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
10.1016/j.celrep.2019.09.082
DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing DataCited by: 120
Author(s): Erica A. K. DePasquale, Daniel Schnell, Pieter-Jan Van Camp, Íñigo Valiente-Alandí, Burns C. Blaxall, H. Leighton Grimes, Harinder Singh, Nathan Salomonis
Software Mentions: 5
Published: about 5 years ago
10.1186/s13024-021-00481-0
Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer’s disease brainsCited by: 9
Author(s): Julio Barrera, Lingyun Song, Julia Gamache, Melanie E. Garrett, Alexias Safi, Young Won Yun, Ivana Premasinghe, Daniel J. Sprague, Danielle Chipman, Jeffrey Li, Hélène Fradin, Karen Soldano, Raluca Gordân, Allison Ashley‐Koch, Gregory E. Crawford, Ornit Chiba‐Falek
Software Mentions: 5
Published: about 3 years ago
10.1186/s13619-020-00042-8
Mapping a mammalian adult adrenal gland hierarchy across species by microwell-seqCited by: 7
Author(s): Shih–Wei Lai, Lifeng Ma, E Weigao, Fang Ye, Haide Chen, Xiaoping Han, Guoji Guo
Software Mentions: 5
Published: over 4 years ago
10.3389/fimmu.2021.627036
Single Cell RNA-Seq and Machine Learning Reveal Novel Subpopulations in Low-Grade Inflammatory Monocytes With Unique Regulatory CircuitsCited by: 8
Author(s): Jiyoung Lee, Shuo Geng, Song Li, Liwu Li
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.62270
The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timelineCited by: 66
Author(s): Danielle Janosevic, Jered Myslinski, Thomas McCarthy, Amy Zollman, Farooq Syed, Xiaoling Xuei, Hongyu Gao, Yunlong Liu, Kimberly S. Collins, Ying‐Hua Cheng, Seth Winfree, Tarek M. El‐Achkar, Bernhard Maier, Ricardo Melo Ferreira, Michael T. Eadon, Takashi Hato, Pierre C. Dagher
Software Mentions: 5
Published: almost 4 years ago
10.3389/fimmu.2021.711980
Characterization of Organ-Specific Regulatory B Cells Using Single-Cell RNA SequencingCited by: 7
Author(s): Si Yu Yang, Jie Long, Meng Huang, Pan Luo, Zhen Bian, Ya Xu, Chengbo Wang, Shu Yang, Li Liang, Carlo Selmi, M. Eric Gershwin, Zhi Bin Zhao, Zhe Xiong Lian
Software Mentions: 5
Published: about 3 years ago
10.7554/eLife.59095
Constitutive activation of cellular immunity underlies the evolution of resistance to infection in DrosophilaCited by: 17
Author(s): Alexandre B. Leitão, Ramesh Arunkumar, Jonathan P. Day, Emma M Geldman, Ismaël Morin-Poulard, Michèle Crozatier, Francis M. Jiggins
Software Mentions: 5
Published: almost 4 years ago
10.7554/eLife.62522
Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genesCited by: 117
Author(s): Allen Wang, Joshua Chiou, Olivier Poirion, Justin Buchanan, Michael J. Valdez, Jamie M. Verheyden, Xiaomeng Hou, Parul Kudtarkar, Sharvari Narendra, Jacklyn Newsome, Minzhe Guo, Dina A. Faddah, Kai Zhang, Randee E. Young, Justinn Barr, Enikö Sajti, Ravi S. Misra, Heidie Huyck, Lisa M. Rogers, Cory Poole, JA Whitsett, Gloria S. Pryhuber, Yan Xu, Kyle J. Gaulton, Sebastian Preißl, Xin Sun
Software Mentions: 5
Published: about 4 years ago
10.1038/s41423-020-00574-8
Single-cell profiling reveals the trajectories of natural killer cell differentiation in bone marrow and a stress signature induced by acute myeloid leukemiaCited by: 48
Author(s): Adeline Crinier, Pierre‐Yves Dumas, Éric Bertrand, Christelle Pipéroglou, Laurine Gil, Arnaud Villacreces, Frédéric Vély, Zoran Ivanović, Pierre Milpied, Émilie Narni-Mancinelli, Éric Vivier
Software Mentions: 5
Published: almost 4 years ago
10.1002/jcsm.12643
Single‐cell RNA sequencing and lipidomics reveal cell and lipid dynamics of fat infiltration in skeletal muscleCited by: 33
Author(s): Zhonglin Xu, Wenjing You, Wentao Chen, Yanbing Zhou, Qiuyun Nong, Teresa G. Valencak, Yizhen Wang, Tizhong Shan
Software Mentions: 5
Published: almost 4 years ago
10.3389/fnmol.2021.712609
NMDARs Drive the Expression of Neuropsychiatric Disorder Risk Genes Within GABAergic Interneuron Subtypes in the Juvenile BrainCited by: 7
Author(s): Vivek Mahadevan, Apratim Mitra, Yajun Zhang, Xitong Yuan, Areg Peltekian, Ramesh Chittajallu, Caroline Esnault, Dragan Maric, C. T. Rhodes, Kenneth A. Pelkey, Ryan Dale, Timothy J. Petros, Chris J. McBain
Software Mentions: 5
Published: about 3 years ago
10.1038/s41421-020-00214-5
Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progressionCited by: 67
