cran: Seurat | Projects | Ecosyste.ms: Papers

10.1186/s12920-018-0433-z

Identification of cancer subtypes from single-cell RNA-seq data using a consensus clustering method
Cited by: 31
Author(s): Yanglan Gan, Ning Li, Guobing Zou, Yongchang Xin, Jihong Guan
Software Mentions: 3
Published: almost 6 years ago

10.1016/j.immuni.2020.06.002

Transcriptional and Functional Analysis of CD1c+ Human Dendritic Cells Identifies a CD163+ Subset Priming CD8+CD103+ T Cells
Cited by: 174
Author(s): Pierre Bourdely, Giorgio Anselmi, Kristine Vaivode, Rodrigo Nalio Ramos, Yoann Missolo-Koussou, Sofía Hidalgo, Jimena Tosselo, Nicolás Gonzalo Núñez, Wilfrid Richer, Anne Vincent‐Salomon, Alka Saxena, Kristie Wood, Álvaro Lladser, Eliane Piaggio, Julie Helft, Pierre Guermonprez
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pbio.3000421

Adult bone marrow progenitors become decidual cells and contribute to embryo implantation and pregnancy
Cited by: 44
Author(s): Reshef Tal, Shafiq Shaikh, Pallavi Pallavi, Aya Tal, Francesc López-Giráldez, Fang Lyu, Yuanyuan Fang, Shruti Chinchanikar, Ying Liu, Harvey J. Kliman, Myles H. Alderman, Nicola Pluchino, Jehanzeb Kayani, Ramanaiah Mamillapalli, Diane S. Krause, Hugh S. Taylor
Software Mentions: 3
Published: about 5 years ago

10.1016/j.xpro.2020.100092

AbSeq Protocol Using the Nano-Well Cartridge-Based Rhapsody Platform to Generate Protein and Transcript Expression Data on the Single-Cell Level
Cited by: 11
Author(s): Jami R. Erickson, Florian Mair, Grace Bugos, Jody Martin, Aaron J. Tyznik, Margaret Nakamoto, Stefanie Mortimer, Martin Prlic
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-021-03957-4

Selecting single cell clustering parameter values using subsampling-based robustness metrics
Cited by: 35
Author(s): Ryan B. Patterson Cross, Ariel J. Levine, Vilas Menon
Software Mentions: 3
Published: almost 4 years ago

10.1155/2021/9548648

Tumor Purity Coexpressed Genes Related to Immune Microenvironment and Clinical Outcomes of Lung Adenocarcinoma
Cited by: 7
Author(s): Ming Bai, Qi Pan, Chen Sun
Software Mentions: 3
Published: over 3 years ago

10.1186/s12967-020-02647-8

Co-expression of cancer driver genes: IDH-wildtype glioblastoma-derived tumorspheres
Cited by: 4
Author(s): Seon‐Jin Yoon, Ho‐Young Son, Jae Yong Shim, Ju Hyung Moon, Eui Hyun Kim, Jong Hee Chang, Wan Yee Teo, Se Hoon Kim, Park Sw, Yong Min Huh, Seok‐Gu Kang
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-020-07223-4

gCAnno: a graph-based single cell type annotation method
Cited by: 0
Author(s): Xiaofei Yang, Shenghan Gao, Ting-Jie Wang, Boyu Yang, Ningxin Dang, Kai Ye
Software Mentions: 3
Published: about 4 years ago

10.1038/s41422-018-0074-y

Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis
Cited by: 228
Author(s): Yao Chen, Yuxuan Zheng, Yun Gao, Zhen Lin, Suming Yang, Tongtong Wang, Qiu Wang, Nannan Xie, Rong Hua, Mingxi Liu, Jiahao Sha, Michael D. Griswold, Jinsong Li, Fuchou Tang, Ming-Han Tong
Software Mentions: 3
Published: over 6 years ago

10.1093/bioinformatics/bty517

iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data
Cited by: 19
Author(s): Mitulkumar V. Patel
Software Mentions: 3
Published: over 6 years ago

10.1186/s41232-021-00170-x

Single-cell and spatial analyses of cancer cells: toward elucidating the molecular mechanisms of clonal evolution and drug resistance acquisition
Cited by: 18
Author(s): Satoi Nagasawa, Yukie Kashima, Ayako Suzuki, Yutaka Suzuki
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-91846-4

High-resolution transcriptional landscape of xeno-free human induced pluripotent stem cell-derived cerebellar organoids
Cited by: 28
Author(s): Samuel Nayler, Devika Agarwal, Fabiola Curion, Rory Bowden, Esther B. E. Becker
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.61973

Improving oligo-conjugated antibody signal in multimodal single-cell analysis
Cited by: 27
Author(s): Terkild Brink Buus, Alberto Herrera, Ellie Ivanova, Eleni P. Mimitou, Anthony Cheng, Ramin S. Herati, Thales Papagiannakopoulos, Peter Smibert, Niels Ødum, Sergei B. Koralov
Software Mentions: 3
Published: over 3 years ago

10.1186/s12967-021-03014-x

Identification of tumor antigens and immune subtypes in lower grade gliomas for mRNA vaccine development
Cited by: 14
Author(s): Liguo Ye, Long Wang, Jian Yang, Ping Hu, Chunyu Zhang, Shiao Tong, Zhennan Liu, Daofeng Tian
Software Mentions: 3
Published: over 3 years ago

