cran: Seurat | Projects | Ecosyste.ms: Papers

10.7150/thno.54741

Kinomic profile in patient-derived glioma cells during hypoxia reveals c-MET-PI3K dependency for adaptation
Cited by: 6
Author(s): Hong Sheng Cheng, Charlie Marvalim, Pengcheng Zhu, Cheng Lui Daniel Law, Zhi Yan Jeremy Low, Yuk Kien Chong, Beng Ti Ang, Carol Tang, Nguan Soon Tan
Software Mentions: 2
Published: almost 4 years ago

10.1101/2020.08.20.258087

SARS-CoV-2 infection dynamics in lungs of African green monkeys
Cited by: 5
Author(s): Emily Speranza, Brandi N. Williamson, Friederike Feldmann, Gail L. Sturdevant, Lizzette Pérez-Pérez, Kimberly Mead-White, Brian J Smith, Jamie Lovaglio, Craig Martens, Vincent J. Munster, Atsushi Okumura, Carl Shaia, Heinz Feldmann, Sonja M. Best, Emmie de Wit
Software Mentions: 2
Published: over 4 years ago

10.1101/2020.10.08.332080

Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data
Cited by: 1
Author(s): Shaoheng Liang, Jun Dou, Ramiz Iqbal, Ken Chen
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-021-04186-5

CDSeqR: fast complete deconvolution for gene expression data from bulk tissues
Cited by: 9
Author(s): Kai Kang, Caizhi Huang, Yuanyuan Li, David M. Umbach, Leping Li
Software Mentions: 2
Published: over 3 years ago

10.1128/mSystems.01095-20

Single-Cell RNA Sequencing Reveals that the Switching of the Transcriptional Profiles of Cysteine-Related Genes Alters the Virulence of Entamoeba histolytica
Cited by: 4
Author(s): Min Feng, Yuhan Zhang, Hang Zhou, Xia Li, Yongfeng Fu, Hiroshi Tachibana, Xunjia Cheng
Software Mentions: 2
Published: almost 4 years ago

10.1093/humrep/dez139

Tissue stiffness at the human maternal–fetal interface
Cited by: 53
Author(s): Yassen Abbas, Alejandro Carnicer‐Lombarte, Lucy Gardner, Jake Thomas, Jan J. Brosens, Ashley Moffett, Andrew Sharkey, Kristian Franze, Graham J. Burton, Michelle L. Oyen
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-020-03700-5

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
Cited by: 15
Author(s): Ji-Hye Choi, Hye In Kim, Hyun Goo Woo
Software Mentions: 2
Published: over 4 years ago

10.1186/s13046-021-01874-1

Single‐cell RNA sequencing in cancer research
Cited by: 104
Author(s): Yijie Zhang, Dan Wang, Peng Miao, Le Tang, Jiawei Ouyang, Fang Xiong, Can Guo, Yue Tang, Yujuan Zhou, Qianjin Liao, Xu Wu, Hui Wang, Jianjun Yu, Yong Li, Xiaoling Li, Guiyuan Li, Zhaoyang Zeng, Yixin Tan, Wei Xiong
Software Mentions: 2
Published: over 3 years ago

10.1186/s13046-021-01944-4

Deciphering the temporal heterogeneity of cancer-associated fibroblast subpopulations in breast cancer
Cited by: 20
Author(s): Freja Albjerg Venning, Kamilla Westarp Zornhagen, Lena Wullkopf, Jonas Sjölund, Carmen Rodriguez-Cupello, Pontus Kjellman, Mikkel Morsing, Morteza Chalabi Hajkarim, Kyoung Jae Won, Janine T. Erler, Chris D. Madsen
Software Mentions: 2
Published: over 3 years ago

