pypi: scanpy | Projects | Ecosyste.ms: Papers

10.15252/msb.20188746

Current best practices in single‐cell RNA‐seq analysis: a tutorial
Cited by: 1,173
Author(s): Malte D. Luecken, Fabian J. Theis
Software Mentions: 20
Published: about 5 years ago

Spatiotemporal analysis of human intestinal development at single-cell resolution
Cited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: over 3 years ago

10.12688/f1000research.15666.3

A systematic performance evaluation of clustering methods for single-cell RNA-seq data
Cited by: 33
Author(s): Angelo Duò, Mark D. Robinson, Charlotte Soneson
Software Mentions: 17
Published: over 3 years ago

10.1371/journal.pcbi.1008625

mbkmeans: Fast clustering for single cell data using mini-batch k-means
Cited by: 27
Author(s): Stephanie C. Hicks, Ruoxi Liu, Yuwei Ni, Elizabeth Purdom, Davide Risso
Software Mentions: 15
Published: over 3 years ago

10.1186/s12859-021-04210-8

Contrastive self-supervised clustering of scRNA-seq data
Cited by: 28
Author(s): Madalina Ciortan, Matthieu Defrance
Software Mentions: 13
Published: about 3 years ago

10.15252/msb.20209522

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma
Cited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: about 3 years ago

10.1186/s13073-020-00786-7

A cell-of-origin epigenetic tracer reveals clinically distinct subtypes of high-grade serous ovarian cancer
Cited by: 11
Author(s): Pietro Lo Riso, Carlo Emanuele Villa, Gilles Gasparoni, Andrea Vingiani, Raffaele Luongo, Anna Manfredi, Annemarie Jungmann, Alessia Bertolotti, Francesca Borgo, Annalisa Garbi, Michela Lupia, Pasquale Laise, Vivek Das, Giancarlo Pruneri, Giuseppe Viale, Nicoletta Colombo, Teresa Manzo, Luigi Nezi, Ugo Cavallaro, Davide Cacchiarelli, Jörn Walter, Giuseppe Testa
Software Mentions: 9
Published: over 3 years ago

10.3389/fimmu.2021.709173

The Role of Hemoglobin Subunit Delta in the Immunopathy of Multiple Sclerosis: Mitochondria Matters
Cited by: 6
Author(s): Afshin Derakhshani, Hossein Safarpour, Behzad Baradaran, Nima Hemmat, Patrizia Leone, Zahra Asadzadeh, Mehrdad Pashazadeh, Behzad Baradaran, Vito Racanelli
Software Mentions: 9
Published: almost 3 years ago

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pgen.1009773

Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline
Cited by: 7
Author(s): Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A. Louwé, Gonneke S. K. Pilgram, Károly Szuhai, Roberto Matorras, Cristina Eguizábal, Lucette van der Westerlaken, Hailiang Mei, Susana M. Chuva de Sousa Lopes
Software Mentions: 9
Published: over 2 years ago

10.1016/j.molcel.2020.04.008

Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets
Cited by: 101
Author(s): Bethan Psaila, Guanlin Wang, Alba Rodríguez-Meira, Rong Li, Elisabeth F. Heuston, Lauren C. Murphy, Daniel Yee, Ian S. Hitchcock, Nikolaos Sousos, Jennifer O’Sullivan, Stacie M. Anderson, Yotis A. Senis, Olga K. Weinberg, Monica L. Calicchio, Deena Iskander, Daniel Royston, Dragana Milojković, Irene Roberts, David M. Bodine, Supat Thongjuea, Adam J. Mead
Software Mentions: 9
Published: about 4 years ago

10.3389/fgene.2020.00295

Single-Cell Transcriptome Data Clustering via Multinomial Modeling and Adaptive Fuzzy K-Means Algorithm
Cited by: 13
Author(s): Liang Chen, Weinan Wang, Yuyao Zhai, Minghua Deng
Software Mentions: 8
Published: about 4 years ago

