Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: Seurat
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/Seurat
Tools for Single Cell Genomics
36 versions
Latest release: about 1 year ago
56 dependent packages
47,302 downloads last month
Papers Mentioning Seurat 1,512
10.7554/eLife.34550
Cellular diversity in the Drosophila midbrain revealed by single-cell transcriptomicsCited by: 198
Author(s): Vincent Croset, Christoph Daniel Treiber, Scott Waddell
Software Mentions: 1
Published: over 6 years ago
10.1073/pnas.2016650117
SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signalingCited by: 383
Author(s): Lisa Miorin, Thomas Kehrer, María Teresa Sánchez-Aparicio, Ke Zhang, Phillip Cohen, Roosheel S. Patel, Anastasija Cupic, Tadashi Makio, Menghan Mei, Elena Moreno, Oded Danziger, Kris M. White, Raveen Rathnasinghe, Melissa B. Uccellini, Shengyan Gao, Teresa Aydillo, Ignacio Mena, Xin Yin, Laura Martin-Sancho, Nevan J. Krogan, Sumit K. Chanda, Michael Schotsaert, Richard W. Wozniak, Yi Ren, Brad R. Rosenberg, Beatriz M. A. Fontoura, Adolfo Garcı́a-Sastre
Software Mentions: 1
Published: about 4 years ago
10.1186/s40478-021-01234-2
Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal DementiaCited by: 3
Author(s): Karthick Natarajan, Jesper Eisfeldt, Maria Hammond, José Miguel Laffita-Mesa, Kalicharan Patra, Behzad Khoshnood, Linn Öijerstedt, Caroline Graff
Software Mentions: 1
Published: over 3 years ago
10.1073/pnas.2016950118
Pluripotent stem cell-derived epithelium misidentified as brain microvascular endothelium requires ETS factors to acquire vascular fateCited by: 103
Author(s): Tyler M. Lu, Sean Houghton, Tarig Magdeldin, José Gabriel Barcia Durán, Andrew P. Minotti, Amanda M. Snead, Andrew A. Sproul, Duc-Huy T. Nguyen, Jenny Xiang, Howard A. Fine, Zev Rosenwaks, Lorenz Studer, Shahin Rafii, Dritan Agalliu, David Redmond, Raphaël Lis
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0243145
Pharmacological inhibition of hematopoietic progenitor kinase 1 positively regulates T-cell functionCited by: 10
Author(s): Yun Wang, Kelvin Zhang, Peter Georgiev, Steven B. Wells, Haiyan Xu, Brian M. Lacey, Zangwei Xu, Jason Laskey, Robbie L. McLeod, Joey L. Methot, Mark Bittinger, Alexander Pasternak, Sheila Ranganath
Software Mentions: 1
Published: almost 4 years ago
10.1093/bioinformatics/btaa087
Statistical significance of cluster membership for unsupervised evaluation of cell identitiesCited by: 19
Author(s): Neo Christopher Chung
Software Mentions: 1
Published: over 4 years ago
10.1186/s12974-021-02202-2
Group 2 innate lymphoid cells are numerically and functionally deficient in the triple transgenic mouse model of Alzheimer’s diseaseCited by: 9
Author(s): Ivan Ting Hin Fung, Yuanyue Zhang, Damian S. Shin, Poornima Sankar, Xiangwan Sun, Shanti S. D’Souza, Renjie Song, Marcy Kuentzel, Sridar V. Chittur, Kristen L. Zuloaga, Qi Yang
Software Mentions: 1
Published: over 3 years ago
10.1172/jci.insight.139019
Epithelial miR-141 regulates IL-13–induced airway mucus productionCited by: 22
Author(s): Sana Siddiqui, Karin Johansson, Alex Joo, Luke R. Bonser, Kyung Duk Koh, Olivier Le Tonquèze, Samaneh Bolourchi, Rodriel A. Bautista, Lorna Zlock, Theodore L. Roth, Alexander Marson, Nirav R. Bhakta, K. Mark Ansel, Walter E. Finkbeiner, David J. Erle, Prescott G. Woodruff
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0233163
Deletion of inositol polyphosphate 4-phosphatase type-II B affects spermatogenesis in miceCited by: 8
Author(s): Yasemin Ceyhan, Manqi Zhang, Jingtao Guo, Carlos G. Sandoval, Jean Vacher, Elena M. Kaftanovskaya, Alexander I. Agoulnik, Irina U. Agoulnik
Software Mentions: 1
Published: over 4 years ago
10.1523/ENEURO.0345-19.2019
Single-Cell Molecular and Cellular Architecture of the Mouse NeurohypophysisCited by: 26
Author(s): Qiyu Chen, Dena Leshkowitz, Janna Blechman, Gil Levkowitz
Software Mentions: 1
Published: almost 5 years ago
10.1172/jci.insight.141851
GLP-1 receptor signaling increases PCSK1 and β cell features in human α cellsCited by: 20
Author(s): Mridusmita Saikia, Marlena M. Holter, Leanne R. Donahue, Isaac S. Lee, Qiaonan C. Zheng, Journey L. Wise, Jenna E Todero, Daryl J. Phuong, Darline Garibay, Reilly W. Coch, Kyle W. Sloop, Adolfo García‐Ocaña, Charles G. Danko, Bethany P. Cummings
Software Mentions: 1
Published: almost 4 years ago
10.1007/s13238-020-00820-9
Sinoatrial node pacemaker cells share dominant biological properties with glutamatergic neuronsCited by: 8