Author(s): Guohe Song, Yang Shi, Meiying Zhang, Shyamal Goswami, Saifullah Afridi, Ling Meng, Jiaqiang Ma, Yi Chen, Youpei Lin, Juan Zhang, Yuming Liu, Zijie Jin, Shenghong Yang, Dongning Rao, Shu Zhang, Aiwu Ke, Xiaoying Wang, Yang Cao, Jian Zhou, Jia Fan, Xiaoming Zhang, Ruibin Xi, Qiang Gao
Software Mentions: 5
Published: almost 4 years ago
10.1186/s40779-021-00336-1
Advances in single-cell sequencing: insights from organ transplantationCited by: 7
Author(s): Ying Wang, Jian‐Ye Wang, Angelika Schnieke, Konrad Fischer
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-020-07300-8
Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™Cited by: 2
Author(s): Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac M. Neuhaus, Alice M. Walsh, Zachary W. Pitluk
Software Mentions: 5
Published: almost 4 years ago
10.1093/gigascience/giy117
Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiationCited by: 16
Author(s): Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Junyan Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J. Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu
Software Mentions: 5
Published: about 6 years ago
10.1038/s41421-020-00236-z
Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy lossCited by: 74
Author(s): Chuang Guo, Pengfei Cai, Lina Jin, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lü Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu
Software Mentions: 5
Published: almost 4 years ago
10.1016/j.medj.2021.01.006
Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosisCited by: 39
Author(s): Max Kaufmann, Hayley G. Evans, Anna-Lena Schaupp, Jan Broder Engler, Gurman Kaur, Anne Willing, Nina Kursawe, Charlotte Schubert, Kathrine E. Attfield, Lars Fugger, Manuel A. Friese
Software Mentions: 5
Published: over 3 years ago
10.1002/eji.201948432
CD73 contributes to anti‐inflammatory properties of afferent lymphatic endothelial cells in humans and miceCited by: 10
Author(s): Dominik Eichin, Alberto Pessia, Akiko Takeda, Joni Laakkonen, Lydia Bellmann, Matti Kankainen, Beat A. Imhof, Patrizia Stoitzner, Jing Tang, Marko Salmi, Sirpa Jalkanen
Software Mentions: 5
Published: about 4 years ago
10.7554/eLife.49424
Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nucleiCited by: 164
Author(s): Jing Ren, Alina Isakova, Drew Friedmann, Jiawei Zeng, Sophie M. Grutzner, Albert Pun, Grace Zhao, Sai Saroja Kolluru, Ruiyu Wang, Rui Lin, Pengcheng Li, Anan Li, Jennifer L. Raymond, Qi Luo, Minmin Luo, Stephen R. Quake, Liqun Luo
Software Mentions: 5
Published: about 5 years ago
10.7554/eLife.55792
An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genesCited by: 56
Author(s): Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Küçükural, Lihua Julie Zhu
Software Mentions: 5
Published: about 4 years ago
10.7554/eLife.51796
A MAC2-positive progenitor-like microglial population is resistant to CSF1R inhibition in adult mouse brainCited by: 44
Author(s): Lihong Zhan, Li Fan, Lay Kodama, Peter Sohn, Man Ying Wong, Gergey Alzaem Mousa, Yungui Zhou, Yaqiao Li, Li Gan
Software Mentions: 5
Published: about 4 years ago
10.15252/embr.202050078
The actin modulator <scp>hMENA</scp> regulates <scp>GAS</scp> 6‐ <scp>AXL</scp> axis and pro‐tumor cancer/stromal cell cooperationCited by: 18
Author(s): Roberta Melchionna, Sheila Spada, Francesca Di Modugno, Daniel D’Andrea, Anna Di Carlo, Mariangela Panetta, Anna Maria Mileo, Isabella Sperduti, Barbara Antoniani, Enzo Gallo, Rita T. Lawlor, Lorenzo Piemonti, Paolo Visca, Michèle Milella, Gian Luca Grazi, Francesco Facciolo, Emily Chen, Aldo Scarpa, Paola Nisticò
Software Mentions: 5
Published: about 4 years ago
10.15252/embr.202050932
Foxm1 regulates neural progenitor fate during spinal cord regenerationCited by: 6
Author(s): Diane Pelzer, Lauren S. Phipps, Raphaël Thuret, Carlos J Gallardo-Dodd, Syed Murtuza Baker, Karel Dorey
Software Mentions: 5
Published: about 3 years ago
10.18632/aging.202559
Infertility network and hub genes for nonobstructive azoospermia utilizing integrative analysisCited by: 6
Author(s): Baoquan Han, Zihui Yan, Shuai Yu, Wei Ge, Yaqi Li, Yan Wang, Bo Yang, Wei Shen, Hui Jiang, Zhongyi Sun
Software Mentions: 5
Published: almost 4 years ago
10.1093/gigascience/giz105
rCASC: reproducible classification analysis of single-cell sequencing dataCited by: 24
Author(s): Luca Alessandrì, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Martina Olivero, Greta Romano, Sergio Rabellino, Nicola Licheri, Gennaro De Libero, Luigia Pace, Raffaele Calogero