10.15252/emmm.202012871

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers
Cited by: 40
Author(s): Christoph H. Mayr, Lukas M. Simon, Gabriela Leuschner, Meshal Ansari, Janine Schniering, Philipp Geyer, Ilias Angelidis, Maximilian Strunz, Pawandeep Singh, Nikolaus Kneidinger, Frank Reichenberger, Edith Silbernagel, Stephan Böhm, Heiko Adler, Michael Lindner, Britta Maurer, Anne Hilgendorff, Antje Prasse, Jürgen Behr, Matthias Mann, Oliver Eickelberg, Fabian J. Theis, Herbert B. Schiller
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.66747

Mapping single-cell atlases throughout Metazoa unravels cell type evolution
Cited by: 98
Author(s): Alexander J. Tarashansky, Jacob M. Musser, Margarita Khariton, Pengyang Li, Detlev Arendt, Stephen R. Quake, Bo Wang
Software Mentions: 8
Published: about 3 years ago

10.1186/s12859-020-03641-z

A rank-based marker selection method for high throughput scRNA-seq data
Cited by: 23
Author(s): Alexander Vargo, Anna C. Gilbert
Software Mentions: 8
Published: over 3 years ago

10.3390/genes12020311

Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model
Cited by: 7
Author(s): Zhenqiu Liu
Software Mentions: 8
Published: over 3 years ago

10.1016/j.celrep.2021.109118

Resident memory T cells in tumor-distant tissues fortify against metastasis formation
Cited by: 14
Author(s): Laura S. Christian, Liuyang Wang, Bryan Jian Wei Lim, Dachuan Deng, Haiyang Wu, Xiaofan Wang, Qi-Jing Li
Software Mentions: 8
Published: about 3 years ago

10.3389/fonc.2020.01254

Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies
Cited by: 39
Author(s): Natasja L. de Vries, Ahmed Mahfouz, Frits Koning, Noel F.C.C. de Miranda
Software Mentions: 8
Published: almost 4 years ago

10.12688/f1000research.15830.2

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
Cited by: 2
Author(s): Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael Reich, Jill P. Mesirov
Software Mentions: 7
Published: about 5 years ago

10.1126/scitranslmed.abe9599

Plasma from patients with bacterial sepsis or severe COVID-19 induces suppressive myeloid cell production from hematopoietic progenitors in vitro
Cited by: 57
Author(s): Miguel Reyes, Michael R. Filbin, Roby P. Bhattacharyya, Abraham Sonny, Arnav Mehta, Kianna Billman, Kyle R. Kays, Mayra Pinilla-Vera, Maura Benson, Lisa A. Cosimi, Deborah T. Hung, Bruce D. Levy, Alexandra Chloé Villani, Moshe Sade-Feldman, Rebecca M. Baron, Marcia B. Goldberg, Paul C. Blainey, Nir Hacohen
Software Mentions: 7
Published: almost 3 years ago

10.15252/emmm.202114123

Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer
Cited by: 33
Author(s): Florian Uhlitz, Philip Bischoff, Stefan Peidli, Anja Sieber, Alexandra Trinks, Mareen Lüthen, Benedikt Obermayer, Eric Blanc, Yana Ruchiy, Thomas Sell, Soulafa Mamlouk, Roberto Arsiè, Tzu-Ting Wei, Kathleen Klotz-Noack, Roland F. Schwarz, Birgit Sawitzki, Carsten Kamphues, Dieter Beule, Markus Landthaler, Christine Sers, David Horst, Nils Blüthgen, Markus Morkel
Software Mentions: 6
Published: almost 3 years ago

10.15252/msb.20199146

Mammalian gene expression variability is explained by underlying cell state
Cited by: 85
Author(s): Robert T. Foreman, Roy Wollman
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-019-1837-6

DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data
Cited by: 162
Author(s): Cédric Arisdakessian, Olivier Poirion, Breck Yunits, Xun Zhu, Lana X. Garmire
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-020-02128-7