Author(s): Dandan Liang, Zhigang Xue, Jinfeng Xue, Duanyang Xie, Kun Xiong, Huixing Zhou, Fulei Zhang, Xuling Su, Guanghua Wang, Qicheng Zou, Yi Liu, Jian Yang, Honghui Ma, Luying Peng, Chunyu Zeng, Gang Li, Li Wang, Yihan Chen
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0237529
Dysregulation of club cell biology in idiopathic pulmonary fibrosisCited by: 21
Author(s): Wu-Lin Zuo, Mahboubeh Rostami, Michelle G. LeBlanc, Robert J. Kaner, Sarah L. O’Beirne, Jason G. Mezey, Philip L. Leopold, Karsten Quast, Sudha Visvanathan, Jay S. Fine, Matthew Thomas, Ronald G. Crystal
Software Mentions: 1
Published: about 4 years ago
10.1177/2045894020908782
Transcriptional profiling of lung cell populations in idiopathic pulmonary arterial hypertensionCited by: 54
Author(s): Didem Saygın, Tracy Tabib, Humberto E. Trejo Bittar, Eleanor Valenzi, John Sembrat, Stephen Y. Chan, Mauricio Rojas, Robert Lafyatis
Software Mentions: 1
Published: almost 5 years ago
10.1080/15476286.2020.1870362
Elucidating the cellular dynamics of the brain with single-cell RNA sequencingCited by: 13
Author(s): Aida Cardona-Alberich, Manon Tourbez, Sarah F Pearce, Christopher R. Sibley
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.59928
Common cell type nomenclature for the mammalian brainCited by: 47
Author(s): Jeremy A. Miller, Nathan W. Gouwens, Bosiljka Tasic, Forrest Collman, Cindy Tj van Velthoven, Trygve E. Bakken, Michael Hawrylycz, Hongkui Zeng, Ed Lein, Amy Bernard
Software Mentions: 1
Published: almost 4 years ago
10.7554/eLife.65745
Unveiling the sensory and interneuronal pathways of the neuroendocrine connectome in DrosophilaCited by: 23
Author(s): Sebastian Hückesfeld, Philipp Schlegel, Anton Miroschnikow, Andreas Schoofs, Ingo Zinke, André N Haubrich, Casey M Schneider-Mizell, James W. Truman, Richard D. Fetter, Albert Cardona, Michael J. Pankratz
Software Mentions: 1
Published: over 3 years ago
10.1002/jnr.24842
ACSA‐2 and GLAST classify subpopulations of multipotent and glial‐restricted cerebellar precursorsCited by: 6
Author(s): Christina Geraldine Kantzer, Elena Parmigiani, Valentina Cerrato, Stefan Tomiuk, Michail Knauel, Melanie Jungblut, Annalisa Buffo, Andreas Bosio
Software Mentions: 1
Published: over 3 years ago
10.21203/rs.3.rs-80476/v1
Distinct B cell subsets give rise to antigen-specific antibody responses against SARS-CoV-2Cited by: 12
Author(s): Patrick C. Wilson, Christopher T. Stamper, Haley L. Dugan, Lei Li, Nicholas Asby, Peter Halfmann, Jenna J. Guthmiller, Na Zheng, Min Huang, Olivia Stovicek, Jiaolong Wang, Maria Lucia Madariaga, Kumaran Shanmugarajah, Maud O. Jansen, Fatima Amanat, Isabelle Stewart, Siriruk Changrob, Henry A. Utset, Jun Huang, Christopher G. Nelson, Ya-Nan Dai, Paige D. Hall, R. Jedrzejczak, Andrzej Joachimiak, Florian Krammer, D.H. Fremont, Yoshihiro Kawaoka
Software Mentions: 1
Published: about 4 years ago
10.21203/rs.3.rs-42999/v1
Severe SARS-CoV-2 infection is defined by a shift in the serum lipidome resulting in dysregulation of eicosanoid lipid immune mediatorsCited by: 6
Author(s): Benjamin Schwarz, Lokesh Sharma, Lydia M. Roberts, Xiaohua Peng, Santos Bermejo, Ian Leighton, Arnau Casanovas‐Massana, Shelli Farhadian, Albert I. Ko, Charles S. Dela Cruz, Catharine M. Bosio
Software Mentions: 1
Published: over 4 years ago
10.21203/rs.3.rs-214352/v1
A Human 3D neural assembloid model for SARS-CoV-2 infectionCited by: 3
Author(s): Joseph G. Gleeson, Lu Wang, David Sievert, Alex E. Clark, Hannah Federman, Benjamin D. Gastfriend, Eric V. Shusta, Sean P. Palecek, Aaron F. Carlin
Software Mentions: 1
Published: almost 4 years ago
10.1093/bioinformatics/btaa611
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing dataCited by: 74
Author(s): Gregor Sturm, Tamás Szabó, Georgios Fotakis, Marlene Haider, Dietmar Rieder, Zlatko Trajanoski, Francesca Finotello
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0254194
Revealing immune responses in the Mycobacterium avium subsp. paratuberculosis-infected THP-1 cells using single cell RNA-sequencingCited by: 3
Author(s): Hong-Tae Park, Woo Bin Park, Suji Kim, Jae Yong Lim, Gyoungju Nah, Han Sang Yoo
Software Mentions: 1
Published: over 3 years ago
10.1111/imcb.12490
A preliminary investigation into the immune cell landscape of schistosome‐associated liver fibrosis in humansCited by: 4
Author(s): Yu Zhang, Junhui Li, Hao Li, Zhaoqin Zhou, Chunguang Guo, Jie Jiang, Yingzi Ming