10.3389/fnins.2020.00538

Brainstem Organoids From Human Pluripotent Stem Cells
Cited by: 42
Author(s): Nobuyuki Eura, Takeshi K. Matsui, Joachim Luginbühl, Masaya Matsubayashi, Hitoki Nanaura, T. Shiota, Kaoru Kinugawa, Naohiko Iguchi, Takao Kiriyama, Canbin Zheng, Tsukasa Kouno, Yan Lan, Pornparn Kongpracha, Pattama Wiriyasermkul, Yoshihiko Sakaguchi, Riko Nagata, Tomoya Komeda, Naritaka Morikawa, Fumika Kitayoshi, Miyong Jong, Shinko Kobashigawa, Mari Nakanishi, Masatoshi Hasegawa, Yasuhiko Saito, Takashi Shiromizu, Yuhei Nishimura, Takahiko Kasai, Maiko Takeda, Hiroshi Kobayashi, Yusuke Inagaki, Yasuhito Tanaka, Manabu Makinodan, Toshifumi Kishimoto, Hiroki Kuniyasu, Shushi Nagamori, Alysson R. Muotri, Jay W. Shin, Kazuma Sugie, Eiichiro Mori
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.00863

DC Respond to Cognate T Cell Interaction in the Antigen-Challenged Lymph Node
Cited by: 16
Author(s): Caterina Curato, Biana Bernshtein, Eva Zupancič, Almut Dufner, Diego Adhemar Jaitin, Amir Giladi, Eyal David, Louise Chappell‐Maor, Dena Leshkowitz, Klaus–Peter Knobeloch, Ido Amit, Helena F. Florindo, Steffen Jung
Software Mentions: 3
Published: over 5 years ago

10.21203/rs.3.rs-279341/v1

A humanized mouse model of chronic COVID-19 to evaluate disease mechanisms and treatment options
Cited by: 7
Author(s): Esen Sefik, Ben Israelow, Jun Zhao, Rihao Qu, Eric Song, Haris Mirza, Eleanna Kaffe, Stephanie Halene, Eric Meffre, Yuval Kluger, Michel C. Nussenzweig, Craig B. Wilen, Akiko Iwasaki, Richard A. Flavell
Software Mentions: 3
Published: over 3 years ago

10.1186/s13287-020-01934-x

Immunosuppressive effects of mesenchymal stem cells on lung B cell gene expression in LPS-induced acute lung injury
Cited by: 18
Author(s): Bing Feng, Jiaqi Zhu, Yanping Xu, Wenyi Chen, Xinyu Sheng, Xudong Feng, Xiaowei Shi, Jingqi Liu, Qiaoling Pan, Jinfeng Yang, Jiong Yu, Lanjuan Li, Cao H
Software Mentions: 3
Published: about 4 years ago

10.3389/fimmu.2020.00340

Enhanced Phenotype Definition for Precision Isolation of Precursor Exhausted Tumor-Infiltrating CD8 T Cells
Cited by: 24
Author(s): Amaia Martinez-Usatorre, Santiago J. Carmona, Céline Godfroid, Céline Yacoub Maroun, Sara Labiano, Pedro Romero
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers12092551

Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells
Cited by: 12
Author(s): Michał Marczyk, Gauri A. Patwardhan, Jun Zhao, Rihao Qu, Xiaotong Li, Vikram B. Wali, Abhishek Kumar Gupta, Manoj M. Pillai, Yuval Kluger, Qin Yan, Christos Hatzis, Lajos Pusztai, Vignesh Gunasekharan
Software Mentions: 3
Published: about 4 years ago

10.1007/s13238-020-00705-x

Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity
Cited by: 43
Author(s): Yugong Ho, Peng Hu, Michael T. Peel, Sixing Chen, Pablo G. Cámara, Douglas J. Epstein, Hao Wu, Stephen A. Liebhaber
Software Mentions: 3
Published: over 4 years ago

10.1038/s41421-021-00260-7

Spatio-temporal landscape of mouse epididymal cells and specific mitochondria-rich segments defined by large-scale single-cell RNA-seq
Cited by: 23
Author(s): Jianwu Shi, Kin Lam Fok, Pengyuan Dai, Feng Qiao, Mengya Zhang, Huage Liu, Mengmeng Sang, Mei Ye, Yang Liu, Yiwen Zhou, Chengniu Wang, Fei Sun, Gangcai Xie, Hao Chen
Software Mentions: 3
Published: over 3 years ago

10.1186/s12859-019-2817-2

A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification
Cited by: 7
Author(s): Douglas N. Abrams, Parveen Kumar, R. Krishna Murthy Karuturi, Joshy George
Software Mentions: 3
Published: over 5 years ago

10.1167/iovs.61.3.33

Expression and Localization ofKcne2in the Vertebrate Retina
Cited by: 1
Author(s): Moritz Lindner, Michael James Gilhooley, Teele Palumaa, A. Jennifer Morton, Steven Hughes, Mark W. Hankins
Software Mentions: 3
Published: over 4 years ago