Tuning parameters of dimensionality reduction methods for single-cell RNA-seq analysis
Cited by: 15
Author(s): Félix Raimundo, Céline Vallot, Jean-Philippe Vert
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13059-021-02280-8

iMAP: integration of multiple single-cell datasets by adversarial paired transfer networks
Cited by: 25
Author(s): Dongfang Wang, Siyu Hou, Lei Zhang, Xiliang Wang, Baolin Liu, Zemin Zhang
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007939

Iterative point set registration for aligning scRNA-seq data
Cited by: 3
Author(s): Amir Alavi, Ziv Bar‐Joseph
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-021-07469-6

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
Cited by: 5
Author(s): Andreas Hoek, Katharina Maibach, Ebru Özmen, Ana Ivonne Vazquez‐Armendariz, Jan Philipp Mengel, Torsten Hain, Susanne Herold, Alexander Goesmann
Software Mentions: 6
Published: about 3 years ago

10.1523/JNEUROSCI.1634-20.2020

Cell Type-Specific Oxidative Stress Genomic Signatures in the Globus Pallidus of Dopamine-Depleted Mice
Cited by: 12
Author(s): Alyssa J. Lawler, Ashley R. Brown, Rachel S. Bouchard, Noelle Toong, Yeonju Kim, Nitinram Velraj, Grant A Fox, Michael Kleyman, Byungsoo Kang, Aryn H. Gittis, Andreas Pfenning
Software Mentions: 5
Published: over 3 years ago

10.3390/biology10060503

Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing
Cited by: 6
Author(s): Aidan S. Marshall, Nick Jones
Software Mentions: 5
Published: almost 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 Tissues
Cited 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: about 4 years ago

10.1111/cpr.12968

Systemic transcriptome comparison between early‐ And late‐onset pre‐eclampsia shows distinct pathology and novel biomarkers
Cited by: 15
Author(s): Fang Guo, Zhenan Bao, Hao Yang, Yixi Fu, Yaning Wang, Jianming Huang, Min Cheng, Xiaobo Li, Zhuo Shen, Li Li, Ping He, Andy Peng Xiang, Shuaiyu Wang, Hongbo Zhang
Software Mentions: 5
Published: over 3 years ago

10.1242/dev.174557

Lgr5+ stem/progenitor cells reside at the apex of a heterogeneous embryonic hepatoblast pool
Cited by: 46
Author(s): Nicole Prior, Christopher J. Hindley, Fabian Rost, Elena Meléndez, Winnie Lau, Berthold Göttgens, Steffen Rulands, Benjamin D. Simons, Meritxell Huch
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-019-1906-x

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation
Cited by: 257
Author(s): Elo Madissoon, Anna Wilbrey-Clark, Ricardo J. Miragaia, Kourosh Saeb‐Parsy, Krishnaa Mahbubani, Nikitas Georgakopoulos, Philippa Harding, Krzysztof Polański, Ni Huang, Karol Nowicki-Osuch, Rebecca C. Fitzgerald, Kevin Loudon, John R. Ferdinand, Menna R. Clatworthy, Anthi Tsingene, Stijn van Dongen, Monika Dąbrowska, Minal Patel, Michael J T Stubbington, Sarah A. Teichmann, Oliver Stegle, Kerstin B. Meyer
Software Mentions: 5
Published: over 4 years ago

10.1186/s13059-021-02414-y

Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
Cited by: 38
Author(s): Melania Barile, Iván Imaz-Rosshandler, Isabella Inzani, Shila Ghazanfar, Jennifer Nichols, John C. Marioni, Carolina Guibentif, Berthold Göttgens
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13059-021-02452-6