Software Mentions: 1
Published: over 3 years ago
10.18632/aging.202288
Phenotyping of immune and endometrial epithelial cells in endometrial carcinomas revealed by single-cell RNA sequencingCited by: 14
Author(s): Yue Guo, Yiran Li, Bailian Cai, Qizhi He, Guofang Chen, Mengfei Wang, Kai Wang, Xiaoping Wan, Yan Qin
Software Mentions: 1
Published: almost 4 years ago
10.1038/s42003-021-02438-x
Butyrophilin-like 2 regulates site-specific adaptations of intestinal γδ intraepithelial lymphocytesCited by: 1
Author(s): Casandra Panea, Ruoyu Zhang, Jeffrey VanValkenburgh, Min Ni, Christina Adler, Yi Wei, Francisca Ochoa, Jennifer Schmahl, Yajun Tang, Chia-Jen Siao, William Poueymirou, Jennifer Espert, Wei Keat Lim, Gurinder S. Atwal, Andrew Murphy, Matthew A. Sleeman, Zaruhi Hovhannisyan, Sokol Haxhinasto
Software Mentions: 1
Published: over 3 years ago
10.21203/rs.3.rs-555275/v1
Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVsCited by: 11
Author(s): Caroline Goujon, Antoine Rebendenne, Priyanka Roy, Boris Bonaventure, Ana Chaves Valadao, Lowiese Desmarets, Yves Rouillé, Marine Tauziet, Mary Arnaud-Arnould, Donatella Giovannini, Yenarae Lee, Peter C DeWeirdt, Mudra Hegde, Francisco Garcia de Gracia, Joe McKellar, Mélanie Wencker, Jean Dubuisson, Sandrine Belouzard, Olivier Moncorgé, John G. Doench
Software Mentions: 1
Published: over 3 years ago
10.18632/aging.102141
Dlx5 and Dlx6 expression in GABAergic neurons controls behavior, metabolism, healthy aging and lifespanCited by: 22
Author(s): Camille de Lombares, Églantine Heude, Gladys Alfama, Anastasia Fontaine, Rim Hassouna, Cécile Vernochet, Fabrice de Chaumont, Christophe Olivo-Marin, Elodie Ey, Sébastien Parnaudeau, François Tronche, Thomas Bourgeron, Serge Luquet, Giovanni Levi, Nicolas Narboux-Nême
Software Mentions: 1
Published: about 5 years ago
10.1186/s13227-020-00162-x
Expression of smooth muscle-like effectors and core cardiomyocyte regulators in the contractile papillae of CionaCited by: 10
Author(s): Christopher Johnson, Florian Razy-Krajka, Alberto Stolfi
Software Mentions: 1
Published: over 4 years ago
10.3390/cancers12051307
Single-Cell Transcriptomic Analysis of Tumor-Derived Fibroblasts and Normal Tissue-Resident Fibroblasts Reveals Fibroblast Heterogeneity in Breast CancerCited by: 124
Author(s): Aimy Sebastian, Nicholas R. Hum, Kelly A. Martin, Sean F. Gilmore, Ivana Peran, Stephen W. Byers, Elizabeth K. Wheeler, Matthew A. Coleman, Gabriela G. Loots
Software Mentions: 1
Published: over 4 years ago
10.1186/s12931-021-01675-2
Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPDCited by: 13
Author(s): Xiuying Li, Guillaume Noell, Tracy Tabib, Alyssa D. Gregory, Humberto E. Trejo Bittar, Ravi Vats, Tomasz W. Kamiński, John Sembrat, Mark E. Snyder, Divay Chandra, Kong Chen, Chunbin Zou, Yingze Zhang, Prithu Sundd, John F. McDyer, Frank C. Sciurba, Mauricio Rojas, Robert Lafyatis, Steve D. Shapiro, Rosa Faner, Toru Nyunoya
Software Mentions: 1
Published: over 3 years ago
10.1186/s12931-021-01709-9
Single-cell characterization of a model of poly I:C-stimulated peripheral blood mononuclear cells in severe asthmaCited by: 6
Author(s): Ailu Chen, Maria P Diaz-Soto, Miguel F. Sanmamed, Taylor Adams, Jonas C. Schupp, Amolika Gupta, Clemente J. Britto, Maor Sauler, Xiting Yan, Qing Liu, Gustavo Niño, Charles S. Dela Cruz, Geoffrey Chupp, José L. Gómez
Software Mentions: 1
Published: over 3 years ago
10.1016/j.immuni.2021.05.005
Identification of a Kupffer cell subset capable of reverting the T cell dysfunction induced by hepatocellular primingCited by: 61
Author(s): Giorgia De Simone, Francesco Andreata, Camille Blériot, Valeria Fumagalli, Chiara Laura, José Manuel García-Manteiga, Pietro Di Lucia, Stefano Gilotto, Xenia Ficht, Federico Ponti, Elisa Bono, Leonardo Giustini, G. Ambrosi, Marta Mainetti, Paola Zordan, Alexandre P. Bénéchet, Micol Ravà, Svetoslav Chakarov, Federica Moalli, Marc Bajénoff, Luca G. Guidotti, Florent Ginhoux, Matteo Iannacone
Software Mentions: 1
Published: about 3 years ago
10.1093/biomethods/bpaa008
Fine-mapping within eQTL credible intervals by expression CROP-seqCited by: 8
Author(s): Yidan Pan, Ruoyu Tian, Ciaran M. Lee, Gang Bao, Greg Gibson
Software Mentions: 1
Published: almost 5 years ago
10.1242/bio.038083
Characterization of spatial and temporal development of Type I and Type II hair cells in the mouse utricle using new cell-type-specific markersCited by: 59