10.1152/ajplung.00128.2019

PDGFRα and αSMA mark two distinct mesenchymal cell populations involved in parenchymal and vascular remodeling in pulmonary fibrosis
Cited by: 30
Author(s): Valentina Biasin, Slaven Crnković, Anita Sahu-Osen, Anna Birnhuber, Elie El Agha, Katharina Sinn, Walter Klepetko, Andrea Olschewski, Savério Bellusci, Leigh M. Marsh, Grażyna Kwapiszewska
Software Mentions: 3
Published: over 4 years ago

10.15252/msb.20209945

MicroRNA governs bistable cell differentiation and lineage segregation via a noncanonical feedback
Cited by: 16
Author(s): Chung-Jung Li, Ee Shan Liau, Yi-Han Lee, Yang-Zhe Huang, Ziyi Liu, Andrew Willems, Victoria C. Garside, Edwina McGlinn, Jun-An Chen, Tian Hong
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.63056

A transcriptomic taxonomy of Drosophila circadian neurons around the clock
Cited by: 62
Author(s): Dingbang Ma, Dariusz Przybylski, Katharine C. Abruzzi, Matthias Schlichting, Qunlong Li, Xi Long, Michael Rosbash
Software Mentions: 3
Published: almost 4 years ago

10.1038/s10038-020-00844-3

Single-cell genomics to understand disease pathogenesis
Cited by: 23
Author(s): Seitaro Nomura
Software Mentions: 3
Published: about 4 years ago

10.7554/eLife.69825

Transcriptomic encoding of sensorimotor transformation in the midbrain
Cited by: 24
Author(s): Zhiyong Xie, Mengdi Wang, Zeyuan Liu, Congping Shang, Changjiang Zhang, Le Sun, Huating Gu, Gengxin Ran, Qing Pei, Qiang Ma, Meizhu Huang, Junjing Zhang, Rui Lin, Youtong Zhou, Jiyao Zhang, Miao Zhao, Minmin Luo, Qian Wu, Peng Cao, Xiaoqun Wang
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2020.585980

Discovery and Validation of a Metastasis-Related Prognostic and Diagnostic Biomarker for Melanoma Based on Single Cell and Gene Expression Datasets
Cited by: 16
Author(s): Qi Wan, Chengxiu Liu, Chang Liu, Weiqin Liu, Xiaoran Wang, Zhichong Wang
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-82914-w

Single-cell RNA sequencing reveals developmental heterogeneity among Plasmodium berghei sporozoites
Cited by: 17
Author(s): Anthony A Ruberto, Caitlin Bourke, Nicolas Mérienne, Thomas Obadia, Rogério Amino, Ivo Müeller
Software Mentions: 3
Published: almost 4 years ago

10.3389/fcell.2021.661243

Ligand–Receptor Interactions Elucidate Sex-Specific Pathways in the Trajectory From Primordial Germ Cells to Gonia During Human Development
Cited by: 11
Author(s): Arend W. Overeem, Yolanda W. Chang, Jeroen Spruit, Celine M. Roelse, Susana M. Chuva de Sousa Lopes
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-02223-w

Single-cell RNA sequencing of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium
Cited by: 8
Author(s): Hyun Je Kim, Joon Ho Shim, Ji-Hye Park, Hyun Tae Shin, Kee–Taek Jang, Woong-Yang Park, Kyung-Hoon Lee, Eun Ji Kwon, Hyung-Suk Jang, Hanseul Yang, Jong Hee Lee, Jun‐Mo Yang, Dong‐Youn Lee
Software Mentions: 3
Published: over 3 years ago

10.3389/fpls.2021.687652

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling
Cited by: 4
Author(s): Renee Dale, S. Oswald, Amogh Prabhav Jalihal, Mary-Francis LaPorte, Daniel McKay Fletcher, Allen Hubbard, Shin-Han Shiu, Andrew D. L. Nelson, Alexander Bucksch
Software Mentions: 3
Published: over 3 years ago

10.1073/pnas.2023070118

BABEL enables cross-modality translation between multiomic profiles at single-cell resolution
Cited by: 55
Author(s): Kevin Wu, Kathryn E. Yost, Howard Y. Chang, James Zou
Software Mentions: 3
Published: over 3 years ago

10.1084/jem.20210790

Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells
Cited by: 27
Author(s): Balthasar A. Heesters, Kyah van Megesen, Ilhan Tomris, Robert P. de Vries, Giuliana Magri, Hergen Spits
Software Mentions: 3
Published: over 3 years ago

10.3390/genes11030240

Estimating the Allele-Specific Expression of SNVs From 10× Genomics Single-Cell RNA-Sequencing Data
Cited by: 11
Author(s): N M Prashant, Hongyu Liu, Pavlos Bousounis, Liam F. Spurr, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Dacian Reece-Stremtan, Anélia Horvath
Software Mentions: 3
Published: over 4 years ago

10.1016/j.crmeth.2021.100008

Double-jeopardy: scRNA-seq doublet/multiplet detection using multi-omic profiling
Cited by: 3
Author(s): Bo Sun, Emmanuel Bugarín-Estrada, Lauren Overend, Catherine Elizabeth Walker, Felicia Anna Tucci, Rachael Bashford-Rogers
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.65921

Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart
Cited by: 40
Author(s): Julia Hesse, Christoph Owenier, Tobias Lautwein, Ria Zalfen, Jonas F Weber, Zhaoping Ding, Christina Alter, Alexander Lang, Maria Grandoch, Norbert Gerdes, Jens W. Fischer, Gunnar W. Klau, Christoph Dieterich, Karl Köhrer, Jürgen Schrader
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-020-07241-2

Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis
Cited by: 8
Author(s): Shaojian Gao, Zhijie Wu, Xingmin Feng, Sachiko Kajigaya, Xujing Wang, Neal S. Young
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1009687

The endogenous cellular protease inhibitor SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity
Cited by: 4
Author(s): Carlos Ramirez Alvarez, Carmon Kee, Ashwini Kumar Sharma, Leonie Thomas, Florian I. Schmidt, Megan L. Stanifer, Steeve Boulant, Carl Herrmann
Software Mentions: 3
Published: over 3 years ago

10.1084/jem.20202178

PGD2 and CRTH2 counteract Type 2 cytokine–elicited intestinal epithelial responses during helminth infection
Cited by: 28
Author(s): Oyebola O. Oyesola, Michael T. Shanahan, Matt Kanke, Bridget Mooney, Lauren M. Webb, Shuchi Smita, Macy K. Matheson, Pamela Campioli, Duc Hung Pham, Simon Früh, John W. McGinty, Madeline J. Churchill, Jordan L. Cahoon, Pavithra Sundaravaradan, Becca A. Flitter, Karthik Mouli, Marija S. Nadjsombati, Elena Kamynina, Seth A. Peng, Rebecca L. Cubitt, Karsten Gronert, James D. Lord, Isabella Rauch, Jakob von Moltke, Praveen Sethupathy, Elia D. Tait Wojno
Software Mentions: 3
Published: over 3 years ago

10.1186/s13395-020-00236-3

A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations
Cited by: 109
Author(s): Andrea De Micheli, Jason A. Spector, Olivier Elemento, Benjamin D. Cosgrove
Software Mentions: 3
Published: over 4 years ago

10.1084/jem.20202489

Germinal center–dependent and –independent memory B cells produced throughout the immune response
Cited by: 47
Author(s): Charlotte Viant, Tobias Wirthmiller, Mohamed ElTanbouly, Spencer Chen, Melissa Cipolla, Víctor Ramos, Thiago Y. Oliveira, Leonidas Stamatatos, Michel C. Nussenzweig
Software Mentions: 3
Published: over 3 years ago

10.1186/s12915-021-00955-z

Single-cell RNA-seq reveals a concomitant delay in differentiation and cell cycle of aged hematopoietic stem cells
Cited by: 18
Author(s): Léonard Hérault, Mathilde Poplineau, Adrien Mazuel, Nadine Platet, Élisabeth Rémy, Estelle Duprez
Software Mentions: 3
Published: almost 4 years ago

10.1074/jbc.RA120.015679

Danish and British dementia ITM2b/BRI2 mutations reduce BRI2 protein stability and impair glutamatergic synaptic transmission
Cited by: 16
Author(s): Tao Yin, Wen Yao, Alexander Lemenze, Luciano D’Adamio
Software Mentions: 3
Published: almost 4 years ago

10.1038/s42003-021-01846-3

Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function in mice
Cited by: 8
Author(s): José Gabriel Barcia Durán, Tyler M. Lu, Sean Houghton, Fuqiang Geng, Ryan Schreiner, Jenny Xiang, Shahin Rafii, David Redmond, Raphaël Lis
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.58040

Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors
Cited by: 53
Author(s): AJ Venkatakrishnan, Arjun Puranik, Akash Anand, David Zemmour, Xiang Yao, Xiaoying Wu, Ramakrishna Chilaka, Dariusz K. Murakowski, Kristopher Standish, Bharathwaj Raghunathan, Tyler Wagner, Enrique Garcia-Rivera, Hugo Solomon, Abhinav Garg, Rakesh Barve, Anuli Anyanwu-Ofili, Najat Khan, Venky Soundararajan
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2019.01036

Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver Lymphatic Endothelial Cells
Cited by: 43
Author(s): Beth Tamburini, Jeffrey M. Finlon, Austin E. Gillen, Michael Kriss, Kent Riemondy, Rui Fu, Ronald P. Schuyler, Jay R. Hesselberth, Hugo R. Rosen, Matthew A. Burchill
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.55730

Cardiac endothelial cells maintain open chromatin and expression of cardiomyocyte myofibrillar genes
Cited by: 22
Author(s): Nora Yucel, Jessie Axsom, Yifan Yang, Li Li, Joshua H. Rhoades, Zoltàn Arany
Software Mentions: 3
Published: almost 4 years ago

10.15252/msb.20209866

TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Cited by: 12
Author(s): Vivekanandan Ramalingam, Malini Natarajan, Jeff Johnston, Julia Zeitlinger
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.ppat.1009647

Sustained viremia suppression by SHIVSF162P3CN-recalled effector-memory CD8+ T cells after PD1-based vaccination
Cited by: 1
Author(s): Yik Chun Wong, Liu Wan, Lok Yan Yim, Xin Li, Hui Wang, Yue Ming, Mang Niu, Lin Cheng, Liuyi Ling, Yanhua Du, Samantha M. Y. Chen, Kmc Cheung, Haibo Wang, Xian Tang, Jiansong Tang, Haoji Zhang, You‐Qiang Song, Lisa A. Chakrabarti, Zhiwei Chen
Software Mentions: 3
Published: over 3 years ago