10.1186/s13046-021-02046-x

Ref-1 redox activity alters cancer cell metabolism in pancreatic cancer: exploiting this novel finding as a potential target
Cited by: 15
Author(s): Silpa Gampala, Fenil Shah, Xiaoyu Lu, Hye-ran Moon, Olivia Babb, Nikkitha Umesh Ganesh, George E. Sandusky, Emily Hulsey, Lee Armstrong, Amber L Mosely, Bumsoo Han, Mircea Ivan, Jing-Ruey Joanna Yeh, Mark R. Kelley, Chi Zhang, Melissa L. Fishel
Software Mentions: 2
Published: over 3 years ago

10.1084/jem.20191236

Dynamics of human monocytes and airway macrophages during healthy aging and after transplant
Cited by: 91
Author(s): Adam Byrne, Joseph E. Powell, B. O’Sullivan, Patricia P. Ogger, Ashley Hoffland, James Cook, Katie Bonner, Richard Hewitt, Simone Wolf, Poonam Ghai, Simone A. Walker, Samuel W. Lukowski, Philip L. Molyneaux, Sejal Saglani, Daniel C. Chambers, Toby M. Maher, Clare M. Lloyd
Software Mentions: 2
Published: almost 5 years ago

10.1084/jem.20202001

Human marginal zone B cell development from early T2 progenitors
Cited by: 40
Author(s): Thomas J Tull, Michael J Pitcher, William Guesdon, Jacqueline Hy Siu, Cristina Lebrero‐Fernández, Yuan Zhao, Nedyalko Petrov, Susanne Heck, Richard J. Ellis, Pawan Dhami, Ulrich D. Kadolsky, Michelle Kleeman, Yogesh Kamra, David Fear, Susan John, Wayel Jassem, Richard Groves, Jeremy Sanderson, Michael G. Robson, David D’Cruz, Mats Bemark, Jo Spencer
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-021-04022-w

PIKE-R2P: Protein–protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction
Cited by: 7
Author(s): Xinnan Dai, Fan Xu, Shike Wang, Piyushkumar A. Mundra, Jie Zheng
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-021-04165-w

SSBER: removing batch effect for single-cell RNA sequencing data
Cited by: 3
Author(s): Yin Zhang, Fei Wang
Software Mentions: 2
Published: over 3 years ago

10.1167/iovs.62.6.18

Dissecting the Transcriptional and Chromatin Accessibility Heterogeneity of Proliferating Cone Precursors in Human Retinoblastoma Tumors by Single Cell Sequencing—Opening Pathways to New Therapeutic Strategies?
Cited by: 11
Author(s): Joseph Collin, Rachel Queen, Darin Zerti, David Steel, Claire Bowen, Manoj Parulekar, Majlinda Lako
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-016-0984-y

pcaReduce: hierarchical clustering of single cell transcriptional profiles
Cited by: 228
Author(s): Justina Žurauskienė, Christopher Yau
Software Mentions: 2
Published: over 8 years ago

10.1155/2021/6619302

Identification of the Different Gene Expression Characteristics from Liver Cirrhosis to Hepatocellular Carcinoma Using Single-Cell Sequencing Analyses
Cited by: 5
Author(s): Xin Xing, Jian Song
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41388-019-0680-2

Isolation and characterization of patient-derived CNS metastasis-associated stromal cell lines
Cited by: 9
Author(s): Ben Yi Tew, Christophe Legendre, Gerald C. Gooden, Kyle N. Johnson, Rae Anne Martinez, Jeff Kiefer, Mark Bernstein, Jennifer Glen, Loren Butry, Aleksander Hinek, Steven Toms, Bodour Salhia
Software Mentions: 2
Published: almost 6 years ago

10.1007/s10911-021-09486-3

Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland
Cited by: 9
Author(s): Samantha Henry, Marygrace C. Trousdell, Samantha L. Cyrill, Yixin Zhao, Mary J. Feigman, Julia M Bouhuis, Dominik A. Aylard, Adam Siepel, Camila O. dos Santos
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.54903

