bioconductor: scran | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1006361

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Cited by: 92
Author(s): Tian Li, Shian Su, Xueyi Dong, Daniela Amann‐Zalcenstein, Christine Biben, Azadeh Seidi, Douglas J. Hilton, Shalin H. Naik, Matthew E. Ritchie
Software Mentions: 21
Published: over 6 years ago

10.1186/s13059-020-02136-7

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools
Cited by: 53
Author(s): Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
Software Mentions: 21
Published: about 4 years ago

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: over 5 years ago

10.3389/fimmu.2020.01691

Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies
Cited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago

10.20517/jtgg.2020.51

Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq
Cited by: 2
Author(s): Brandon Lieberman, Meena Kusi, Chia-Nung Hung, Chih-Wei Chou, Ning He, Yen‐Yi Ho, Josephine A. Taverna, Tim Hui-Ming Huang, Chun-Liang Chen
Software Mentions: 18
Published: almost 5 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: about 4 years ago

10.1016/j.stem.2019.07.008

Defining the Identity and Dynamics of Adult Gastric Isthmus Stem Cells
Cited by: 85
Author(s): Seungmin Han, J. Lynn Fink, David J. Jörg, Eunmin Lee, Min Kyu Yum, Lemonia Chatzeli, Sebastian R. Merker, Manon Josserand, Teodora Trendafilova, Amanda Andersson-Rolf, Catherine Dabrowska, Hyunki Kim, Ronald Naumann, Ji–Hyun Lee, Nobuo Sasaki, Richard L. Mort, Onur Basak, Hans Clevers, Daniel E. Stange, Anna Philpott, Jong Kim, Benjamin D. Simons, Bon‐Kyoung Koo
Software Mentions: 17
Published: about 5 years ago

10.1126/sciimmunol.abd6832

Natural killer cell immunotypes related to COVID-19 disease severity
Cited by: 315
Author(s): Christopher Maucourant, Iva Filipovic, Andrea Ponzetta, Soo Aleman, Martin Cornillet, Laura Hertwig, Benedikt Strunz, Antonio Lentini, Björn Reinius, Demi Brownlie, Angélica Cuapio, Eivind Heggernes Ask, Ryan M. Hull, Alvaro Haroun-Izquierdo, Marie Schaffer, Jonas Klingström, Elin Folkesson, Marcus Buggert, Johan K. Sandberg, Lars Eriksson, Olav Rooyackers, Hans‐Gustaf Ljunggren, Karl‐Johan Malmberg, Jakob Michaëlsson, Nicole Marquardt, Quirin Hammer, Kristoffer Strålin, Niklas K. Björkström
Software Mentions: 16
Published: over 4 years ago

10.1186/s13059-020-02132-x

A systematic evaluation of single-cell RNA-sequencing imputation methods
Cited by: 156
Author(s): Wenpin Hou, Zhicheng Ji, Hongkai Ji, Stephanie Hicks
Software Mentions: 15
Published: about 4 years ago

10.1093/gigascience/giy123

PiGx: reproducible genomics analysis pipelines with GNU Guix
Cited by: 51
Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Software Mentions: 15
Published: about 6 years ago

10.3390/life11070716

Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering
Cited by: 0
Author(s): Yunhe Liu, Aoshen Wu, Xueqing Peng, Xiaona Liu, Gang Liu, Lei Liu
Software Mentions: 15
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: almost 4 years ago

10.1093/bioinformatics/btw777

Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
Cited by: 1,059
Author(s): Davis J. McCarthy, Kieran R Campbell, Aaron T. L. Lun, Quin F. Wills
Software Mentions: 14
Published: almost 8 years ago

10.1038/s42003-019-0554-8

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome
Cited by: 37
Author(s): Weiyan Chen, Samuel Morabito, Kai Kessenbrock, Tariq Enver, Kerstin B. Meyer, Andrew E. Teschendorff
Software Mentions: 14
Published: over 5 years ago

10.1186/s40478-020-0880-6

Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Cited by: 147
Author(s): Osama Al‐Dalahmah, Alexander A. Sosunov, Ayesha Shaik, Kenneth Ofori, Yang Liu, Jean Paul Vonsattel, István Adorján, Vilas Menon, James E. Goldman
Software Mentions: 14
Published: almost 5 years ago