10.1038/s42003-021-02142-w

A combined approach for single-cell mRNA and intracellular protein expression analysis
Cited by: 52
Author(s): Johan Reimegård, Marcel Tarbier, Marcus Danielsson, Jens Schuster, Sathishkumar Baskaran, Styliani Panagiotou, Niklas Dahl, Marc R. Friedländer, Caroline J. Gallant
Software Mentions: 3
Published: over 3 years ago

10.1038/s41421-020-00213-6

Characterization and generation of human definitive multipotent hematopoietic stem/progenitor cells
Cited by: 18
Author(s): Yanling Zhu, Tianyu Wang, Jiaming Gu, Ke Huang, Tian Zhang, Zhishuai Zhang, He Liu, Jun Tang, Yuchan Mai, Yanqi Zhang, Yuhang Li, Yashu Feng, Baoqiang Kang, Jinbing Li, Yongli Shan, Qianyu Chen, Jian Zhang, Bing Liang, Junwei Wang, Minghui Gao, Di Zhang, Min Zhou, Xiaofen Zhong, Jiekai Chen, Duanqing Pei, Jinfu Nie, Bing Liu, Guangjin Pan
Software Mentions: 3
Published: almost 4 years ago

10.3389/fimmu.2020.01999

Validation of a Combined Transcriptome and T Cell Receptor Alpha/Beta (TRA/TRB) Repertoire Assay at the Single Cell Level for Paucicellular Samples
Cited by: 3
Author(s): Nicolle H.R. Litjens, Anton W. Langerak, Amy C. J. van der List, Mariska Klepper, Maaike de Bie, Zakia Azmani, Alexander T. den Dekker, Rutger W. W. Brouwer, M. Betjes, Wilfred F. J. van IJcken
Software Mentions: 3
Published: about 4 years ago

10.3389/fncel.2021.624826

Single Cell Transcriptome Data Analysis Defines the Heterogeneity of Peripheral Nerve Cells in Homeostasis and Regeneration
Cited by: 28
Author(s): Bing Chen, Matthew C. Banton, Lolita Singh, David B. Parkinson, Xin‐Peng Dun
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0205883

Single-cell RNA sequencing of the mammalian pineal gland identifies two pinealocyte subtypes and cell type-specific daily patterns of gene expression
Cited by: 33
Author(s): Joseph C. Mays, Michael C. Kelly, Steven L. Coon, Lynne A. Holtzclaw, Martin F. Rath, Matthew W. Kelley, David C. Klein
Software Mentions: 3
Published: about 6 years ago

10.1126/scitranslmed.abe8146

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys
Cited by: 128
Author(s): Emily Speranza, Brandi N. Williamson, Friederike Feldmann, Gail L. Sturdevant, Lizzette Pérez-Pérez, Kimberly Meade-White, Brian J Smith, Jamie Lovaglio, Craig Martens, Vincent J. Munster, Atsushi Okumura, Carl Shaia, Heinz Feldmann, Sonja M. Best, Emmie de Wit
Software Mentions: 3
Published: almost 4 years ago

10.3389/fendo.2021.690387

L-Cell Expression of Melanocortin-4-Receptor Is Marginal in Most of the Small Intestine in Mice and Humans and Direct Stimulation of Small Intestinal Melanocortin-4-Receptors in Mice and Rats Does Not Affect GLP-1 Secretion
Cited by: 1
Author(s): Rune Ehrenreich Kuhre, Ida M. Modvig, Sara L. Jepsen, Hüsün Sheyma Kizilkaya, Cecilie Bæch-Laursen, Christopher A. Smith, Frank Reimann, Fiona M. Gribble, Mette M. Rosenkilde, Jens J. Holst
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2021.648917

Deciphering the Prognostic Implications of the Components and Signatures in the Immune Microenvironment of Pancreatic Ductal Adenocarcinoma
Cited by: 34
Author(s): Rong Tang, Xiaomeng Liu, Chen Liang, Jie Hua, Jin Xu, Wei Wang, Qingcai Meng, Jiang Liu, Bo Zhang, Xianjun Yu, Si Shi
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.ppat.1008660

Identification of oncolytic vaccinia restriction factors in canine high-grade mammary tumor cells using single-cell transcriptomics
Cited by: 3
Author(s): Béatrice Cambien, Kévin Lebrigand, Alberto Baeri, Nicolas Nottet, Catherine Compin, Audrey Lamit, Olivier Ferraris, Christophe N. Peyrefitte, Virginie Magnone, Jérôme Henriques, Laure‐Emmanuelle Zaragosi, Sophie Giorgetti‐Peraldi, Fréd́eric Bost, Marine Gautier-Isola, Roger Rezzonico, Pascal Barbry, Robert Barthel, Bernard Mari, Georges Vassaux
Software Mentions: 3
Published: about 4 years ago

10.1186/s12859-021-04267-5

Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing
Cited by: 8
Author(s): Lior Galanti, Dennis Shasha, Kristin C. Gunsalus
Software Mentions: 3
Published: over 3 years ago