Sfaira accelerates data and model reuse in single cell genomics
Cited by: 16
Author(s): David Fischer, Leander Dony, Martin König, Abdul Moeed, Luke Zappia, Lukas Heumos, Sophie Tritschler, Olle Holmberg, Hananeh Aliee, Fabian J. Theis
Software Mentions: 5
Published: almost 3 years ago

10.1093/gigascience/giz105

rCASC: reproducible classification analysis of single-cell sequencing data
Cited 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: almost 5 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 genes
Cited 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: over 3 years ago

10.1186/s13059-021-02364-5

scSNV: accurate dscRNA-seq SNV co-expression analysis using duplicate tag collapsing
Cited by: 6
Author(s): Gavin Wilson, Mathieu Derouet, Gail Darling, Jonathan C. Yeung
Software Mentions: 4
Published: about 3 years ago

10.1111/all.14633

Single‐cell molecular profiling provides a high‐resolution map of basophil and mast cell development
Cited by: 29
Author(s): Fiona Hamey, Winnie Lau, Iwo Kuciński, Xiaonan Wang, Evangelia Diamanti, Nicola K. Wilson, Berthold Göttgens, Joakim S. Dahlin
Software Mentions: 4
Published: over 3 years ago

10.1016/j.exphem.2019.08.009

Machine learning predicts putative hematopoietic stem cells within large single-cell transcriptomics data sets
Cited by: 32
Author(s): Fiona Hamey, Berthold Göttgens
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.65857

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing
Cited by: 17
Author(s): Eyal Ben-David, James Boocock, Longhua Guo, Stefan Zdraljevic, Joshua S. Bloom, Leonid Kruglyak
Software Mentions: 4
Published: about 3 years ago

10.1093/gigascience/giaa136

Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma
Cited by: 8
Author(s): Lauren Sanders, Allison Cheney, Lucas Seninge, Anouk van den Bout, Marissa Chen, Holly C. Beale, Ellen Kephart, Jacob Pfeil, Katrina Learned, A. Geoffrey Lyle, Isabel Bjork, David Haussler, Sofie R. Salama, Olena M. Vaske
Software Mentions: 4
Published: over 3 years ago

10.1016/j.stem.2020.06.020

Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration
Cited by: 251
Author(s): Jinwook Choi, Jong-Eun Park, Georgia Tsagkogeorga, Motoko Yanagita, Bon‐Kyoung Koo, Namshik Han, Joo Hyeon Lee
Software Mentions: 4
Published: almost 4 years ago

10.1093/gigascience/giaa122

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data
Cited by: 9
Author(s): Lukas M. Simon, Fangfang Yan, Zhongming Zhao
Software Mentions: 4
Published: over 3 years ago

10.1016/j.devcel.2020.11.010

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease
Cited by: 139
Author(s): Rasa Elmentaite, Alex Ross, Kenny Roberts, Kylie R. James, Daniel Ortmann, Tomás Gomes, Komal Nayak, Liz Tuck, Sophie Pritchard, Ömer Bayraktar, Robert Heuschkel, Ludovic Vallier, Sarah A. Teichmann, Matthias Zilbauer
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2021.644211

CBA: Cluster-Guided Batch Alignment for Single Cell RNA-seq
Cited by: 1
Author(s): Wenbo Yu, Ahmed Mahfouz, Marcel J. T. Reinders
Software Mentions: 3
Published: about 3 years ago

10.1186/s13024-021-00443-6

The CD33 short isoform is a gain-of-function variant that enhances Aβ1–42 phagocytosis in microglia
Cited by: 41
Author(s): Abhishek Bhattacherjee, J. Jung, Sameera Zia, Madelene F. S. Ho, Ghazaleh Eskandari‐Sedighi, Chris D. St. Laurent, Kelli A. McCord, Arjun Bains, Gaurav Sidhu, Susmita Sarkar, Jason R. Plemel, Matthew Macauley
Software Mentions: 3
Published: about 3 years ago