Author(s): Stephen McInturff, J. C. Burns, Matthew W. Kelley
Software Mentions: 1
Published: about 6 years ago
10.1097/HS9.0000000000000034
Single-Cell Sequencing in Normal and Malignant HematopoiesisCited by: 11
Author(s): Nicola K. Wilson, Berthold Göttgens
Software Mentions: 1
Published: over 6 years ago
10.1186/s13227-019-0134-5
Cnidofest 2018: the future is bright for cnidarian researchCited by: 10
Author(s): Shuonan He, Juris A. Grasis, Matthew L. Nicotra, Celina E. Juliano, Christine E. Schnitzler
Software Mentions: 1
Published: about 5 years ago
10.1016/j.xpro.2021.100590
Dissociation of microdissected mouse brain tissue for artifact free single-cell RNA sequencingCited by: 12
Author(s): Lu Liu, Simon Besson-Girard, Hao Ji, K. Gehring, Buket Bulut, Tuğberk Kaya, Fumere Usifo, Mikael Simons, Özgün Gökçe
Software Mentions: 1
Published: over 3 years ago
10.1016/j.heliyon.2020.e05810
Methods for isolation and transcriptional profiling of individual cells from the human heartCited by: 9
Author(s): Neha Pimpalwar, Tomasz Czuba, Melanie H. Smith, Johan Nilsson, Olof Gidlöf, J. G. Smith
Software Mentions: 1
Published: almost 4 years ago
10.1242/bio.058172
The SARS-CoV-2 receptor and other key components of the Renin-Angiotensin-Aldosterone System related to COVID-19 are expressed in enterocytes in larval zebrafishCited by: 13
Author(s): John H. Postlethwait, Michelle S. Massaquoi, Dylan Farnsworth, Yi‐Lin Yan, Karen Guillemin, Adam C. Miller
Software Mentions: 1
Published: over 3 years ago
10.1126/sciadv.abf0787
Dissecting the microenvironment around biosynthetic scaffolds in murine skin wound healingCited by: 63
Author(s): Changwei Hu, Chenyu Chu, Li Liu, Chenbing Wang, Shue Jin, Renli Yang, Shengan Rung, Jidong Li, Yang Qu, Yi Man
Software Mentions: 1
Published: over 3 years ago
10.1093/gigascience/giaa126
D-EE: Distributed software for visualizing intrinsic structure of large-scale single-cell dataCited by: 1
Author(s): Shaokun An, Jingcheng Huang, Lin Wan
Software Mentions: 1
Published: about 4 years ago
10.1186/s12920-021-00977-0
In silico analysis suggests disruption of interactions between HAMP from hepatocytes and SLC40A1 from macrophages in hepatocellular carcinomaCited by: 5
Author(s): Liang Hu, Chao Wu
Software Mentions: 1
Published: over 3 years ago
10.1038/sdata.2019.31
Single-cell RNA-seq of cultured human adipose-derived mesenchymal stem cellsCited by: 52
Author(s): Xuanyu Liu, Qinqin Xiang, Fengming Xu, Jiuzuo Huang, Nanze Yu, Qixu Zhang, Xiao Long, Zhou Zhou
Software Mentions: 1
Published: over 5 years ago
10.1155/2021/7643209
Single-Cell Transcriptomics-Based Study of Transcriptional Regulatory Features in the Mouse Brain VasculatureCited by: 19
Author(s): Weiwei Lin, Lingxiao Xu, Yisheng Chen, Ken Go, Chenyu Sun, Yongjian Zhu
Software Mentions: 1
Published: over 3 years ago
10.1002/eji.201848053
Single‐cell transcriptomes of murine bone marrow stromal cells reveal niche‐associated heterogeneityCited by: 26
Author(s): Richard Addo, Frederik Heinrich, Gitta Anne Heinz, Daniel Schulz, Özen Sercan, Katrin Lehmann, Cam Loan Tran, Markus Bardua, Mareen Matz, Max Löhning, Anja E. Hauser, Andrey Kruglov, Hyun‐Dong Chang, Pawel Durek, Andreas Radbruch, Mir‐Farzin Mashreghi
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0253178
Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterationsCited by: 4
Author(s): Iliana Kerzeli, Martin Lord, Milena Doroszko, Ramy Elgendy, Aikaterini Chourlia, I Stĕpánek, Elinor Larsson, Luuk van Hooren, Sven Nelander, Per‐Uno Malmström, Anca Dragomir, Ulrika Segersten, Sara M. Mangsbo
Software Mentions: 1
Published: over 3 years ago
10.1038/s41597-021-00972-1
Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cellsCited by: 1
Author(s): Doreen Becker, Rosemarie Weikard, Frieder Hadlich, Christa Kühn
Software Mentions: 1
Published: over 3 years ago
10.21105/joss.02061
scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing dataCited by: 2
Author(s): Juan Sebastian Paez, Michael K. Wendt, Nadia A. Lanman
Software Mentions: 1
Published: over 4 years ago
10.1038/s41413-021-00141-5
Mapping the immune microenvironment for mandibular alveolar bone homeostasis at single-cell resolutionCited by: 49
Author(s): Weimin Lin, Qiwen Li, Danting Zhang, Xiaohan Zhang, Xu Qi, Qian Wang, Yaqian Chen, Caojie Liu, Hanwen Li, Shiwen Zhang, Yuan Wang, Bin Shao, Li Zhang, Quan Yuan
Software Mentions: 1
Published: over 3 years ago
10.1038/s42003-021-02522-2