10.3389/fonc.2021.749398

A Tumor-Infiltration CD8+ T Cell-Based Gene Signature for Facilitating the Prognosis and Estimation of Immunization Responses in HPV+ Head and Neck Squamous Cell Cancer
Cited by: 7
Author(s): Yingning Wu, Lingzhang Meng, Kai Cai, Jingjie Zhao, Siyuan He, Jiajia Shen, Qiuju Wei, Zechen Wang, Suren R. Sooranna, Li Hengguo, Jian Song
Software Mentions: 3
Published: about 3 years ago

10.3389/fimmu.2021.613810

Göttingen Minipigs as a Model to Evaluate Longevity, Functionality, and Memory of Immune Response Induced by Pertussis Vaccines
Cited by: 3
Author(s): Céline Vaure, Véronique Grégoire-Barou, Virginie Courtois, Émilie Chautard, Cyril Dégletagne, Yuanqing Liu
Software Mentions: 2
Published: over 3 years ago

10.3390/cells10092222

Modeling Notch-Induced Tumor Cell Survival in the Drosophila Ovary Identifies Cellular and Transcriptional Response to Nuclear NICD Accumulation
Cited by: 5
Author(s): Allison Jevitt, Yi-Chun Huang, Su-Mei Zhang, Deeptiman Chatterjee, Xianfeng Wang, Gengqiang Xie, Wu-Min Deng
Software Mentions: 2
Published: about 3 years ago

10.3390/cells10051214

Sex-Specific Isolation and Propagation of Human Premeiotic Fetal Germ Cells and Germ Cell-Like Cells
Cited by: 11
Author(s): Swati Mishra, Jasin Taelman, Yolanda W. Chang, Annekatrien Boel, Petra De Sutter, Björn Heindryckx, Susana M. Chuva de Sousa Lopes
Software Mentions: 2
Published: over 3 years ago

10.3390/cells9040920

scRNA-seq Profiling of Human Testes Reveals the Presence of the ACE2 Receptor, A Target for SARS-CoV-2 Infection in Spermatogonia, Leydig and Sertoli Cells
Cited by: 441
Author(s): Zhengpin Wang, Xiaojiang Xu
Software Mentions: 2
Published: over 4 years ago

10.1002/ctm2.321

Single‐cell transcriptomics provides new insights into the role of fibroblasts during peritoneal fibrosis
Cited by: 8
Author(s): Jinhua Zhang, Yuxian Chen, Tufeng Chen, Benchun Miao, Zuofu Tang, Xiao Hu, Yilun Luo, Tong Zheng, Ning Na
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.50354

Single cell transcriptome atlas of the Drosophila larval brain
Cited by: 83
Author(s): Clarisse Brunet Avalos, Gernot Maier, Rémy Bruggmann, Simon G. Sprecher
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-021-02099-w

Cryptic developmental events determine medulloblastoma radiosensitivity and cellular heterogeneity without altering transcriptomic profile
Cited by: 10
Author(s): Daniel Malawsky, Seth Weir, Jennifer K. Ocasio, Benjamin Babcock, Taylor Dismuke, Abigail H. Cleveland, Andrew M. Donson, Rajeev Vibhakar, Kirk C. Wilhelmsen, Timothy R. Gershon
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.05042

Response to Nodal morphogen gradient is determined by the kinetics of target gene induction
Cited by: 85
Author(s): Julien Dubrulle, Benjamin M Jordan, Laila Akhmetova, Jeffrey A. Farrell, Seok-Hyung Kim, Lilianna Solnica‐Krezel, Alexander F. Schier
Software Mentions: 2
Published: over 9 years ago

10.1038/s42003-019-0487-2

Canine osteosarcoma genome sequencing identifies recurrent mutations in DMD and the histone methyltransferase gene SETD2
Cited by: 67
Author(s): Heather L. Gardner, Karthigayini Sivaprakasam, Natalia Briones, Victoria Zismann, Nieves Perdigones, Kevin Drenner, Salvatore Facista, Ryan Richholt, Winnie S. Liang, Jessica Aldrich, Jeffrey M. Trent, Peter G. Shields, Nicholas A. Robinson, Jeremy Johnson, Susan E. Lana, Peter J. Houghton, Joelle M. Fenger, Gwendolen Lorch, Katherine A. Janeway, Cheryl A. London, William P.D. Hendricks
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-020-0763-1

Recurrent pregnancy loss is associated with a pro-senescent decidual response during the peri-implantation window
Cited by: 132
Author(s): Emma S. Lucas, Pavle Vrljicak, Joanne Muter, Maria Diniz-da-Costa, Paul J. Brighton, Chow-Seng Kong, Julia Lipecki, Katherine Fishwick, Joshua Odendaal, Lauren J. Ewington, Siobhán Quenby, Sascha Ott, Jan J. Brosens
Software Mentions: 2
Published: almost 5 years ago

10.1038/s42003-019-0618-9

Single-cell RNA-sequencing analysis of estrogen- and endocrine-disrupting chemical-induced reorganization of mouse mammary gland
Cited by: 28
Author(s): Noriko Kanaya, Gregory Chang, Xiwei Wu, Kohei Saeki, Lauren Bernal, Hyun-Jeong Shim, Jinhui Wang, Charles Warden, Takuro Yamamoto, Jay Li, June-Soo Park, Timothy W. Synold, Steve Vonderfecht, Michele Rakoff, Susan L. Neuhausen, Shiuan Chen
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers12102946

Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers
Cited by: 6
Author(s): Emmanuel Dollinger, Daniel Bergman, Peijie Zhou, Scott X. Atwood, Qing Nie
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-020-01522-y

Molecularly targeted photothermal ablation improves tumor specificity and immune modulation in a rat model of hepatocellular carcinoma
Cited by: 13
Author(s): Nina M. Muñoz, Crystal Dupuis, Madison H. Williams, Kathleen Dixon, Amanda McWatters, Rony Avritscher, Richard R. Bouchard, Ahmed O. Kaseb, Kyle M. Schachtschneider, Arvind Rao, Rahul A. Sheth
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.csbj.2020.10.016

Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives
Cited by: 26
Author(s): Geyang Luo, Qian Gao, Shuye Zhang, Bo Yan
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.csbj.2021.06.043

UCell: Robust and scalable single-cell gene signature scoring
Cited by: 158
Author(s): Massimo Andreatta, Santiago J. Carmona
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13054-021-03481-0

Identification and characterization of neutrophil heterogeneity in sepsis
Cited by: 32
Author(s): Xinxin Qi, Yang Yu, Ran Sun, Jiamin Huang, Lu Liu, Yunxi Yang, Rui Tao, Bo Sun
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.devcel.2020.12.004

Inducible Stem-Cell-Derived Embryos Capture Mouse Morphogenetic Events In Vitro
Cited by: 64
Author(s): Gianluca Amadei, Kasey Y.C. Lau, Joachim De Jonghe, Carlos W. Gantner, Berna Sözen, Christopher Chan, Meng Zhu, Christos Kyprianou, Florian Hollfelder, Magdalena Zernicka‐Goetz
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.59445

High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human ESC gastruloid cultures
Cited by: 54
Author(s): Kyaw Thu Minn, Yaotian Fu, Shenghua He, Sabine Dietmann, Steven C. George, Mark A. Anastasio, Samantha A. Morris, Lilianna Solnica‐Krezel
Software Mentions: 2
Published: about 4 years ago

10.1242/dmm.044404

Quantitative single-cell interactomes in normal and virus-infected mouse lungs
Cited by: 13
Author(s): Margo P. Cain, Belinda Hernández, Jichao Chen
Software Mentions: 2
Published: almost 5 years ago

10.15252/embj.2019103476

Multilineage murine stem cells generate complex organoids to model distal lung development and disease
Cited by: 35
Author(s): Ana Ivonne Vazquez‐Armendariz, Monika Heiner, Elie El Agha, Isabelle Salwig, Andreas Hoek, Marie Christin Hessler, Irina Shalashova, Amit Shrestha, Gianni Carraro, Jan Philip Mengel, Andreas Günther, Rory E. Morty, István Vadász, Martin Schwemmle, Wolfgang Kummer, Torsten Hain, Alexander Goesmann, Savério Bellusci, Werner Seeger, Thomas Braun, Susanne Herold
Software Mentions: 2
Published: about 4 years ago

10.15252/emmm.201910515

Targeting <scp>TGF</scp> βR2‐mutant tumors exposes vulnerabilities to stromal <scp>TGF</scp> β blockade in pancreatic cancer
Cited by: 46
Author(s): Huocong Huang, Yuqing Zhang, Valerie Gallegos, Noah Sorrelle, Mohamed Zaid, Jamie Toombs, Wenting Du, Steven H. Wright, Moriah M. Hagopian, Zhaoning Wang, Abdel Hosein, Adwait Amod Sathe, Chao Xing, Eugene J. Koay, Kyla E. Driscoll, Rolf A. Brekken
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers13051067

Dive into Single, Seek Out Multiple: Probing Cancer Metastases via Single-Cell Sequencing and Imaging Techniques
Cited by: 3
Author(s): Shang Su, Xiaohong Li
Software Mentions: 2
Published: over 3 years ago

10.1002/advs.202100629

Pulmonary Aerosol Delivery of Let‐7b microRNA Confers a Striking Inhibitory Effect on Lung Carcinogenesis through Targeting the Tumor Immune Microenvironment
Cited by: 13
Author(s): Qi Zhang, Jing Pan, Donghai Xiong, Yian Wang, Mark Steven Miller, Shizuko Sei, Robert H. Shoemaker, Alberto Izzotti, Ming You
Software Mentions: 2
Published: over 3 years ago

10.1080/22221751.2020.1781551

Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site
Cited by: 40
Author(s): Xi Jin, Kangli Xu, Penglei Jiang, Jiangshan Lian, Shaorui Hao, Hang‐Ping Yao, Hongyu Jia, Yimin Zhang, Lin Zheng, Nuoheng zheng, Dong Chen, Jinmei Yao, Jianhua Hu, Gao J, Liang Wen, Jian Shen, Yue Ren, Guodong Yu, Xiaoyan Wang, Yingfeng Lu, Xiaopeng Yu, Liang Yu, Da‐Xiong Xiang, Nanping Wu, Xiangyun Lu, Linfang Cheng, Fumin Liu, Haibo Wu, Changzhong Jin, Xiaofeng Yang, Pengxu Qian, Yunqing Qiu, Jifang Sheng, Tingbo Liang, Lanjuan Li, Yida Yang
Software Mentions: 2
Published: almost 5 years ago