10.1016/j.cell.2021.04.048

Integrated analysis of multimodal single-cell data
Cited by: 4,423
Author(s): Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, William M. Mauck, Shiwei Zheng, Andrew Butler, Madeline Lee, Aaron J. Wilk, Charlotte A. Darby, Michael Zager, Paul Hoffman, Marlon Stoeckius, Efthymia Papalexi, Eleni P. Mimitou, Jaison Jain, Avi Srivastava, T.A. Stuart, Lamar M. Fleming, Bertrand Z. Yeung, Angela J. Rogers, Juliana McElrath, Catherine A. Blish, Raphaël Gottardo, Peter Smibert, Rahul Satija
Software Mentions: 13
Published: over 3 years ago

10.1186/s13059-019-1739-7

CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data
Cited by: 33
Author(s): Rebekka Wegmann, Marilisa Neri, Sven Schuierer, Bilada Bilican, Huyen Hartkopf, Florian Nigsch, Felipa Mapa, Annick Waldt, Rachel Cuttat, Max R. Salick, Joe Raymond, Ajamete Kaykas, Guglielmo Roma, Caroline Gubser Keller
Software Mentions: 13
Published: over 5 years ago

10.1371/journal.pcbi.1007113

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes
Cited by: 28
Author(s): Claire Bomkamp, Shreejoy J. Tripathy, Carolina Bengtsson Gonzales, Jens Hjerling-Leffler, Ann Marie Craig, Paul Pavlidis
Software Mentions: 13
Published: over 5 years ago

10.3389/fgene.2021.665888

A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells
Cited by: 2
Author(s): Simon Haile, Richard Corbett, Véronique G. LeBlanc, Lisa L. Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin Coope, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, İnanç Birol, Steven J.M. Jones, Marco A. Marra
Software Mentions: 13
Published: over 3 years ago

10.12688/f1000research.9501.2

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
Cited by: 693
Author(s): Aaron T. L. Lun, Davis J. McCarthy, John C. Marioni
Software Mentions: 12
Published: about 8 years ago

10.26508/lsa.202001004

CellMixS: quantifying and visualizing batch effects in single-cell RNA-seq data
Cited by: 21
Author(s): Almut Luetge, Joanna Zyprych-Walczak, Urszula Brykczynska Kunzmann, Helena L. Crowell, Daniela Calini, Dheeraj Malhotra, Charlotte Soneson, Mark D. Robinson
Software Mentions: 12
Published: over 3 years ago

10.12688/f1000research.15809.2

Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data
Cited by: 90
Author(s): Saskia Freytag, Tian Li, Ingrid Lönnstedt, Milica Ng, Melanie Bahlo
Software Mentions: 12
Published: almost 6 years ago

10.1242/dev.177428

Novel dynamics of human mucociliary differentiation revealed by single-cell RNA sequencing of nasal epithelial cultures
Cited by: 182
Author(s): Sandra Ruiz García, Marie Deprez, Kévin Lebrigand, Amélie Cavard, Agnès Paquet, Marie-Jeanne Arguel, Virginie Magnone, Marin Truchi, Ignacio Caballero, Sylvie Leroy, Charles‐Hugo Marquette, Brice Marcet, Pascal Barbry, Laure‐Emmanuelle Zaragosi
Software Mentions: 11
Published: about 5 years ago

10.1371/journal.pcbi.1006135

beachmat: A Bioconductor C++ API for accessing high-throughput biological data from a variety of R matrix types
Cited by: 13
Author(s): Aaron T. L. Lun, Hervé Pagès, Mike L. Smith
Software Mentions: 10
Published: over 6 years ago

10.1038/s42003-020-0842-3

Loss of the branched-chain amino acid transporter CD98hc alters the development of colonic macrophages in mice
Cited by: 17
Author(s): Philipp Wuggenig, Berna Kaya, Hassan Melhem, C. Korcan Ayata, Swiss Ibd Cohort Investigators, Petr Hrúz, Emre Sayan, Hideki Tsumura, Morihiro Ito, Julien Roux, Jan Hendrik Niess
Software Mentions: 10
Published: over 4 years ago