Distinct immune microenvironment profiles of therapeutic responders emerge in combined TGFβ/PD-L1 blockade-treated squamous cell carcinomaCited by: 11
Author(s): Alexander A. Strait, Rachel A. Woolaver, Spencer Hall, Christian D. Young, Sana D. Karam, Antonio Jimeno, Yan Lan, David Raben, Jing H. Wang, Xiaojing Wang
Software Mentions: 1
Published: about 3 years ago
10.1038/s41413-019-0075-6
Mesenchymal VEGFA induces aberrant differentiation in heterotopic ossificationCited by: 35
Author(s): Charles Hwang, Simone Marini, Amanda K. Huber, David M. Stepien, Michael Sorkin, Shawn Loder, Chase A. Pagani, John Li, Noelle D. Visser, Kaetlin Vasquez, Mohamed A. Garada, Shuli Li, Jiajia Xu, Ching Yun Hsu, Paul B. Yu, Aaron W. James, Yuji Mishina, Shailesh Agarwal, Jun Li, Benjamin Lévi
Software Mentions: 1
Published: almost 5 years ago
10.15252/embr.201949555
A cell atlas of adult muscle precursors uncovers early events in fibre‐type divergence in <i>Drosophila</i>Cited by: 14
Author(s): María Paula Zappia, Lucia de Castro, Majd M. Ariss, Holly Jefferson, Abul B.M.M.K. Islam, Maxim V. Frolov
Software Mentions: 1
Published: over 4 years ago
10.1038/s41413-019-0073-8
Focal adhesion protein Kindlin-2 regulates bone homeostasis in miceCited by: 42
Author(s): Huiling Cao, Qinnan Yan, Dong Wang, Yisheng Lai, Bo Zhou, Qi Zhang, Wenfei Jin, Simin Lin, Yiming Lei, Li‐Ting Ma, Yuxi Guo, Yishu Wang, Yilin Wang, Xia Bai, Chuanju Liu, Jian Q. Feng, Chuanyue Wu, Di Chen, Xu Cao, Guozhi Xiao
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pone.0254024
Single-cell transcriptome analysis of the zebrafish embryonic trunkCited by: 8
Author(s): Sanjeeva Metikala, Satish Casie Chetty, Saulius Sumanas
Software Mentions: 1
Published: over 3 years ago
10.1038/s42003-021-02571-7
Generation and characterization of cardiac valve endothelial-like cells from human pluripotent stem cellsCited by: 12
Author(s): Linxi Cheng, Minghui Xie, Weihua Qiao, Yu Song, YanYong Zhang, Yingchao Geng, Weilin Xu, Lin Wang, Zheng Wang, Kai Huang, Nianguo Dong, Yuhua Sun
Software Mentions: 1
Published: about 3 years ago
10.1038/srep24607
A somatic reference standard for cancer genome sequencingCited by: 57
Author(s): David W. Craig, Sara Nasser, Richard Corbett, Simon K. Chan, Lisa Murray, Christophe Legendre, Waibhav Tembe, Jonathan Adkins, Nancy Kim, Shukmei Wong, Angela Baker, Daniel Enríquez, Stephanie J. K. Pond, Erin Pleasance, Andrew J. Mungall, Richard A. Moore, Timothy K. McDaniel, Yussanne Ma, Steven J.M. Jones, Marco A. Marra, John D. Carpten, Winnie S. Liang
Software Mentions: 1
Published: over 8 years ago
10.1038/s41419-020-02787-1
High-dimensional single-cell analysis delineates radiofrequency ablation induced immune microenvironmental remodeling in pancreatic cancerCited by: 32
Author(s): Qinglin Fei, Yu Pan, Wentao Lin, Yuanyuan Zhou, Xingxing Yu, Zelin Hou, Xunbin Yu, Xianchao Lin, Ronggui Lin, Fang Lü, Hongdan Guan, Heguang Huang
Software Mentions: 1
Published: over 4 years ago
10.1038/s41413-020-0097-0
Comparison of skeletal and soft tissue pericytes identifies CXCR4+ bone forming mural cells in human tissuesCited by: 22
Author(s): Jiajia Xu, Dongqing Li, Ching Yun Hsu, Ye Tian, Leititia Zhang, Yiyun Wang, Robert J. Tower, Leslie Chang, Carolyn A. Meyers, Yongxing Gao, Kristen Broderick, Carol D. Morris, Jody E. Hooper, Sridhar Nimmagadda, Bruno Péault, Aaron W. James
Software Mentions: 1
Published: over 4 years ago
10.1186/s13073-020-00722-9
Single-cell transcriptome analysis reveals TOX as a promoting factor for T cell exhaustion and a predictor for anti-PD-1 responses in human cancerCited by: 89
Author(s): Kyung-Soo Kim, Sung Yong Park, Gamin Kim, Jae Won Cho, Da Hee Kim, Young Min Park, Yoon Woo Koh, Sang Jun Ha, Insuk Lee
Software Mentions: 1
Published: over 4 years ago
10.1038/s42003-020-01557-1
Age-related injury responses of human oligodendrocytes to metabolic insults: link to BCL-2 and autophagy pathwaysCited by: 15
Author(s): Milton Guilherme Forestieri Fernandes, Julia Xiao Xuan Luo, Qiao‐Ling Cui, Kelly Perlman, Florian Pernin, Moein Yaqubi, Jeffery A. Hall, Roy Dudley, Myriam Srour, Céline Couturier, Kevin Petrecca, Catherine Larochelle, Luke M. Healy, Jo Anne Stratton, Timothy E. Kennedy, Jack Antel
Software Mentions: 1
Published: almost 4 years ago
10.1002/advs.202100921
Characterization of Cellular Heterogeneity and an Immune Subpopulation of Human MegakaryocytesCited by: 25
