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Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
Liu, Yunqing, Zhao, Jiayi, Adams, Taylor S., Wang, Ningya, Schupp, Jonas C., Wu, Weimiao, McDonough, John E., Chupp, Geoffrey L., Kaminski, Naftali, Wang, Zuoheng, Yan, Xiting
Published in BMC bioinformatics (19.10.2023)
Published in BMC bioinformatics (19.10.2023)
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Journal Article
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects
Liu, Yunqing, Zhao, Jiayi, Adams, Taylor S., Wang, Ningya, Schupp, Jonas C., Wu, Weimiao, McDonough, John E., Chupp, Geoffrey L., Kaminski, Naftali, Wang, Zuoheng, Yan, Xiting
Published in BMC bioinformatics (22.08.2023)
Published in BMC bioinformatics (22.08.2023)
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Journal Article
Identification of Subject-Specific Immunoglobulin Alleles From Expressed Repertoire Sequencing Data
Gadala-Maria, Daniel, Gidoni, Moriah, Marquez, Susanna, Vander Heiden, Jason A., Kos, Justin T., Watson, Corey T., O'Connor, Kevin C., Yaari, Gur, Kleinstein, Steven H.
Published in Frontiers in immunology (13.02.2019)
Published in Frontiers in immunology (13.02.2019)
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Journal Article
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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Journal Article
Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles
Gadala-Maria, Daniel, Yaari, Gur, Uduman, Mohamed, Kleinstein, Steven H.
Published in Proceedings of the National Academy of Sciences - PNAS (24.02.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (24.02.2015)
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Journal Article
Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis
Yang, Lu, Ng, Yan Er, Sun, Haipeng, Li, Ying, Chini, Lucas C. S., LeBrasseur, Nathan K., Chen, Jun, Zhang, Xu
Published in BMC biology (20.10.2023)
Published in BMC biology (20.10.2023)
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Journal Article
Comparison of tet (X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects
Ding, Yichen, Er, Shuan, Tan, Abel, Gounot, Jean-Sebastien, Saw, Woei-Yuh, Tan, Linda Wei Lin, Teo, Yik Ying, Nagarajan, Niranjan, Seedorf, Henning
Published in Microbiology spectrum (02.04.2024)
Published in Microbiology spectrum (02.04.2024)
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Journal Article
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) (01.08.2025)
Published in Bioinformatics (Oxford, England) (01.08.2025)
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Journal Article
High-throughput muscle fiber typing from RNA sequencing data
Oskolkov, Nikolay, Santel, Malgorzata, Parikh, Hemang M., Ekström, Ola, Camp, Gray J., Miyamoto-Mikami, Eri, Ström, Kristoffer, Mir, Bilal Ahmad, Kryvokhyzha, Dmytro, Lehtovirta, Mikko, Kobayashi, Hiroyuki, Kakigi, Ryo, Naito, Hisashi, Eriksson, Karl-Fredrik, Nystedt, Björn, Fuku, Noriyuki, Treutlein, Barbara, Pääbo, Svante, Hansson, Ola
Published in Skeletal muscle (02.07.2022)
Published in Skeletal muscle (02.07.2022)
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Journal Article
scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Shao, Xin, Liao, Jie, Lu, Xiaoyan, Xue, Rui, Ai, Ni, Fan, Xiaohui
Published in iScience (27.03.2020)
Published in iScience (27.03.2020)
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Journal Article
Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data
Kircher, Berenike, Woltemate, Sabrina, Gutzki, Frank, Schlüter, Dirk, Geffers, Robert, Bähre, Heike, Vital, Marius
Published in Gut microbes (31.12.2022)
Published in Gut microbes (31.12.2022)
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Journal Article
A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data
Ainscough, Benjamin J., Barnell, Erica K., Ronning, Peter, Campbell, Katie M., Wagner, Alex H., Fehniger, Todd A., Dunn, Gavin P., Uppaluri, Ravindra, Govindan, Ramaswamy, Rohan, Thomas E., Griffith, Malachi, Mardis, Elaine R., Swamidass, S. Joshua, Griffith, Obi L.
Published in Nature genetics (01.12.2018)
Published in Nature genetics (01.12.2018)
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Journal Article
Identification of recurrent pathogenic alleles using exome sequencing data: Proof-of-concept study of Russian subjects
Orlov, Igor E., Laidus, Tatiana A., Tumakova, Anastasia V., Yanus, Grigoriy A., Iyevleva, Aglaya G., Sokolenko, Anna P., Bizin, Ilya V., Imyanitov, Evgeny N., Suspitsin, Evgeny N.
Published in European journal of medical genetics (01.02.2022)
Published in European journal of medical genetics (01.02.2022)
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Journal Article
Detecting and phasing minor single-nucleotide variants from long-read sequencing data
Feng, Zhixing, Clemente, Jose C., Wong, Brandon, Schadt, Eric E.
Published in Nature communications (24.05.2021)
Published in Nature communications (24.05.2021)
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Journal Article
16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis
Zuo, Wenxuan, Wang, Beibei, Bai, Xin, Luan, Yihui, Fan, Yingying, Michail, Sonia, Sun, Fengzhu
Published in Scientific reports (19.04.2022)
Published in Scientific reports (19.04.2022)
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Journal Article
Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects
Kim, Ju Han, Lee, Sang-Do, Lee, Jae Seung, Lim, Jae Hyun, Kim, Woo Jin, Oh, Yeon-Mok
Published in International journal of genomics (01.01.2015)
Published in International journal of genomics (01.01.2015)
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Journal Article