10.1016/j.celrep.2019.10.024

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis
Cited by: 227
Author(s): Ross Dobie, John Wilson-Kanamori, Beth E. P. Henderson, J. F. Smith, Kylie P. Matchett, Jordan Raymond Portman, Karolina Wallenborg, Simone Picelli, Анна Загорска, Swetha Pendem, Thomas E. Hudson, Max C. Wu, Grant R. Budas, David G. Breckenridge, Ewen M Harrison, Damian J. Mole, Stephen J. Wigmore, Prakash Ramachandran, Chris P. Ponting, Sarah A. Teichmann, John C. Marioni, Neil C. Henderson
Software Mentions: 10
Published: about 5 years ago

10.3389/fgene.2019.01253

Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering Methods
Cited by: 56
Author(s): Monika Krzak, Yordan P. Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini
Software Mentions: 9
Published: almost 5 years ago

10.1186/s13059-019-1662-y

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Cited by: 518
Author(s): Aaron T. L. Lun, Samantha J. Riesenfeld, Tallulah Andrews, Tomás Gomes, John C. Marioni
Software Mentions: 9
Published: over 5 years ago

10.1186/s13059-021-02407-x

Optimizing expression quantitative trait locus mapping workflows for single-cell studies
Cited by: 30
Author(s): Anna Cuomo, Giordano Alvari, Christina B. Azodi, Davis J. McCarthy, Marc Jan Bonder
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.33105

Single-cell RNA-seq reveals hidden transcriptional variation in malaria parasites
Cited by: 152
Author(s): Adam J. Reid, Arthur M. Talman, Hayley M. Bennett, Ana Gomes, Mandy Sanders, Christopher J. R. Illingworth, Oliver Billker, Matthew Berriman, Mara Lawniczak
Software Mentions: 9
Published: over 6 years ago

10.1371/journal.pcbi.1008778

Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells
Cited by: 4
Author(s): Jared Brown, Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Michael P. Schwartz, Amy Van Aartsen, John Steill, Scott Swanson, Ron Stewart, James A. Thomson, Christina Kendziorski
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.60188

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells
Cited by: 42
Author(s): Kristen L. Wells, Corey N. Miller, Andreas R. Gschwind, Wei Wu, Jonah D Phipps, Mark S. Anderson, Lars M. Steinmetz
Software Mentions: 9
Published: almost 4 years ago

10.1016/j.celrep.2020.108661

Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets
Cited by: 47
Author(s): Michael Fitzpatrick, Nicholas M. Provine, Lucy C. Garner, Kate Powell, Ali Amini, Sophie Irwin, Helen Ferry, Tim Ambrose, Peter J. Friend, Georgios Vrakas, Srikanth Reddy, Elizabeth Soilleux, Paul Klenerman, Philip Allan
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13073-020-00731-8

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Cited by: 28
Author(s): Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Hans‐Georg Rammensee, Jens Bedke, Stefan Stevanović, Matthias Schwab, Elke Schaeffeler
Software Mentions: 9
Published: over 4 years ago

10.3390/genes11050532

Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-seq Data
Cited by: 9
Author(s): Weilai Chi, Minghua Deng
Software Mentions: 9
Published: over 4 years ago

10.7554/eLife.69065

Cross-species analysis defines the conservation of anatomically segregated VMH neuron populations
Cited by: 16
Author(s): Alison H. Affinati, Paul V. Sabatini, Cadence True, Abigail J. Tomlinson, Melissa A. Kirigiti, Sarah R. Lindsley, Chien Li, David P. Olson, Paul Kievit, Martin G. Myers, Alan C. Rupp
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-017-1188-0

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
Cited by: 391
Author(s): Peijie Lin, Michael Troup, Joshua W. K. Ho
Software Mentions: 8
Published: over 7 years ago

10.3389/fgene.2020.00041

Normalization Methods on Single-Cell RNA-seq Data: An Empirical Survey
Cited by: 46
Author(s): Nicholas Lytal, Ran Di, Lingling An
Software Mentions: 8
Published: almost 5 years ago