Software Mentions: 5
Published: about 5 years ago
10.15252/emmm.202113953
Intrathecal activation of CD8 <sup>+</sup> memory T cells in IgG4‐related disease of the brain parenchymaCited by: 5
Author(s): Mirco Friedrich, Niklas Kehl, Niko Engelke, Josephine Kraus, Katharina A.M. Lindner, Philipp Münch, Iris Mildenberger, Christoph Groden, Achim Gass, Nima Etminan, Marc Fatar, Andreas von Deimling, David Reuß, Michael Platten, Lukas Bunse
Software Mentions: 5
Published: over 3 years ago
10.1038/s41419-021-03936-w
Valproic acid stimulates myogenesis in pluripotent stem cell-derived mesodermal progenitors in a NOTCH-dependent mannerCited by: 9
Author(s): Natacha Breuls, Nefele Giarratana, Laura Yedigaryan, Gabriel Miró Garrido, Paolo Carai, Stéphane Heymans, Adrian Ranga, Christophe M. Deroose, Maurilio Sampaolesi
Software Mentions: 5
Published: over 3 years ago
10.1038/s41419-021-03740-6
Single-cell analysis reveals urothelial cell heterogeneity and regenerative cues following cyclophosphamide-induced bladder injuryCited by: 12
Author(s): Xiaomu Cheng, Huadong Lai, Wenqin Luo, Man Zhang, Juju Miao, Weichen Song, Shunpeng Xing, Jia Wang, Wei‐Qiang Gao
Software Mentions: 5
Published: over 3 years ago
10.1016/j.jtos.2021.03.010
A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cellsCited by: 84
Author(s): Joseph Collin, Rachel Queen, Darin Zerti, Sanja Bojić, Birthe Dorgau, Nicky Moyse, Marina Moya Molina, Chunbo Yang, Sunanda Dey, Gary Reynolds, Rafiqul Hussain, Jonathan Coxhead, Steven Lisgo, Deborah J. Henderson, Agatha Joseph, Paul Rooney, Saurabh Ghosh, Lucy Clarke, Che J. Connon, Muzlifah Haniffa, Francisco C Figueiredo, Lyle Armstrong, Majlinda Lako
Software Mentions: 5
Published: over 3 years ago
10.3389/fcvm.2020.00052
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic VasculatureCited by: 86
Author(s): Menglan Xiang, Rubén Adrián Grosso, Akiko Takeda, Junliang Pan, Tove Bekkhus, Kevin Brulois, Denis Đermadi, Sofia Nordling, Michael Vanlandewijck, Sirpa Jalkanen, Maria H. Ulvmar, Eugene C. Butcher
Software Mentions: 5
Published: over 4 years ago
10.1038/s41388-021-01940-0
Human cell transformation by combined lineage conversion and oncogene expressionCited by: 10
Author(s): Biswajyoti Sahu, Päivi Pihlajamaa, Kaiyang Zhang, Kimmo Palin, Saija Ahonen, Alejandra Cervera, Ari Ristimäki, Lauri A. Aaltonen, Sampsa Hautaniemi, Jussi Taipale
Software Mentions: 5
Published: over 3 years ago
10.1186/s13073-021-00885-z
Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysisCited by: 24
Author(s): Sunny Z. Wu, Daniel Roden, Ghamdan Al-Eryani, Nenad Bartoniček, Kate Harvey, Aurélie Cazet, Chia-Ling Chan, Simon Junankar, Mun Hui, Ewan A. Millar, Julia Beretov, Lisa Kristina Horvath, Anthony M. Joshua, Phillip D. Stricker, James S. Wilmott, Camelia Quek, Georgina V. Long, Richard A. Scolyer, Bertrand Z. Yeung, Davendra Segara, Cindy Mak, Sanjay Warrier, Joseph E. Powell, Sandra A. O’Toole, Elgene Lim, Alexander Swarbrick
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.53839
Cancer systems immunologyCited by: 12
Author(s): Nathan E. Reticker-Flynn, Edgar G. Engleman
Software Mentions: 5
Published: over 4 years ago
10.1242/dmm.040147
Dynamic MAPK signaling activity underlies a transition from growth arrest to proliferation in <i>Drosophila scribble</i> mutant tumorsCited by: 17
Author(s): Tiantian Ji, Lina Zhang, Mingxi Deng, Shan Huang, Jiguang Wang, Tri Pham, Andrew A. Smith, Varun Sridhar, Clemens Cabernard, Yan Yan
Software Mentions: 5
Published: almost 6 years ago
10.1186/s13059-021-02505-w
Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seqCited by: 23
Author(s): Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Yahan Liang, B Wold, A Mortazavi
Software Mentions: 5
Published: about 3 years ago
10.1016/j.cell.2020.04.035
SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across TissuesCited by: 1,817