10.7554/eLife.65762

A sustained type I IFN-neutrophil-IL-18 axis drives pathology during mucosal viral infection
Cited by: 13
Author(s): Tania Lebratti, Ying Shiang Lim, Adjoa Cofie, Prabhakar S. Andhey, Xiaoping Jiang, Jason Scott, Maria Rita Fabbrizi, Ayşe Naz Ozantürk, Christine Pham, Regina A. Clemens, Maxim N. Artyomov, Mary C. Dinauer, Haina Shin
Software Mentions: 2
Published: over 3 years ago

10.1016/j.exphem.2018.09.004

The Human Cell Atlas bone marrow single-cell interactive web portal
Cited by: 152
Author(s): Stuart Hay, Kyle Ferchen, Kashish Chetal, H. Leighton Grimes, Nathan Salomonis
Software Mentions: 2
Published: almost 6 years ago

10.12688/f1000research.24163.2

Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency
Cited by: 0
Author(s): Maryam Zand, Jianhua Ruan
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0244743

Transcriptional profiling of pediatric cholestatic livers identifies three distinct macrophage populations
Cited by: 20
Author(s): Sarah Taylor, Shang-Yang Chen, Gaurav Gadhvi, Liang Feng, Kyle D. Gromer, Hiam Abdala‐Valencia, Ki-Won Nam, Salina Dominguez, Anna B. Montgomery, Paul A. Reyfman, Lorena Ostilla, Joshua B. Wechsler, Carla M. Cuda, Richard M. Green, Harris Perlman, Deborah R. Winter
Software Mentions: 2
Published: almost 4 years ago

10.3389/fnagi.2021.731180

Microglia Mediate the Occurrence and Development of Alzheimer’s Disease Through Ligand-Receptor Axis Communication
Cited by: 13
Author(s): Chongdong Jian, Lei Wei, Ruikang Mo, Rongjie Li, Lucong Liang, Liechun Chen, Chun Zou, Youshi Meng, Ying Liu, Donghua Zou
Software Mentions: 2
Published: about 3 years ago

10.3389/fbioe.2020.564057

Cell Development Deficiency and Gene Expression Dysregulation of Trisomy 21 Retina Revealed by Single-Nucleus RNA Sequencing
Cited by: 2
Author(s): Fangyuan Hu, Feng‐Juan Gao, Ping Xu, Shenghai Zhang
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.36865

Pdgfra marks a cellular lineage with distinct contributions to myofibroblasts in lung maturation and injury response
Cited by: 119
Author(s): Rongbo Li, Ksenija Bernau, Nathan Sandbo, Jing Gu, Sebastian Preißl, Xin Sun
Software Mentions: 2
Published: about 6 years ago

10.3389/fcvm.2020.00042

Single Cell Analysis in Vascular Biology
Cited by: 46
Author(s): Nicholas W. Chavkin, Karen K. Hirschi
Software Mentions: 2
Published: over 4 years ago

10.3389/fcvm.2019.00165

Single Cell Analysis of Endothelial Cells Identified Organ-Specific Molecular Signatures and Heart-Specific Cell Populations and Molecular Features
Cited by: 64
Author(s): Wei Feng, Lyuqin Chen, Patricia K. Nguyen, Sean M. Wu, Guang Li
Software Mentions: 2
Published: almost 5 years ago

10.3389/fcell.2021.662903

Genetic Defects in DNAH2 Underlie Male Infertility With Multiple Morphological Abnormalities of the Sperm Flagella in Humans and Mice
Cited by: 16
Author(s): Jae Yeon Hwang, Shoaib Nawaz, Jungmin Choi, Huafeng Wang, Shabir Hussain, Mehboob Nawaz, Francesc López-Giráldez, Kyungjo Jeong, Weilai Dong, Jong Nam Oh, Kaya Bilgüvar, Shrikant Mane, Chang Kyu Lee, Christopher Bystroff, Richard P. Lifton, Wasim Ahmad, Jin‐Ho Chung
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.54501

Semiochemical responsive olfactory sensory neurons are sexually dimorphic and plastic
Cited by: 18
Author(s): Aashutosh Vihani, Xiaoyang Serene Hu, Sivaji Gundala, Sachiko Koyama, Eric Block, Hiroaki Matsunami
Software Mentions: 2
Published: almost 4 years ago

10.3389/fcell.2021.622519

Connecting the Dots: Resolving the Bone Marrow Niche Heterogeneity
Cited by: 41
Author(s): Igor Dolgalev, Anastasia Tikhonova
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.657149

The Transcription Regulator Patz1 Is Essential for Neural Stem Cell Maintenance and Proliferation
Cited by: 5
Author(s): Sara Mancinelli, Marianna Vitiello, Maria Donnini, Francesca Mantile, Giuseppe Palma, Antonio Luciano, Claudio Arra, Laura Cerchia, Giovanna L. Liguori
Software Mentions: 2
Published: over 3 years ago

Projects: cran: Seurat

Papers Mentioning Seurat 1,512