10.7554/eLife.58810

Single-cell RNA-sequencing reveals distinct patterns of cell state heterogeneity in mouse models of breast cancer
Cited by: 38
Author(s): Syn Kok Yeo, Xiaoting Zhu, Takaaki Okamoto, Mingang Hao, Cailian Wang, Peixin Lu, Long Lu, Jun‐Lin Guan
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0210571

Deterministic column subset selection for single-cell RNA-Seq
Cited by: 0
Author(s): Shannon R. McCurdy, Vasilis Ntranos, Lior Pachter
Software Mentions: 8
Published: almost 6 years ago

10.1038/s41422-018-0053-3

Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis
Cited by: 162
Author(s): Xiaoying Fan, Ji Dong, Shaobo Zhong, Wei Yuan, Qian Wu, Liying Yan, Jun Yong, Le Sun, Xiaoye Wang, Yangyu Zhao, Wei Wang, Jie Yan, Xiaoqun Wang, Jie Qiao, Fuchou Tang
Software Mentions: 8
Published: over 6 years ago

10.1186/s13073-020-00799-2

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities
Cited by: 20
Author(s): Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg, Olli Lohi, Merja Heinäniemi
Software Mentions: 8
Published: about 4 years ago

10.1186/s13073-019-0615-0

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney
Cited by: 144
Author(s): Alexander N. Combes, Luke Zappia, Pei X. Er, Alicia Oshlack, Melissa H. Little
Software Mentions: 8
Published: almost 6 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

10.3389/fimmu.2018.01553

Single Cell RNA Sequencing of Rare Immune Cell Populations
Cited by: 88
Author(s): Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I. Croucher, Tri Giang Phan
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.53360

Dual histone methyl reader ZCWPW1 facilitates repair of meiotic double strand breaks in male mice
Cited by: 25
Author(s): Mohamed Mahgoub, Jacob Paiano, Melania Bruno, Wei Wu, Sarath Pathuri, Xing Zhang, Sherry Ralls, Xiaodong Cheng, André Nussenzweig, Todd S. Macfarlan
Software Mentions: 7
Published: over 4 years ago

10.1186/s12935-021-02154-w

Study of cellular heterogeneity and differential dynamics of autophagy in human embryonic kidney development by single-cell RNA sequencing
Cited by: 2
Author(s): Wenjin Chen, Xiuwu Pan, Jian Chu, Da Xu, Jia-Xin Chen, Weijie Chen, Linhui Wang, Xingang Cui
Software Mentions: 7
Published: about 3 years ago

10.1371/journal.pgen.1008506

Latent transcriptional variations of individual Plasmodium falciparum uncovered by single-cell RNA-seq and fluorescence imaging
Cited by: 21
Author(s): Katelyn A. Walzer, Hélène Fradin, Liane Y. Emerson, David L. Corcoran, Jen‐Tsan Chi
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pcbi.1009290

miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
Cited by: 23
Author(s): Ariel A. Hippen, Matías M. Falco, Lukas M. Weber, Erdoğan Pekcan Erkan, Kaiyang Zhang, Jennifer A. Doherty, Anna Vähärautio, Casey S. Greene, Stephanie C. Hicks
Software Mentions: 7
Published: about 3 years ago

10.1186/s13059-018-1438-9

UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Cited by: 80
Author(s): Wenan Chen, Yán Li, John Easton, David Finkelstein, Gang Wu, Xiang Chen
Software Mentions: 7
Published: over 6 years ago

10.3389/fimmu.2021.665312

An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells
Cited by: 8
Author(s): James Davies, Andrés F. Vallejo, Sofía Sirvent, Gemma Porter, Kalum Clayton, Yamkela Qumbelo, Patrick S. Stumpf, Jonathan West, Clive M. Gray, Nyaradzo T. L. Chigorimbo‐Murefu, Ben D. MacArthur, Marta E. Polak
Software Mentions: 7
Published: over 3 years ago

10.3390/ijms22094917

The Cellular Composition of Bovine Coccygeal Intervertebral Discs: A Comprehensive Single-Cell RNAseq Analysis
Cited by: 24
Author(s): Martina Caliò, Benjamin Gantenbein, Marcel Egli, Lucy Poveda, Fabian Ille
Software Mentions: 7
Published: over 3 years ago