Author(s): Carly G.K. Ziegler, Samuel J. Allon, Sarah K. Nyquist, Ian Mbano, Vincent N. Miao, Constantine N. Tzouanas, Yuming Cao, Ashraf S. Yousif, Julia Bals, Blake M. Hauser, Jared Feldman, Christoph Muus, Marc H. Wadsworth, Samuel W. Kazer, Travis Hughes, Benjamin Doran, G. James Gatter, Marko Vukovic, Faith Taliaferro, Benjamin E. Mead, Zhiru Guo, Jennifer Wang, Delphine Gras, Magali Plaisant, Meshal Ansari, Ilias Angelidis, Heiko Adler, Jennifer M.S. Sucre, Chase J. Taylor, Brian M. Lin, Avinash Waghray, Vanessa Mitsialis, Daniel F. Dwyer, Kathleen M. Buchheit, Joshua A. Boyce, Nora A. Barrett, Tanya M. Laidlaw, Shaina L. Carroll, Lucrezia Colonna, Victor Tkachev, Christopher W. Peterson, Alison Yu, Hengqi Zheng, Hannah P. Gideon, Caylin G. Winchell, Philana Ling Lin, Colin D. Bingle, Scott B. Snapper, Jonathan A. Kropski, Fabian J. Theis, Herbert B. Schiller, Laure‐Emmanuelle Zaragosi, Pascal Barbry, Alasdair Leslie, Hans–Peter Kiem, JoAnne L. Flynn, Sarah M. Fortune, Bonnie Berger, Robert W. Finberg, Leslie S. Kean, Manuel Garber, Aaron Schmidt, Daniel Lingwood, Alex K. Shalek, José Ordovás-Montañés, Nicholas E. Banovich, Alvis Brāzma, Tushar J. Desai, Thao Duong, Oliver Eickelberg, Christine S. Falk, Michael Farzan, Ian A. Glass, Muzlifah Haniffa, Péter Horváth, Deborah T. Hung, Naftali Kaminski, Mark A. Krasnow, Malte Kühnemund, Robert Lafyatis, Haeock Lee, Sylvie Leroy, Sten Linnarson, Joakim Lundeberg, Kerstin B. Meyer, Alexander V. Misharin, Martijn C. Nawijn, M Nikolíc, Dana Pe’er, Joseph E. Powell, Stephen R. Quake, Jay Rajagopal, Purushothama Rao Tata, Emma L. Rawlins, Aviv Regev, Paul A. Reyfman, Mauricio Rojas, Orit Rosen, Kourosh Saeb‐Parsy, Christos Samakovlis, Herbert B. Schiller, Joachim L. Schultze, Max A. Seibold, Douglas P. Shepherd, Jason R. Spence, Avrum Spira, Xin Sun, Sarah A. Teichmann, Fabian J. Theis, Alexander M. Tsankov, Maarten van den Berge, Michael von Papen, Jeffrey A. Whitsett, Ramnik J. Xavier, Yan Xu, Kun Zhang
Software Mentions: 5
Published: over 4 years ago
10.1016/j.cell.2019.05.047
Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human TumorsCited by: 147
Author(s): Andrea Ponzetta, Roberta Carriero, Silvia Carnevale, Marialuisa Barbagallo, Martina Molgora, Chiara Perucchini, Elena Magrini, Francesca Gianni, Paolo Kunderfranco, Nadia Polentarutti, Fabio Pasqualini, Sabrina Di Marco, Domenico Supino, Clelia Peano, Ferdinando Carlo Maria Cananzi, Piergiuseppe Colombo, Silvana Pilotti, Suliman Yousef Alomar, Eduardo Bonavita, Maria Rosaria Galdiero, Cecília Garlanda, Alberto Mantovani, Sébastien Jaillon
Software Mentions: 5
Published: over 5 years ago
10.1016/j.cell.2020.09.062
M. tuberculosis Reprograms Hematopoietic Stem Cells to Limit Myelopoiesis and Impair Trained ImmunityCited by: 126
Author(s): Nargis Khan, Jeffrey Downey, Joaquín Sanz, Eva Kaufmann, Birte Blankenhaus, Alain Pacis, Erwan Pernet, Eisha Ahmed, Sílvia Cardoso, Anastasia Nijnik, Bruce Mazer, Christopher M. Sassetti, Marcel A. Behr, Miguel P. Soares, Luis B. Barreiro, Maziar Divangahi
Software Mentions: 5
Published: about 4 years ago
10.1186/s13059-021-02313-2
Schema: metric learning enables interpretable synthesis of heterogeneous single-cell modalitiesCited by: 19
Author(s): Rohit Singh, Brian Hie, Ashwin Narayan, Bonnie Berger
Software Mentions: 5
Published: over 3 years ago
10.3390/cancers13051097
Functional States in Tumor-Initiating Cell Differentiation in Human Colorectal CancerCited by: 10
Author(s): Martina K. Zowada, Stephan M. Tirier, Sebastian M. Dieter, Teresa G Krieger, Ava Oberlack, Robert Lorenz Chua, Mario Huerta, Foo Wei Ten, Karin Laaber, Jeongbin Park, Katharina Jechow, Torsten Müller, Mathias Kalxdorf, Mark Kriegsmann, Katharina Kriegsmann, Friederike Herbst, Jeroen Krijgsveld, Martin Schneider, Roland Eils, Hanno Glimm, Christian Conrad, Claudia R. Ball
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-021-02302-5
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomicsCited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 3 years ago
10.1242/dev.183855
Aging induces aberrant state transition kinetics in murine muscle stem cellsCited by: 50
Author(s): Jacob C. Kimmel, Ara B. Hwang, Annarita Scaramozza, Wallace F. Marshall, Andrew S. Brack
Software Mentions: 5
Published: almost 5 years ago
10.1242/dev.184143
A single cell transcriptome atlas of the developing zebrafish hindbrainCited by: 33
Author(s): Monica Tambalo, Richard Mitter, David Wilkinson
Software Mentions: 5
Published: almost 5 years ago
10.1093/bib/bbaa339
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric testCited by: 9
Author(s): Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed Lein, Richard H. Scheuermann
Software Mentions: 5
Published: almost 4 years ago
10.7554/eLife.63930
An in vitro stem cell model of human epiblast and yolk sac interactionCited by: 16