10.7554/eLife.58534

Heterogeneity of murine periosteum progenitors involved in fracture healing
Cited by: 48
Author(s): Brya G. Matthews, Sanja Novak, Francesca Sbrana, Jessica L Funnell, Ye Cao, Emma J. Buckels, Danka Grčević, Ivo Kalajzić
Software Mentions: 3
Published: over 3 years ago

10.1186/s12920-021-00872-8

XenoCell: classification of cellular barcodes in single cell experiments from xenograft samples
Cited by: 6
Author(s): Stefano Cheloni, Roman Hillje, Lucilla Luzi, Pier Giuseppe Pelicci, Elena Gatti
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-019-6053-y

Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data
Cited by: 17
Author(s): Di Feng, Charles E. Whitehurst, Dechao Shan, Jon Hill, Yong Yue
Software Mentions: 3
Published: almost 5 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: over 3 years ago

10.1242/dev.185595

Single cell sequencing of radial glia progeny reveals diversity of newborn neurons in the adult zebrafish brain
Cited by: 45
Author(s): Christian Lange, Fabian Rost, Anja Machate, Susanne Reinhardt, Matthias Lesche, Anke Weber, Veronika Kuscha, Andreas Dahl, Steffen Rulands, Michael Brand
Software Mentions: 3
Published: over 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: over 3 years ago

10.7554/eLife.54129

A single-parasite transcriptional atlas of Toxoplasma Gondii reveals novel control of antigen expression
Cited by: 43
Author(s): Yuan Xue, Terence C. Theisen, Suchita Rastogi, Abel Ferrel, Stephen R. Quake, John C. Boothroyd
Software Mentions: 2
Published: over 4 years ago

10.1186/s13619-021-00078-4

Forkhead box family transcription factors as versatile regulators for cellular reprogramming to pluripotency
Cited by: 7
Author(s): Meijun Fu, Huan Chen, Zepo Cai, Yihang Yang, Ziyu Feng, Meiqin Zeng, Lijun Chen, Yue Qin, Baomei Cai, Pinghui Zhu, Chunhua Zhou, Shengyong Yu, Jing Guo, Jing Liu, Shuiyan Cao, Duanqing Pei
Software Mentions: 2
Published: almost 3 years ago

10.3389/fmicb.2020.578795

PARMAP: A Pan-Genome-Based Computational Framework for Predicting Antimicrobial Resistance
Cited by: 7
Author(s): Xuefei Li, Jingxia Lin, Yongfei Hu, Jiajian Zhou
Software Mentions: 2
Published: over 3 years ago

10.15252/msb.20209682

A single cell atlas of the human liver tumor microenvironment
Cited by: 77
Author(s): Hassan Massalha, Keren Bahar Halpern, Samir Abu‐Gazala, Tamar Jana, Efi E. Massasa, Andreas E. Moor, Lisa Buchauer, Milena Rozenberg, Eli Pikarsky, Ido Amit, Gideon Zamir, Shalev Itzkovitz
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.70514

Activity-dependent modulation of synapse-regulating genes in astrocytes
Cited by: 48
Author(s): Isabella Farhy-Tselnicker, Matthew Boisvert, Hanqing Liu, Cari Dowling, Galina Erikson, Elena Blanco‐Suarez, Chen Farhy, Maxim N. Shokhirev, Joseph R. Ecker, Nicola J. Allen
Software Mentions: 2
Published: over 2 years ago

10.3389/fncel.2020.592005

Organotypic Brain Slice Culture Microglia Exhibit Molecular Similarity to Acutely-Isolated Adult Microglia and Provide a Platform to Study Neuroinflammation
Cited by: 27
Author(s): Alex R. D. Delbridge, Dann Huh, Margot Brickelmaier, Jeremy C. Burns, Chris Roberts, Ravi Challa, Naideline Raymond, Patrick Cullen, Thomas M. Carlile, Katelin A. Ennis, Mei Liu, Chao Sun, Norm Allaire, Marianna Foos, Hui-Hsin Tsai, Nathalie Franchimont, Richard M. Ransohoff, Cherié Butts, Michaël Mingueneau
Software Mentions: 2
Published: over 3 years ago