10.1002/1878-0261.12569

Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progression
Cited by: 34
Author(s): Bo Pang, Jiu Hua Xu, Jing Hu, Fenghua Guo, Linyun Wan, Mingjiang Cheng, Lin Pang
Software Mentions: 7
Published: about 5 years ago

10.12688/f1000research.11290.1

Gene length and detection bias in single cell RNA sequencing protocols
Cited by: 71
Author(s): Belinda Phipson, Luke Zappia, Alicia Oshlack
Software Mentions: 7
Published: over 7 years ago

10.1038/s42003-021-01897-6

Identification of a targetable KRAS-mutant epithelial population in non-small cell lung cancer
Cited by: 9
Author(s): Giorgia Maroni, Mahmoud A. Bassal, Indira Krishnan, Chee Wai Fhu, Virginia Savova, Rapolas Žilionis, Valerie A. Maymi, Nicole Pandell, Eva Csizmadia, Junyan Zhang, Barbara Storti, Julio Castaño, Riccardo Panella, Jia Li, Corinne E. Gustafson, Sam Fox, Rachel Levy, Claire Meyerovitz, Peter J. Tramontozzi, Kimberly Vermilya, Assunta De Rienzo, Stefania Crucitta, Daniela S. Bassères, Marla Weetall, Art Branstrom, Alessandra Giorgetti, Raffaele Ciampi, Marzia Del Re, Romano Danesi, Ranieri Bizzarri, Henry Yang, Olivier Kocher, Allon M. Klein, Robert S. Welner, Raphael Bueno, Maria Cristina Magli, John G. Clohessy, Azhar Ali, Daniel G. Tenen, Elena Levantini
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.41627

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming
Cited by: 38
Author(s): Mirko Francesconi, Bruno Di Stefano, Clara Berenguer, Luísa de Andrés-Aguayo, Marcos Plana-Carmona, María Méndez-Lago, Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Marta Gut, Holger Heyn, Ben Liu, Thomas Graf
Software Mentions: 7
Published: over 5 years ago

10.1523/ENEURO.0066-20.2020

Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth
Cited by: 33
Author(s): Jeremy S. Toma, Konstantina Karamboulas, Matthew Carr, Adelaida Kolaj, Scott A. Yuzwa, Neemat Mahmud, Mekayla Storer, David R. Kaplan, Freda D. Miller
Software Mentions: 6
Published: over 4 years ago

10.1186/s12915-020-00842-z

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo
Cited by: 19
Author(s): Jialin Liu, Michael Frochaux, Vincent Gardeux, Bart Deplancke, Marc Robinson‐Rechavi
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-021-07435-2

Blinatumomab-induced T cell activation at single cell transcriptome resolution
Cited by: 11
Author(s): Yi Huo, Zhonghua Sheng, Daniel Lu, Daniel C. Ellwanger, Chi-Ming Li, Oliver Homann, Songli Wang, Hong Mei Yin, Ruibao Ren
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-020-07358-4

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling
Cited by: 33
Author(s): Tracy M. Yamawaki, Daniel Lu, Daniel C. Ellwanger, Dev Bhatt, Paolo Manzanillo, Vanessa Arias, Hong Zhou, Oh Kyu Yoon, Oliver Homann, Songli Wang, Chi-Ming Li
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pbio.2006687

Quantitative assessment of cell population diversity in single-cell landscapes
Cited by: 40
Author(s): Qi Liu, Charles A. Herring, Quanhu Sheng, Jie Ping, Alan J. Simmons, Bob Chen, Amrita Banerjee, Wei Li, Guoqiang Gu, Robert J. Coffey, Yu Shyr, Ken S. Lau
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pgen.1007552

High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor
Cited by: 56
Author(s): Tetsuji Yamashita, Fei Zheng, David Finkelstein, Zoe Kellard, Caroline Robert, Celeste Rosencrance, Ken Sugino, John Easton, Charles Gawad, Jian Zuo
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0243360