Author(s): Cuicui Liu, Dan Wu, Meijuan Xia, Minmin Li, Zhiqiang Sun, Biao Shen, Yiying Liu, Erlie Jiang, Hongtao Wang, Pei Su, Lihong Shi, Zhijian Xiao, Xiaofan Zhu, Wen Zhou, Qian-fei Wang, Xin Gào, Tao Cheng, Jiaxi Zhou
Software Mentions: 1
Published: over 3 years ago
10.1038/s41598-018-30047-y
High-density single cell mRNA sequencing to characterize circulating tumor cells in hepatocellular carcinomaCited by: 63
Author(s): Delia D’Avola, Carlos Villacorta-Martín, Sebastião N. Martins-Filho, Amanda Craig, Ismaïl Labgaa, Johann von Felden, Kimaada Allette, Antoinette Bonaccorso, Parissa Tabrizian, Boris Hartmann, Robert Sebra, Myron Schwartz, Augusto Villanueva
Software Mentions: 1
Published: over 6 years ago
10.26508/lsa.202000680
Single-cell RNA sequencing of human breast tumour-infiltrating immune cells reveals a γδ T-cell subtype associated with good clinical outcomeCited by: 6
Author(s): Katerina Boufea, Víctor González-Huici, Marcus Lindberg, Stefan N. Symeonides, Olga Oikonomidou, Nizar N. Batada
Software Mentions: 1
Published: almost 4 years ago
10.26508/lsa.202000949
Single-cell RNA sequencing of mouse islets exposed to proinflammatory cytokinesCited by: 15
Author(s): Jennifer S. Stancill, Moujtaba Y. Kasmani, Achia Khatun, Weiguo Cui, John A. Corbett
Software Mentions: 1
Published: over 3 years ago
10.1038/s41422-020-0391-9
Dysregulated adaptive immune response contributes to severe COVID-19Cited by: 59
Author(s): Kuai Yu, Jingjing He, Yongjian Wu, Baosong Xie, Xuefei Liu, Bo Wei, Haibo Zhou, Bingliang Lin, Zhixiang Zuo, Wen Wen, Wenxiong Xu, Bin Zou, Lai Wei, Xi Huang, Penghui Zhou
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-019-40923-w
Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterusCited by: 38
Author(s): Michael L. Mucenski, Robert Mahoney, Mike Adam, Andrew Potter, S. Steven Potter
Software Mentions: 1
Published: over 5 years ago
10.3390/cancers12082235
Single-Cell RNA-seq Reveals Obesity-Induced Alterations in the Brca1-Mutated Mammary Gland MicroenvironmentCited by: 5
Author(s): Pang-Kuo Lo, Yuan Yao, Qun Zhou
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-019-41141-0
Molecular profiling of resident and infiltrating mononuclear phagocytes during rapid adult retinal degeneration using single-cell RNA sequencingCited by: 64
Author(s): Kaitryn E. Ronning, Sarah J. Karlen, Eric B. Miller, Marie E. Burns
Software Mentions: 1
Published: over 5 years ago
10.26508/lsa.202000986
PieParty: visualizing cells from scRNA-seq data as pie chartsCited by: 1
Author(s): Stefan Kurtenbach, James Jarad Dollar, Anthony Cruz, Michael A. Durante, Christina L. Decatur, J. William Harbour
Software Mentions: 1
Published: over 3 years ago
10.1186/s13059-020-02044-w
Direct-seq: programmed gRNA scaffold for streamlined scRNA-seq in CRISPR screenCited by: 7
Author(s): Qingkai Song, Ke Ni, Min Liu, Yini Li, Lixia Wang, Yingying Wang, Yingzheng Liu, Zhenxing Yu, Yinyao Qi, Zhike Lu, Lijia Ma
Software Mentions: 1
Published: over 4 years ago
10.1002/advs.201801361
Multiplexed, Sequential Secretion Analysis of the Same Single Cells Reveals Distinct Effector Response Dynamics Dependent on the Initial Basal StateCited by: 25
Author(s): Zhuo Chen, Yao Lu, Kerou Zhang, Yang Xiao, Jun Lü, Rong Fan
Software Mentions: 1
Published: over 5 years ago
10.15252/emmm.202114745
LAG3 is not expressed in human and murine neurons and does not modulate α‐synucleinopathiesCited by: 36
Author(s): Marc Emmenegger, Elena De Cecco, Marián Hruška-Plocháň, Timo Eninger, Matthias M. Schneider, Michael Barth, Elena Tantardini, Pierre De Rossi, Mehtap Bacioglu, Rebekah G. Langston, Alice Kaganovich, Nora Bengoa-Vergniory, Andrés González-Guerra, Merve Avar, Daniel Heinzer, Regina Reimann, Lisa M. Häsler, Therese W. Herling, Naunehal S. Matharu, Natalie Landeck, Kelvin C. Luk, Ronald Melki, Philipp J. Kahle, Simone Hornemann, Tuomas P. J. Knowles, Mark Cookson, Magdalini Polymenidou, Mathias Jucker, Adriano Aguzzi
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.54096
An abundant quiescent stem cell population in Drosophila Malpighian tubules protects principal cells from kidney stonesCited by: 19
Author(s): Chenhui Wang, Allan C. Spradling
Software Mentions: 1
Published: over 4 years ago
10.3390/cancers12041023
Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell LinesCited by: 5
Author(s): Alexander Lang, Patcharawalai Whongsiri, Merve Yılmaz, Tobias Lautwein, Patrick Petzsch, Annemarie Greife, Çagatay Güneş, Karl Köhrer, Günter Niegisch, Michèle J. Hoffmann, Wolfgang A. Schulz