10.1038/s41398-021-01263-4

Exome-wide age-of-onset analysis reveals exonic variants in ERN1 and SPPL2C associated with Alzheimer’s disease
Cited by: 12
Author(s): Liang He, Yury Loika, Yong‐Jin Park, David A. Bennett, M Kellis, Alexander M. Kulminski, Alzheimer’s Disease Neuroimaging Initiative
Software Mentions: 2
Published: over 3 years ago

10.3389/fcell.2021.653308

Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells
Cited by: 6
Author(s): Jiayi Xie, Qi Lou, Yunxin Zeng, Yingying Liang, Siyu Xie, Quanhui Xu, Lisha Yuan, Jin Wang, Linjia Jiang, Lisha Mou, Dongjun Lin, Meng Zhao
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.43803

Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq
Cited by: 212
Author(s): Dylan Kotliar, Adrian Veres, Martina Nagy, Shervin Tabrizi, Eran Hodis, Douglas A. Melton, Pardis C. Sabeti
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmed.2021.603374

Single-Cell RNA-seq Reveals Angiotensin-Converting Enzyme 2 and Transmembrane Serine Protease 2 Expression in TROP2+ Liver Progenitor Cells: Implications in Coronavirus Disease 2019-Associated Liver Dysfunction
Cited by: 26
Author(s): Justine Jia Wen Seow, Rhea Pai, A. N. Mishra, Edwin Shepherdson, Tony Kiat Hon Lim, Brian K. P. Goh, Jerry Ky Chan, Pierce K. H. Chow, Florent Ginhoux, Ramanuj DasGupta, Ankur Sharma
Software Mentions: 2
Published: about 3 years ago

10.7554/eLife.60317

Somatostatin-expressing parafacial neurons are CO2/H+ sensitive and regulate baseline breathing
Cited by: 7
Author(s): Colin Cleary, Brenda M Milla, Fu-Shan Kuo, Shaun James, William F. Flynn, Paul Robson, Daniel K. Mulkey
Software Mentions: 2
Published: about 3 years ago

10.26508/lsa.202000924

Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice
Cited by: 12
Author(s): Ruth Karlina, Dominik Lutter, Viktorian Miok, David Fischer, Irem Altun, Theresa Schöttl, Kenji Schorpp, Andreas Israel, Cheryl Cero, James W. Johnson, Ingrid Kapser-Fischer, Anika Böttcher, Susanne Keipert, Annette Feuchtinger, Elisabeth Graf, Tim M. Strom, Axel Walch, Heiko Lickert, Thomas Walzthoeni, Matthias Heinig, Fabian J. Theis, Cristina García‐Cáceres, Aaron M. Cypess, Siegfried Ussar
Software Mentions: 2
Published: over 3 years ago

10.1186/s41065-020-00168-4

Mediators of SARS-CoV-2 entry are preferentially enriched in cardiomyocytes
Cited by: 22
Author(s): Jing Yang, Cheng Tan, Zhou Yafeng
Software Mentions: 1
Published: over 3 years ago

10.3389/fcell.2021.646252

CXCL11 Correlates With Antitumor Immunity and an Improved Prognosis in Colon Cancer
Cited by: 66
Author(s): Yingying Cao, Nanlin Jiao, Tiantian Sun, Yanru Ma, Xinyu Zhang, Haoyan Chen, Jie Hong, Youwei Zhang
Software Mentions: 1
Published: about 3 years ago

10.1186/s13059-021-02288-0

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants
Cited by: 54
Author(s): Yanping Long, Zhijian Liu, Jinbu Jia, Weipeng Mo, Liang Fang, Dongdong Lu, Bo Liu, Zhang Hong, Wei Chen, Jixian Zhai
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: scanpy

Papers Mentioning scanpy 68