
Published in Nature communications (25.01.2022)
Published in Nature communications (25.01.2022)
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Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing
Cohen, Yael C., Zada, Mor, Wang, Shuang-Yin, Bornstein, Chamutal, David, Eyal, Moshe, Adi, Li, Baoguo, Shlomi-Loubaton, Shir, Gatt, Moshe E., Gur, Chamutal, Lavi, Noa, Ganzel, Chezi, Luttwak, Efrat, Chubar, Evgeni, Rouvio, Ory, Vaxman, Iuliana, Pasvolsky, Oren, Ballan, Mouna, Tadmor, Tamar, Nemets, Anatoly, Jarchowcky-Dolberg, Osnat, Shvetz, Olga, Laiba, Meirav, Shpilberg, Ofer, Dally, Najib, Avivi, Irit, Weiner, Assaf, Amit, Ido
Published in Nature medicine (01.03.2021)
Published in Nature medicine (01.03.2021)
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A comprehensive method to analyze single-cell vibrations
Al-Khaz’Aly, Ali, Ghandorah, Salim, Topham, Jared J., Osman, Nasir, Louie, Taye, Farshidfar, Farshad, Amrein, Matthias
Published in Biophysical journal (07.01.2025)
Published in Biophysical journal (07.01.2025)
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Severely ill COVID-19 patients display impaired exhaustion features in SARS-CoV-2-reactive CD8 + T cells
Kusnadi, Anthony, Ramírez-Suástegui, Ciro, Fajardo, Vicente, Chee, Serena J, Meckiff, Benjamin J, Simon, Hayley, Pelosi, Emanuela, Seumois, Grégory, Ay, Ferhat, Vijayanand, Pandurangan, Ottensmeier, Christian H
Published in Science immunology (21.01.2021)
Published in Science immunology (21.01.2021)
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Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types
Cheung, Leonard Y M, George, Akima S, McGee, Stacey R, Daly, Alexandre Z, Brinkmeier, Michelle L, Ellsworth, Buffy S, Camper, Sally A
Published in Endocrinology (Philadelphia) (01.12.2018)
Published in Endocrinology (Philadelphia) (01.12.2018)
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NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data
He, Liang, Davila-Velderrain, Jose, Sumida, Tomokazu S., Hafler, David A., Kellis, Manolis, Kulminski, Alexander M.
Published in Communications Biology (26.05.2021)
Published in Communications Biology (26.05.2021)
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Simulating paired and longitudinal single-cell RNA sequencing data with rescueSim
Wynn, Elizabeth A, Mould, Kara J, Vestal, Brian E, Moore, Camille M
Published in Bioinformatics (Oxford, England) (14.08.2025)
Published in Bioinformatics (Oxford, England) (14.08.2025)
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Cerebrospinal Fluid and Peripheral Blood Lymphomonocyte Single-Cell Transcriptomics in a Subject with Multiple Sclerosis Acutely Infected with HIV
Pinnetti, Carmela, Rozera, Gabriella, Messina, Francesco, Spezia, Pietro Giorgio, Lazzari, Elisabetta, Fabeni, Lavinia, Chillemi, Giovanni, Pietrucci, Daniele, Haggiag, Shalom, Mastrorosa, Ilaria, Vergori, Alessandra, Girardi, Enrico, Antinori, Andrea, Maggi, Fabrizio, Abbate, Isabella
Published in International journal of molecular sciences (01.10.2024)
Published in International journal of molecular sciences (01.10.2024)
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BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
Vallejos, Catalina A., Marioni, John C., Richardson, Sylvia
Published in PLoS computational biology (01.06.2015)
Published in PLoS computational biology (01.06.2015)
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