Author(s): Kirsty Mackinlay, Bailey A. T. Weatherbee, Viviane Souza Rosa, Charlotte E. Handford, George R. Hudson, Tim Coorens, Lygia V. Pereira, Sam Behjati, Ludovic Vallier, Marta Shahbazi, Magdalena Zernicka‐Goetz
Software Mentions: 5
Published: over 3 years ago
10.3389/fcell.2021.624711
Single-Cell RNA Sequencing With Combined Use of Bulk RNA Sequencing to Reveal Cell Heterogeneity and Molecular Changes at Acute Stage of Ischemic Stroke in Mouse Cortex Penumbra AreaCited by: 22
Author(s): Kang Guo, Jianing Luo, Dayun Feng, Lin Wu, Xin Wang, Xia Li, Kai Tao, Xun Wu, Wenxing Cui, Yijie He, Bing Wang, Zhenwei Zhao, Zhiguo Zhang
Software Mentions: 5
Published: over 3 years ago
10.1016/j.csbj.2020.06.033
Integration of single-cell multi-omics for gene regulatory network inferenceCited by: 37
Author(s): Xinlin Hu, Yaohua Hu, Fanjie Wu, Ricky Wai Tak Leung, Jing Qin
Software Mentions: 5
Published: almost 5 years ago
10.1038/s42003-021-02320-w
A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levelsCited by: 13
Author(s): Guste Urbonaite, Jimmy Tsz Hang Lee, Ping Liu, Guillermo E. Parada, Martin Hemberg, Murat Açar
Software Mentions: 5
Published: over 3 years ago
10.3389/fgene.2020.615680
Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic CholangiocarcinomaCited by: 5
Author(s): Miao Su, Kuangyuan Qiao, Xing Xie, Xinying Zhu, Fu-Lai Gao, Changjuan Li, Dongqiang Zhao
Software Mentions: 5
Published: almost 4 years ago
10.1186/s13059-020-02048-6
Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflowsCited by: 289
Author(s): Elena Denisenko, Belinda Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, C Olivier, Rebecca K. Simmons, Ryan Lister, Alistair R.R. Forrest
Software Mentions: 5
Published: over 4 years ago
10.1186/s13059-020-02054-8
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing dataCited by: 14
Author(s): Zijian Ni, Shuyang Chen, Jared Brown, Christina Kendziorski
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2019.00958
Single-Cell Analysis of Circulating Tumor Cells: How Far Have We Come in the -Omics Era?Cited by: 52
Author(s): Elisabetta Rossi, Rita Zamarchi
Software Mentions: 5
Published: about 5 years ago
10.1186/s13059-020-02027-x
Accounting for cell type hierarchy in evaluating single cell RNA-seq clusteringCited by: 19
Author(s): Zhijin Wu, Hao Wu
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0239711
Reproducibility across single-cell RNA-seq protocols for spatial ordering analysisCited by: 5
Author(s): Morten Seirup, Li‐Fang Chu, Srikumar Sengupta, Ning Leng, Hadley Browder, Kevin Kapadia, Christina M. Shafer, Bret Duffin, Angela L. Elwell, Jennifer M. Bolin, Scott Swanson, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 5
Published: about 4 years ago
10.1186/s13059-020-02210-0
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organsCited by: 98
Author(s): Shuai He, Lin He Wang, Yang Liu, Yi Qi Li, Hai Tian Chen, Jing Xu, Peng Wan, Guo Wang Lin, Pan Wei, Bo Li, Xiaojun Xia, Dan Wang, Jin Xin Bei, Xiaoshun He, Zhiyong Guo
Software Mentions: 5
Published: almost 4 years ago
10.3389/fgene.2021.666771
scGPS: Determining Cell States and Global Fate Potential of SubpopulationsCited by: 1
Author(s): Michael Thompson, Maika Matsumoto, Tianqi Ma, Anne Senabouth, Nathan J. Palpant, Joseph E. Powell, Quan Nguyen
Software Mentions: 5
Published: over 3 years ago
10.3390/biology10060503
Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC SequencingCited by: 6
Author(s): Aidan S. Marshall, Nick Jones
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-020-02032-0
Sampling time-dependent artifacts in single-cell genomics studiesCited by: 50
Author(s): Ramón Massoni-Badosa, Giovanni Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elı́as Campo, Antonio Julià, José I. Martín‐Subero, Holger Heyn
Software Mentions: 5
Published: over 4 years ago
10.1038/s41398-020-00994-0
Presynaptic dysfunction in CASK-related neurodevelopmental disordersCited by: 25
Author(s): Martin Becker, Francesca Mastropasqua, Jan Philipp Reising, Simon Maier, Mai‐Lan Ho, Ielyzaveta Rabkina, Danyang Li, Janina Neufeld, Lea Ballenberger, Lynnea Myers, Viveka Moritz, Malin Kele, Josephine Wincent, Charlotte Willfors, Rouslan Sitnikov, Eric Herlenius, Britt‐Marie Anderlid, Anna Falk, Sven Bölte, Kristiina Tammimies
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pone.0215987