DSAVE: Detection of misclassified cells in single-cell RNA-Seq data
Cited by: 2
Author(s): Johan Gustafsson, Jonathan L. Robinson, Juan Salvador Inda-Díaz, Elias Björnson, Rebecka Jörnsten, Jens Nielsen
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.celrep.2020.107628

Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth
Cited by: 156
Author(s): Sarah Davidson, Mirjana Efremova, Angela Riedel, Bidesh Mahata, Jhuma Pramanik, Jani Huuhtanen, Gozde Kar, Roser Vento‐Tormo, Tzachi Hagai, Xi Chen, Muzlifah Haniffa, Jacqueline D. Shields, Sarah A. Teichmann
Software Mentions: 6
Published: over 4 years ago

10.1016/j.devcel.2018.06.028

Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development
Cited by: 36
Author(s): Magdalena K. Sznurkowska, Édouard Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher J. Hindley, Jennifer Nichols, Berthold Göttgens, Meritxell Huch, Anna Philpott, Benjamin D. Simons
Software Mentions: 6
Published: over 6 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: about 4 years ago

10.1093/gigascience/giy059

zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: over 6 years ago

10.1084/jem.20192386

Transcription cofactor GRIP1 differentially affects myeloid cell–driven neuroinflammation and response to IFN-β therapy
Cited by: 4
Author(s): Sanda Mimouna, David A. Rollins, Gayathri Shibu, Bowranigan Tharmalingam, Dinesh K Deochand, Xi Chen, David J. Oliver, Yurii Chinenov, Inez Rogatsky
Software Mentions: 6
Published: about 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: over 3 years ago

10.1371/journal.pone.0239711

Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis
Cited 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

10.1371/journal.pbio.3000704

Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
Cited by: 83
Author(s): Noriki Fujimoto, Yuliang He, Marco D’Addio, Carlotta Tacconi, Michael Detmar, Lothar C. Dieterich
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 data
Cited by: 14
Author(s): Zijian Ni, Shuyang Chen, Jared Brown, Christina Kendziorski
Software Mentions: 5
Published: over 4 years ago

10.3389/fcvm.2020.00052

A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature
Cited 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

10.1016/j.immuni.2019.05.002

Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow
Cited by: 85
Author(s): Jennifer Walker, Paula A. Clark, Alastair Crisp, Jillian L. Barlow, Aydan C H Szeto, Ana Carolina Franco Ferreira, Batika M. J. Rana, Helen E. Jolin, Noé Rodríguez-Rodríguez, Meera Sivasubramaniam, Richard Pannell, James Cruickshank, Maria Daly, Liora Haim-Vilmovsky, Sarah A. Teichmann, Andrew N. J. McKenzie
Software Mentions: 5
Published: over 5 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: almost 6 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: over 4 years ago

10.1126/sciimmunol.abc3582

TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes
Cited by: 754
Author(s): Ruochen Zang, María Florencia Gómez Castro, Broc T. McCune, Qiru Zeng, Paul W. Rothlauf, Naomi Sonnek, Zhuoming Liu, Kevin Brulois, Xin Wang, Harry B. Greenberg, Michael S. Diamond, Matthew A. Ciorba, Sean P. J. Whelan, Siyuan Ding
Software Mentions: 5
Published: over 4 years ago

10.1038/s41422-018-0099-2

The adult human testis transcriptional cell atlas
Cited by: 381
Author(s): Jingtao Guo, Edward J. Grow, Hana Mlčochová, Geoffrey J. Maher, Cecilia Lindskog, Xiaolu Nie, Yixuan Guo, Yodai Takei, Jina Yun, Long Cai, Robin Kim, Douglas T. Carrell, Anne Goriely, James M. Hotaling, Bradley R. Cairns
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.55474

An atlas of cell types in the mouse epididymis and vas deferens
Cited by: 45
Author(s): Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Küçükural, Onur Yukselen, Manuel Garber, Upasna Sharma, Oliver J. Rando
Software Mentions: 5
Published: over 4 years ago

10.1016/j.devcel.2020.11.013

Diverse Routes toward Early Somites in the Mouse Embryo
Cited by: 40
Author(s): Carolina Guibentif, J. B. Griffiths, Iván Imaz-Rosshandler, Shila Ghazanfar, Jennifer Nichols, Valerie Wilson, Berthold Göttgens, John C. Marioni
Software Mentions: 5
Published: almost 4 years ago