Software Mentions: 1
Published: over 4 years ago
10.1002/advs.202001724
Oncogenic State and Cell Identity Combinatorially Dictate the Susceptibility of Cells within Glioma Development Hierarchy to IGF1R TargetingCited by: 12
Author(s): Anhao Tian, Bo Kang, Baizhou Li, Biying Qiu, Wenhong Jiang, Feng Shao, Qingqing Gao, Rui Li, Chengwei Cai, Rui Jiang, Wei Wang, Pengxiang Chen, Qinghui Liang, Lili Bao, Jianghong Man, Yan Wang, Yu Shi, Jin Li, Minmin Yang, Lisha Wang, Jianmin Zhang, Simon Hippenmeyer, Junming Zhu, Xiu‐Wu Bian, Yingjie Wang, Chong Liu
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-59827-1
Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in HumansCited by: 15
Author(s): Ying Hu, Mohini Ranganathan, Chang Shu, Xiaoyu Liang, Suhas Ganesh, Awo Osafo-Addo, Chunhua Yan, Xin Yu Zhang, Bradley E. Aouizerat, John H. Krystal, Deepak Cyril D’Souza, Ke Xu
Software Mentions: 1
Published: over 4 years ago
10.7554/eLife.39636
Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult miceCited by: 208
Author(s): Chelsea Hepler, Bo Shan, Qianbin Zhang, Gervaise H. Henry, Mengle Shao, Lavanya Vishvanath, Alexandra L. Ghaben, Angela B. Mobley, Douglas W. Strand, Gary C. Hon, Rana K. Gupta
Software Mentions: 1
Published: about 6 years ago
10.1097/MD.0000000000016916
Single-cell transcriptional profiling reveals the heterogenicity in colorectal cancerCited by: 20
Author(s): Weier Dai, Fangbin Zhou, Donge Tang, Liping Lin, Chang Zou, Wenyong Tan, Yong Dai
Software Mentions: 1
Published: over 5 years ago
10.1186/s13059-019-1861-6
Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial modelCited by: 275
Author(s): F. William Townes, Stephanie Hicks, Martin J. Aryee, Rafael A. Irizarry
Software Mentions: 1
Published: almost 5 years ago
10.1038/s41598-020-67730-y
Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritisCited by: 131
Author(s): Ching‐Heng Chou, Vaibhav Jain, Jason Gibson, David E. Attarian, C. Haraden, Christopher B. Yohn, Rémi-Martin Laberge, Simon Gregory, Virginia B. Kraus
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-67691-2
Functional and transcriptional characterization of complex neuronal co-culturesCited by: 24
Author(s): Heather A. Enright, Doris Lam, Aimy Sebastian, Ana Paula Sales, José Cadena, Nicholas R. Hum, Joanne Osburn, Sandra K. G. Peters, Bryan Petkus, David A. Soscia, Kristen S. Kulp, Gabriela G. Loots, Elizabeth K. Wheeler, Nicholas O. Fischer
Software Mentions: 1
Published: over 4 years ago
10.1002/mgg3.1442
Single‐cell RNA sequencing analysis of human kidney reveals the presence of ACE2 receptor: A potential pathway of COVID‐19 infectionCited by: 26
Author(s): Qiyu He, Tsz Ngai Mok, Yun Liang, Chengbo He, Jieruo Li, Jian Pan
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-68223-8
Anti-integrin αv therapy improves cardiac fibrosis after myocardial infarction by blunting cardiac PW1+ stromal cellsCited by: 23
Author(s): Marion Bouvet, Olivier Claude, M Roux, Daniel A. Skelly, Nihar Masurkar, Nathalie Mougenot, Sophie Nadaud, Catherine Blanc, Clément Delacroix, Solenne Chardonnet, Cédric Pionneau, Claire Perret, Elisa Yaniz–Galende, Nadia Rosenthal, David‐Alexandre Trégouët, Giovanna Marazzi, Jean‐Sébastien Silvestre, David Sassoon, Jean‐Sébastien Hulot
Software Mentions: 1
Published: over 4 years ago
10.3390/ijms22041939
Guide Cells Support Muscle Regeneration and Affect Neuro-Muscular Junction OrganizationCited by: 12
Author(s): Flavio Lorenzo Ronzoni, Nefele Giarratana, Stefania Crippa, Mattia Quattrocelli, Marco Cassano, Gabriele Ceccarelli, Laura Benedetti, Jens Van Herck, Maria Gabriella Cusella De Angelis, Marco Vitale, Daniela Galli, Maurilio Sampaolesi
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13024-021-00473-0
Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer’s diseaseCited by: 50
Author(s): Christel Claes, Emma Danhash, Jonathan Hasselmann, Jean Paul Chadarevian, Sepideh Kiani Shabestari, Whitney England, Tau En Lim, Jorge Luis Silva Hidalgo, Robert C. Spitale, Hayk Davtyan, Mathew Blurton‐Jones
Software Mentions: 1
Published: over 3 years ago
10.1038/s41380-020-0745-1
Neuronal activity increases translocator protein (TSPO) levelsCited by: 63
Author(s): Tina Notter, Sina M. Schalbetter, Nicholas E. Clifton, Daniele Mattei, Juliet Richetto, Kerrie L. Thomas, Urs Meyer, Jérémy Hall
Software Mentions: 1
Published: over 4 years ago