Maf and Mafb control mouse pallial interneuron fate and maturation through neuropsychiatric disease gene regulation
Cited by: 18
Author(s): Emily Ling-Lin Pai, Jin Chen, Siavash Fazel Darbandi, Frances S. Cho, Jiapei Chen, Susan Lindtner, Julia Chu, Jeanne T. Paz, Daniel Vogt, Mercedes F. Paredes, John L.R. Rubenstein
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.69765

Sex-specific pubertal and metabolic regulation of Kiss1 neurons via Nhlh2
Cited by: 11
Author(s): Silvia León, Rajae Talbi, Elizabeth McCarthy, Kaitlin Ferrari, Chrysanthi Fergani, Lydie Naulé, Ji Hae Choi, Rona S. Carroll, Ursula B. Kaiser, Carlos F. Aylwin, Alejandro Lomniczi, Víctor Navarro
Software Mentions: 2
Published: about 3 years ago

10.1186/s40478-021-01183-w

Combined epigenetic/genetic study identified an ALS age of onset modifier
Cited by: 6
Author(s): Ming Zhang, Zhengrui Xi, Sara Sáez-Atiénzar, Ruth Chia, Danielle Moreno, Christine Sato, Mahdi Montazer Haghighi, Bryan J. Traynor, Lorne Zinman, Ekaterina Rogaeva
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.63092

Subcellular sequencing of single neurons reveals the dendritic transcriptome of GABAergic interneurons
Cited by: 42
Author(s): Julio Pérez, Susanne tom Dieck, Beatriz Alvarez‐Castelao, Georgi Tushev, I.C.W. Chan, Erin M. Schuman
Software Mentions: 2
Published: almost 4 years ago

10.7554/eLife.55732

Novel C1q receptor-mediated signaling controls neural stem cell behavior and neurorepair
Cited by: 17
Author(s): Francisca Benavente, Katja Piltti, Mitra J. Hooshmand, Aileen A Nava, Anita Lakatos, Brianna G Feld, Dana Creasman, Paul D. Gershon, Aileen J. Anderson
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.61413

Mapping endothelial-cell diversity in cerebral cavernous malformations at single-cell resolution
Cited by: 38
Author(s): Fabrizio Orsenigo, Lei Liu Conze, Suvi Jauhiainen, Monica Corada, Francesca Lazzaroni, Matteo Malinverno, Veronica Sundell, Sara I. Cunha, Johan Brännström, Maria Ascención Globisch, Claudio Maderna, Maria Grazia Lampugnani, Peetra U. Magnusson, Elisabetta Dejana
Software Mentions: 2
Published: about 4 years ago

10.1128/JVI.01819-20

A Comparative Analysis of SARS-CoV-2 Antivirals Characterizes 3CL pro Inhibitor PF-00835231 as a Potential New Treatment for COVID-19
Cited by: 88
Author(s): Maren de Vries, Adil Mohamed, Rachel A Prescott, Ana M. Valero-Jimenez, Ludovic Desvignes, Rebecca E. O’Connor, Claire M. Steppan, Joseph C. Devlin, Ellie Ivanova, Alberto Herrera, Austin Schinlever, Paige Loose, Kelly V. Ruggles, Sergei B. Koralov, Annaliesa S. Anderson, Joseph Binder, Meike Dittmann
Software Mentions: 2
Published: over 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: over 3 years ago

10.7554/eLife.66192

Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation
Cited by: 25
Author(s): Hyeogsun Kwon, Mubasher Mohammed, Oscar Franzén, Johan Ankarklev, Ryan C. Smith
Software Mentions: 2
Published: over 3 years ago