10.1038/s42003-020-0837-0

Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells
Cited by: 39
Author(s): Jackson A. Hoffman, Brian N. Papas, Kevin W. Trotter, Trevor Archer
Software Mentions: 4
Published: over 4 years ago

10.1016/j.immuni.2018.07.004

The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages
Cited by: 142
Author(s): Charlotte Scott, Wouter T’Jonck, Liesbet Martens, Helena Todorov, Dorine Sichien, Bieke Soen, Johnny Bonnardel, Sofie De Prijck, Niels Vandamme, Robrecht Cannoodt, Wouter Saelens, Bavo Vanneste, Wendy Toussaint, Pieter De Bleser, Nozomi Takahashi, Peter Vandenabeele, Sandrine Henri, Clare Pridans, David Hume, Bart N. Lambrecht, Patrick De Baetseĺier, Simon Milling, Jo A. Van Ginderachter, Bernard Malissen, Geert Berx, Alain Beck, Yvan Saeys, Martin Guilliams
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.49262

Pathologic evolution-related Gene Analysis based on both single-cell and bulk transcriptomics in Colorectal Cancer
Cited by: 3
Author(s): Jiali Li, Zhao-Yi Zeng, Jiarui Chen, Xingyu Liu, Xueping Jiang, Wenjie Sun, Yuan Luo, Jiangbo Ren, Yan Gong, Conghua Xie
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.56221

Ageing compromises mouse thymus function and remodels epithelial cell differentiation
Cited by: 83
Author(s): Jeanette Baran-Gale, Michael D. Morgan, Stefano Maio, Fatima Dhalla, Irene Calvo‐Asensio, Mary E. Deadman, Adam E. Handel, Ashley Maynard, Steven Chen, Foad Green, Rene Sit, Norma Neff, Spyros Darmanis, Weilun Tan, Andy P May, John C. Marioni, Chris P. Ponting, Georg A. Holländer
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pbio.3000711

Single-cell transcription analysis of Plasmodium vivax blood-stage parasites identifies stage- and species-specific profiles of expression
Cited by: 49
Author(s): Juliana M. Sá, Matthew Cannon, Ramoncito L. Caleon, Thomas E. Wellems, David Serre
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2019.01036

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

10.3389/fncel.2020.00059

Cell Type-Specific Gene Network-Based Analysis Depicts the Heterogeneity of Autism Spectrum Disorder
Cited by: 8
Author(s): Jinting Guan, Yiping Lin, Guoli Ji
Software Mentions: 3
Published: over 4 years ago

10.3389/fcell.2020.00288

Hybrid Stem Cell States: Insights Into the Relationship Between Mammary Development and Breast Cancer Using Single-Cell Transcriptomics
Cited by: 18
Author(s): Tasha Thong, Yutong Wang, Michael Brooks, Christopher T. Lee, Clayton Scott, Laura Balzano, Max S. Wicha, Justin A. Colacino
Software Mentions: 3
Published: over 4 years ago

10.12688/f1000research.16613.2

False signals induced by single-cell imputation
Cited by: 99
Author(s): Tallulah Andrews, Martin Hemberg
Software Mentions: 3
Published: over 5 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: almost 5 years ago

10.1093/molbev/msz290

Distinct Evolutionary Trajectories of Neuronal and Hair Cell Nicotinic Acetylcholine Receptors
Cited by: 26
Author(s): Irina Marcovich, Marcelo J. Moglie, Agustín Eduardo Carpaneto Freixas, Anabella Paola Trigila, Lucía F. Franchini, Paola V. Plazas, Marcela Lipovsek, Ana Belén Elgoyhen
Software Mentions: 3
Published: almost 5 years ago

10.1016/j.devcel.2020.09.001

Abscission Couples Cell Division to Embryonic Stem Cell Fate
Cited by: 26
Author(s): Agathe Chaigne, Céline Labouesse, Ian J. White, Meghan Agnew, Édouard Hannezo, Kevin J. Chalut, Ewa K. Paluch
Software Mentions: 3
Published: about 4 years ago