Insights from deconvolution of cell subtype proportions enhance the interpretation of functional genomic dataCited by: 18
Author(s): Yu Kong, Deepa Rastogi, Cathal Seoighe, John M. Greally, Masako Suzuki
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pntd.0009306
The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infectionCited by: 4
Author(s): Zhiyuan Yao, Fabio Zanini, Sathish Kumar, Marwah Karim, Sirle Saul, Nishank Bhalla, Nuttada Panpradist, Avery Muniz, Aarthi Narayanan, Stephen R. Quake, Shirit Einav
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-019-1922-x
DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencingCited by: 31
Author(s): Zilu Zhou, Baocheng Xu, Andy J. Minn, Nancy R. Zhang
Software Mentions: 5
Published: almost 5 years ago
10.1038/s41598-021-86070-z
A flexible microfluidic system for single-cell transcriptome profiling elucidates phased transcriptional regulators of cell cycleCited by: 7
Author(s): Karen Davey, Daniel Wong, Filip A. Konopacki, Eugene Kwa, Tony Ly, Heike Fiegler, Christopher R. Sibley
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pgen.1009018
The causal effect of obesity on prediabetes and insulin resistance reveals the important role of adipose tissue in insulin resistanceCited by: 24
Author(s): Min‐Hua Zong, Marcus Alvarez, Arthur Ko, Yash V. Bhagat, Elior Rahmani, Brandon Jew, Sini Heinonen, Liliana Muñóz-Hernández, Miguel Francisco Herrera-Hernández, Carlos A. Aguilar-Salinas, Teresa Tusié-Luna, Karen L. Mohlke, Markku Laakso, Kirsi H. Pietiläinen, Eran Halperin, Päivi Pajukanta
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pcbi.1006555
Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing MapsCited by: 53
Author(s): Camden Jansen, Ricardo N. Ramirez, Nicole El-Ali, David Green, Jesper Tegnér, Matthias Merkenschlager, Ana Conesa, A Mortazavi
Software Mentions: 5
Published: about 5 years ago
10.1038/s42003-021-02201-2
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesisCited by: 28
Author(s): Kohei Saeki, Gregory Chang, Noriko Kanaya, Xiwei Wu, Jinhui Wang, Lauren Bernal, Desiree Ha, Susan L. Neuhausen, Shiuan Chen
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-019-1764-6
BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypesCited by: 94
Author(s): Tongxin Wang, Travis Johnson, Wei Shao, Zixiao Lu, Bryan R. Helm, Jie Zhang, Kun Huang
Software Mentions: 5
Published: over 5 years ago
10.3389/fendo.2021.736286
Gene Signatures of NEUROGENIN3+ Endocrine Progenitor Cells in the Human PancreasCited by: 2
Author(s): Hyo Jeong Yong, Gengqiang Xie, Chengyang Liu, Wei Wang, Ali Naji, Jerome Irianto, Yue J. Wang
Software Mentions: 5
Published: about 3 years ago
10.3389/fendo.2021.679582
Transcriptomic Profiling of Human Placenta in Gestational Diabetes Mellitus at the Single-Cell LevelCited by: 31
Author(s): Yuqi Yang, Fang Guo, Yue Peng, Rong Chen, Wenbo Zhou, Huihui Wang, Jun Ouyang, Bin Yu, Zhengfeng Xu
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-019-57110-6
Single-cell transcriptional profiles in human skeletal muscleCited by: 160
Author(s): Aliza Rubenstein, Gregory R. Smith, Ulrika Raue, Gwénaëlle Begue, Kiril Minchev, Frederique Ruf-Zamojski, Venugopalan D. Nair, Xingyu Wang, Lan Zhou, Elena Zaslavsky, Todd A. Trappe, Scott Trappe, Stuart C. Sealfon
Software Mentions: 5
Published: almost 5 years ago
10.1371/journal.pcbi.1007794
Scedar: A scalable Python package for single-cell RNA-seq exploratory data analysisCited by: 10
Author(s): Yuanchao Zhang, Man S. Kim, Erin R. Reichenberger, Benjamin Stear, Deanne Taylor
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2021.681206
LISA2: Learning Complex Single-Cell Trajectory and Expression TrendsCited by: 1
Author(s): Yang Chen, Yuping Zhang, Kairong Li, Zhengqing Ouyang
Software Mentions: 5
Published: about 3 years ago
10.1038/s41598-018-24725-0
Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencingCited by: 68
Author(s): Söeren Lukassen, Elisabeth Bosch, Arif B. Ekici, Andreas Winterpacht
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-020-59808-4
Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturationCited by: 29
Author(s): Ian M. Traniello, Syed Bukhari, Jessica L. Kevill, Amy Cash Ahmed, Adam R. Hamilton, Nicholas L. Naeger, Declan C. Schroeder, Gene E. Robinson
Software Mentions: 5
Published: almost 5 years ago