10.1038/s41380-020-00988-w
Hippocampal neurons respond to brain activity with functional hypoxiaCited by: 23
Author(s): Umer Javed Butt, Agnes A. Steixner-Kumar, Constanze Depp, Ting Sun, Imam Hassouna, Liane Wüstefeld, Sahab Arinrad, Matthias R. Zillmann, Nadine Schopf, Laura Fernandez Garcia-Agudo, Leonie Mohrmann, Ulli Bode, Anja Ronnenberg, Martin Hindermann, Sandra Goebbels, Stefan Bonn, Dörthe M. Katschinski, Kamilla Woznica Miskowiak, Klaus‐Armin Nave
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13059-016-0931-2
The potential of single-cell profiling in plantsCited by: 75
Author(s): Idan Efroni, Kenneth D. Birnbaum
Software Mentions: 1
Published: over 8 years ago
10.1038/s41598-020-70786-5
Multi-omic single cell analysis resolves novel stromal cell populations in healthy and diseased human tendonCited by: 65
Author(s): A Kendal, T. B. Layton, Hussein Al-Mossawi, Louise Appleton, Stephanie G. Dakin, Robert G. Brown, Constantinos Loizou, M.J. Rogers, Robert Sharp, Andrew Carr
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-72181-6
The immune response after noise damage in the cochlea is characterized by a heterogeneous mix of adaptive and innate immune cellsCited by: 29
Author(s): Vikrant Rai, Megan Beers Wood, Hao Feng, N. Max Schabla, Shu Tu, Jian Zuo
Software Mentions: 1
Published: about 4 years ago
10.7554/eLife.50616
Axon-like protrusions promote small cell lung cancer migration and metastasisCited by: 29
Author(s): Dian Yang, Fangfei Qu, Hongchen Cai, Chen-Hua Chuang, Jing Shan Lim, Nadine S. Jahchan, Barbara M. Grüner, Christin S. Kuo, Christina S. Kong, Madeleine J. Oudin, Monte M. Winslow, Julien Sage
Software Mentions: 1
Published: almost 5 years ago
10.3390/genes12071098
The Trifecta of Single-Cell, Systems-Biology, and Machine-Learning ApproachesCited by: 7
Author(s): Taylor M. Weiskittel, Cristina Correia, Grace T Yu, Choong Yong Ung, Scott H. Kaufmann, Daniel D. Billadeau, Li Hu
Software Mentions: 1
Published: over 3 years ago
10.15252/msb.20209610
The protein expression profile of ACE2 in human tissuesCited by: 657
Author(s): Feria Hikmet, Loren Méar, Åsa Edvinsson, Patrick Micke, Mathias Uhlén, Cecilia Lindskog
Software Mentions: 1
Published: over 4 years ago
10.3390/genes12010019
Structural Variability, Expression Profile, and Pharmacogenetic Properties of TMPRSS2 Gene as a Potential Target for COVID-19 TherapyCited by: 21
Author(s): А. А. Зарубин, В. Г. Степанов, А. В. Марков, Н. А. Колесников, Andrey Marusin, I. Yu. Khitrinskaya, M. G. Swarovskaya, Sergey Litvinov, Natalia Ekomasova, Murat Dzhaubermezov, Н. Р. Максимова, A. S. Syromyatnikova, О. В. Штыгашева, Э. К. Хуснутдинова, М. О. Раджабов, V. N. Kharkov
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41598-020-76488-2
SARS-CoV-2 receptor is co-expressed with elements of the kinin–kallikrein, renin–angiotensin and coagulation systems in alveolar cellsCited by: 39
Author(s): Davi Sidarta-Oliveira, Carlos Poblete Jara, Adriano J. Ferruzzi, Munir S. Skaf, William H. Velander, Eliana P. Araújo, Lı́cio A. Velloso
Software Mentions: 1
Published: about 4 years ago
10.3390/genes11060645
Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal TractCited by: 56
Author(s): Jaewon J. Lee, Scott Kopetz, Eduardo Vilar, John Paul Shen, Ken Chen, Anirban Maitra
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-76972-9
Characterisation of CD4+ T-cell subtypes using single cell RNA sequencing and the impact of cell number and sequencing depthCited by: 14
Author(s): Julia Ding, Samantha Smith, Gisela Orozco, Anne Barton, Steve Eyre, Paul Martin
Software Mentions: 1
Published: about 4 years ago
10.1038/s41598-020-77373-8
Concerted cell and in vivo screen for pancreatic ductal adenocarcinoma (PDA) chemotherapeuticsCited by: 3
Author(s): Somayeh Layeghi-Ghalehsoukhteh, Shreoshi Pal Choudhuri, Ozhan Ocal, Yalda Zolghadri, Victor Pashkov, Hanspeter Niederstrasser, Bruce A. Posner, Havish S. Kantheti, Ana Clara P. Azevedo-Pouly, Huocong Huang, Luc Girard, Raymond J. MacDonald, Rolf A. Brekken, Thomas M. Wilkie
Software Mentions: 1
Published: almost 4 years ago
10.1038/s41598-020-78250-0
Single-cell RNA-seq reveals CD16- monocytes as key regulators of human monocyte transcriptional response to ToxoplasmaCited by: 8
Author(s): Anirudh Patir, Anton Gossner, Prakash Ramachandran, Joana Alves, Tom C. Freeman, Neil C. Henderson, Mick Watson, Musa A. Hassan
Software Mentions: 1
Published: almost 4 years ago