10.1016/j.devcel.2017.04.004

Multi-site Neurogenin3 Phosphorylation Controls Pancreatic Endocrine Differentiation
Cited by: 60
Author(s): Roberta Azzarelli, Christopher A. Hurley, Magdalena K. Sznurkowska, Steffen Rulands, Laura J.A. Hardwick, Ivonne Gamper, Fahad Ali, Laura McCracken, Christopher J. Hindley, Fiona Kate Elizabeth McDuff, Sonia Nestorowa, Richard Kemp, Kenneth Alan Jones, Berthold Göttgens, Meritxell Huch, Gérard I. Evan, Benjamin D. Simons, Douglas J. Winton, Anna Philpott
Software Mentions: 3
Published: over 7 years ago

10.1016/j.stem.2020.05.004

Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease
Cited by: 302
Author(s): Elisa Giacomelli, Viviana Meraviglia, Giulia Campostrini, Amy Cochrane, Xu Cao, Ruben W.J. van Helden, Ana Krotenberg Garcia, Maria Mircea, Sarantos Kostidis, Richard P. Davis, Berend J. van Meer, Carolina R. Jost, Abraham J. Koster, Hailiang Mei, David G. Míguez, Aat A. Mulder, Mario Ledesma-Terrón, Giulio Pompilio, Luca Sala, Daniela Salvatori, Roderick C. Slieker, Elena Sommariva, Antoine A.F. de Vries, Martin Giera, Stefan Semrau, Leon G.J. Tertoolen, Valeria V. Orlova, Milena Bellin, Christine L. Mummery
Software Mentions: 3
Published: over 4 years ago

10.1186/s13073-021-00894-y

Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq
Cited by: 36
Author(s): Wenting Zhao, Athanassios Dovas, Eleonora F. Spinazzi, Hanna Mendes Levitin, Matei Banu, Pavan S. Upadhyayula, Tejaswi Sudhakar, Tamara Marie, Marc L. Otten, Michael B. Sisti, Jeffrey N. Bruce, Peter Canoll, Peter A. Sims
Software Mentions: 3
Published: over 3 years ago

10.1186/s12967-020-02690-5

An analytical method for the identification of cell type-specific disease gene modules
Cited by: 5
Author(s): Jinting Guan, Yiping Lin, Yang Wang, Junchao Gao, Guoli Ji
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-88875-4

Synthetic single cell RNA sequencing data from small pilot studies using deep generative models
Cited by: 5
Author(s): Martin Treppner, Adrián Salas-Bastos, Moritz Hess, Stefan Lenz, Tanja Vogel, Harald Binder
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-97059-z

Gelatin methacrylate hydrogels culture model for glioblastoma cells enriches for mesenchymal-like state and models interactions with immune cells
Cited by: 6
Author(s): Nameeta Shah, Pavan M. Hallur, Raksha A. Ganesh, Pranali Sonpatki, Divya Naik, Komal Prasad Chandrachari, Ralph B. Puchalski, Aditya Chaubey
Software Mentions: 3
Published: about 3 years ago

10.1186/s12920-019-0532-5

Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells
Cited by: 25
Author(s): Yanding Zhao, Caroline Robert, Sivaraman Natarajan, Frederick S. Varn, Duane A. Compton, Charles Gawad, Chao Cheng, Kristina Godek
Software Mentions: 3
Published: over 5 years ago

10.1038/s41421-021-00296-9

Dysregulated hematopoiesis in bone marrow marks severe COVID-19
Cited by: 34
Author(s): Xin Wang, Yanling Wen, Xiaowei Xie, Yang Liu, Xiaohua Tan, Qing-Qing Cai, Yawen Zhang, Lin Cheng, Gang Xu, Shengyuan Zhang, Haiyan Wang, Lanlan Wei, Xian Tang, Furong Qi, Juanjuan Zhao, Jing Yuan, Lei Liu, Ping Zhu, Florent Ginhoux, Shuye Zhang, Tao Cheng, Zheng Zhang
Software Mentions: 3
Published: over 3 years ago

Projects: bioconductor: scran

Papers Mentioning scran 113