10.1038/s41598-021-90797-0
Targeting of the CD80/86 proinflammatory axis as a therapeutic strategy to prevent severe COVID-19Cited by: 9
Author(s): Antonio Julià, Irene Bonafonte-Pardàs, Antonio Gómez, María López-Lasanta, Mireia López-Corbeto, Sergio H Martínez-Mateu, Jordi Lladós, Iván Rodríguez-Nunez, R Myers, Sara Marsal
Software Mentions: 5
Published: over 3 years ago
10.7554/eLife.52004
Single cell transcriptional signatures of the human placenta in term and preterm parturitionCited by: 173
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Edward Sendler, Yi Xu, Valeria Garcia‐Flores, Yaozhu Leng, Francesca Luca, Sonia S. Hassan, Nardhy Gomez-López
Software Mentions: 5
Published: almost 5 years ago
10.1186/s13059-018-1426-0
Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencingCited by: 79
Author(s): Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo Cheng Yuan, Guoji Guo
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pbio.3000705
Vascularized human cortical organoids (vOrganoids) model cortical development in vivoCited by: 178
Author(s): Yingchao Shi, Le Sun, Mengdi Wang, Jianwei Liu, Shaobo Zhong, Rui Li, Peng Li, Dadong Guo, Fang Ai, Ruiguo Chen, Woo Ping Ge, Qian Wu, Xiaoqun Wang
Software Mentions: 4
Published: over 4 years ago
10.1093/bioinformatics/btaa919
ILoReg: a tool for high-resolution cell population identification from single-cell RNA-seq dataCited by: 3
Author(s): Johannes Smolander, Sini Junttila, Mikko S Venäläinen, Laura L. Elo
Software Mentions: 4
Published: almost 4 years ago
10.1002/ctm2.462
Diversity and intratumoral heterogeneity in human gallbladder cancer progression revealed by single‐cell RNA sequencingCited by: 16
Author(s): Peizhan Chen, Yueqi Wang, Jingquan Li, Xiaobo Bo, Jie Wang, Lingxi Nan, Changcheng Wang, Qian Ba, Houbao Liu, Hui Wang
Software Mentions: 4
Published: over 3 years ago
10.1126/sciadv.abg5982
Single-cell analyses unravel cell type–specific responses to a vitamin D analog in prostatic precancerous lesionsCited by: 9
Author(s): Mohamed A. Abu el Maaty, Élise Grelet, Céline Keime, Anna‐Isavella Rerra, Justine Gantzer, C. Emprou, Julie Terzic, Régis Lutzing, Jean‐Marc Bornert, Gilles Laverny, Daniel Metzger
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pbio.3000187
Single-cell RNA sequencing reveals regulatory mechanism for trophoblast cell-fate divergence in human peri-implantation conceptusesCited by: 49
Author(s): Bo Lv, Qin An, Qiao Zeng, Xunyi Zhang, Ping Lü, Yanqiu Wang, Xianmin Zhu, Yao Ji, Guoping Fan, Zhigang Xue
Software Mentions: 4
Published: about 5 years ago
10.1161/CIRCULATIONAHA.120.046672
Stem Cell Pluripotency Genes Klf4 and Oct4 Regulate Complex SMC Phenotypic Changes Critical in Late-Stage Atherosclerotic Lesion PathogenesisCited by: 192
Author(s): Gabriel F. Alencar, Katherine Owsiany, Santosh Karnewar, Katyayani Sukhavasi, Giuseppe Mocci, Anh Nguyen, Corey Williams, Sohel Shamsuzzaman, Michal Mokrý, Christopher A. Henderson, Ryan M. Haskins, Richard A. Baylis, Aloke V. Finn, Coleen A. McNamara, Eli R. Zunder, Vamsidhar R M Venkata, Gérard Pasterkamp, Johan Björkegren, Stefan Bekiranov, Gary K. Owens
Software Mentions: 4
Published: almost 4 years ago
10.3390/genes11040377
Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type IdentificationCited by: 15
Author(s): Maryam Zand, Jianhua Ruan
Software Mentions: 4
Published: over 4 years ago
10.1186/s13104-020-05357-y
Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cellsCited by: 4
Author(s): Xin Zhao, Shaojian Gao, Sachiko Kajigaya, Qingguo Liu, Zhijie Wu, Xingmin Feng, Fengkui Zhang, Neal S. Young
Software Mentions: 4
Published: about 4 years ago
10.3389/fcell.2021.699263
Spatiotemporal and Functional Heterogeneity of Hematopoietic Stem Cell-Competent Hemogenic Endothelial Cells in Mouse EmbryosCited by: 5
Author(s): Yunqiao Li, Yandong Gong, Siyuan Hou, Tao Huang, Haizhen Wang, Di Liu, Yanli Ni, Chaojie Wang, Junliang Wang, Jun Hou, Ruihua Yang, Yan Jing, Guangyu Zhang, Bing Liu, Yu Lan
Software Mentions: 4
Published: over 3 years ago
10.3389/fcell.2021.735307
Transcriptomic Signatures of Airway Epithelium Infected With SARS-CoV-2: A Balance Between Anti-infection and Virus LoadCited by: 3
Author(s): Lingzhang Meng, Houji Qin, Jingjie Zhao, Siyuan He, Qiuju Wei, Zechen Wang, Jiajia Shen, Suren R. Sooranna, Jian Song
Software Mentions: 4
Published: about 3 years ago
10.3390/cells8101117
Meta-Analysis of Human and Mouse Biliary Epithelial Cell Gene ProfilesCited by: 8
Author(s): Stefaan Verhulst, Tania Roskams, Pau Sancho–Bru, Leo A. van Grunsven
Software Mentions: 4
Published: about 5 years ago
10.3390/genes11060709
Extensive Involvement of Alternative Polyadenylation in Single-Nucleus NeuronsCited by: 3
Author(s): Ying Wang, Weixing Feng, Siwen Xu, Bo He
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-018-1416-2
Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesisCited by: 135
Author(s): Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 6 years ago
10.1126/sciimmunol.abe1670
MAIT cell activation and dynamics associated with COVID-19 disease severityCited by: 138
Author(s): Tiphaine Parrot, Jean‐Baptiste Gorin, Andrea Ponzetta, Kimia T. Maleki, Tobias Kammann, Johanna Emgård, André Perez‐Potti, Takuya Sekine, Olga Rivera‐Ballesteros, Sara Gredmark‐Russ, Olav Rooyackers, Elin Folkesson, Lars Eriksson, Anna Norrby‐Teglund, Hans‐Gustaf Ljunggren, Niklas K. Björkström, Soo Aleman, Marcus Buggert, Jonas Klingström, Kristoffer Strålin, Johan K. Sandberg
Software Mentions: 4
Published: about 4 years ago
10.21203/rs.3.rs-333578/v1
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19Cited by: 2
Author(s): Brian Le, Gaia Andreoletti, Tomiko Oskotsky, Albert Vallejo-Gracia, Romel Rosales, Katharine Yu, Idit Kosti, Kristoffer E. Leon, Daniel Bunis, Christine Li, G. Renuka Kumar, Kris M. White, Adolfo Garcı́a-Sastre, Mélanie Ott, Marina Sirota
Software Mentions: 4
Published: over 3 years ago
10.3389/fphar.2021.754933
Immune Cell Landscape of Patients With Diabetic Macular Edema by Single-Cell RNA AnalysisCited by: 10
Author(s): Pingping Ma, Ping Zhang, Shuxia Chen, Wen Shi, Jinguo Ye, Shida Chen, Rong Ju, Bingqian Liu, Yingfeng Zheng, Yizhi Liu
Software Mentions: 4
Published: about 3 years ago
10.3390/cells9091938
Detecting Interactive Gene Groups for Single-Cell RNA-Seq Data Based on Co-Expression Network Analysis and Subgraph LearningCited by: 10
Author(s): Xiucai Ye, Weihang Zhang, Yasunori Futamura, Tetsuya Sakurai
Software Mentions: 4
Published: over 4 years ago
10.1534/g3.120.401160
Evaluation of STAR and Kallisto on Single Cell RNA-Seq Data AlignmentCited by: 31
Author(s): Yuheng Du, Qizhao Huang, Cédric Arisdakessian, Lana X. Garmire
Software Mentions: 4
Published: over 4 years ago
10.1186/s12859-021-04136-1
scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropyCited by: 3
Author(s): Zechuan Chen, Zeruo Yang, Xi Yuan, Xiaoming Zhang, Pei Hao
Software Mentions: 4
Published: over 3 years ago
10.3389/fonc.2020.569985
Diverse Macrophage Populations Contribute to the Inflammatory Microenvironment in Premalignant Lesions During Localized InvasionCited by: 16
Author(s): Ayman Ibrahim, Matthew Moss, Zane Gray, Michelle D. Rojo, Caitlin M. Burke, Kathryn L. Schwertfeger, Camila O. dos Santos, Heather L. Machado
Software Mentions: 4
Published: about 4 years ago
10.3390/cells10030692
CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte DiseaseCited by: 2
Author(s): Sweta Talyan, Samantha Filipów, Michael Ignarski, Magdalena Smieszek, He Chen, Lucas Kühne, Linus Butt, Heike Göbel, Karla Johanna Ruth Hoyer-Allo, Felix C. Koehler, Janine Altmüller, Paul Brinkkötter, Bernhard Schermer, Thomas Benzing, Martin Kann, Roman‐Ulrich Müller, Christoph Dieterich
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.ppat.1009665
Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infectionCited by: 17
Author(s): Qing Wang, Cheng Yuan Peng, Min Yang, Fengqi Huang, Xuzhuo Duan, Shaowen Wang, Huitao Cheng, Huirong Yang, Haifeng Zhao, Qiwei Qin
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.ppat.1009804
Identification of immune correlates of fatal outcomes in critically ill COVID-19 patientsCited by: 34
Author(s): Jonathan Youngs, Nicholas M. Provine, Nicholas Lim, Hannah Sharpe, Ali Amini, Yi‐Ling Chen, Jian Luo, Matthew Edmans, Panagiota Zacharopoulou, Wentao Chen, Oliver Sampson, Robert S Paton, William J Hurt, David A. Duncan, Anna L McNaughton, Vincent N. Miao, Susannah Leaver, Duncan Wyncoll, Jonathan Ball, P Hopkins, Donal Skelly, Eleanor Barnes, Susanna Dunachie, Graham Ogg, Teresa Lambe, Ian D. Pavord, Alex K. Shalek, Craig Thompson, Luzheng Xue, Derek C. Macallan, Philip Goulder, Paul Klenerman, Tihana Bicanic
Software Mentions: 4
Published: about 3 years ago