10.1016/j.ajhg.2021.02.015

Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy
Cited by: 11
Author(s): Ambrin Fatima, Jan Hoeber, Jens Schuster, Eriko Koshimizu, Carolina Maya-González, Boris Keren, Cyril Mignot, Talia Akram, Zafar Ali, Satoko Miyatake, Junpei Tanigawa, Takayoshi Koike, Mitsuhiro Kato, Yoshiko Murakami, Uzma Abdullah, Muhammad Ali, Rein Fadoul, Loora Laan, Casimiro Castillejo-López, Maarika Liik, Zhe Jin, Bryndis Birnir, Naomichi Matsumoto, Shahid Mahmood Baig, Joakim Klar, Niklas Dahl
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.63907

A cell atlas of the chick retina based on single-cell transcriptomics
Cited by: 66
Author(s): Masahito Yamagata, Wenjun Yan, Joshua R. Sanes
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13195-021-00850-3

Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment
Cited by: 89
Author(s): Yadi Zhou, Jielin Xu, Yuan Hou, James B. Leverenz, Asha R. Kallianpur, Reena Mehra, Yunlong Liu, Haiyuan Yu, Andrew A. Pieper, Lara Jehi, Feixiong Cheng
Software Mentions: 2
Published: over 3 years ago

10.1186/s12967-021-02965-5

HLA-dependent heterogeneity and macrophage immunoproteasome activation during lung COVID-19 disease
Cited by: 11
Author(s): Christophe Desterke, Ali G Turhan, Annelise Bennaceur‐Griscelli, Frank Griscelli
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.42940

eIF2B activator prevents neurological defects caused by a chronic integrated stress response
Cited by: 109
Author(s): Yao Liang Wong, Lauren LeBon, Ana M. Basso, Kathy L. Kohlhaas, Arthur L. Nikkel, Holly M. Robb, Diana L. Donnelly‐Roberts, Janani Prakash, Andrew M. Swensen, Nimrod D. Rubinstein, Sadagopan Krishnan, Fiona E. McAllister, Nicole V Haste, Jonathon O’Brien, Margaret Roy, Andrea Ireland, Jennifer M. Frost, Lei Shi, Stephan Riedmaier, Kathleen A. Martin, Michael J. Dart, Carmela Sidrauski
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12967-018-1578-4

PBMC fixation and processing for Chromium single-cell RNA sequencing
Cited by: 95
Author(s): Jinguo Chen, Foo Cheung, Rongye Shi, Huizhi Zhou, Wenrui Lu
Software Mentions: 2
Published: over 6 years ago

10.1186/s13195-019-0524-x

A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain
Cited by: 119
Author(s): Jorge L. Del‐Aguila, Zeran Li, Umber Dube, Kathie A. Mihindukulasuriya, John Budde, María Victoria Fernández, Laura Ibáñez, Joseph Bradley, Fengxian Wang, Kristy Bergmann, Richard Davenport, John C. Morris, David M. Holtzman, Richard J. Perrin, Bruno A. Benítez, Joseph D. Dougherty, Carlos Cruchaga, Oscar Harari
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.62586

Single-cell RNA-seq reveals transcriptomic heterogeneity mediated by host–pathogen dynamics in lymphoblastoid cell lines
Cited by: 26
Author(s): Elliott D. SoRelle, Joanne Dai, Emmanuela N Bonglack, Emma M Heckenberg, Jeffrey Y. Zhou, Stephanie N Giamberardino, Jeffrey A. Bailey, Simon Gregory, Cliburn Chan, Micah A. Luftig
Software Mentions: 2
Published: almost 4 years ago

10.1111/acel.13168

Individual variation of the SARS‐CoV‐2 receptor ACE2 gene expression and regulation
Cited by: 316
Author(s): Jiawei Chen, Quanlong Jiang, Xian Xia, Kangping Liu, Zhiping Yu, Wanyu Tao, W. X. Gong, Jing‐Dong J. Han
Software Mentions: 2
Published: over 4 years ago

10.18632/aging.104015

Single-cell expression profiles of ACE2 and TMPRSS2 reveals potential vertical transmission and fetus infection of SARS-CoV-2
Cited by: 23
Author(s): Mengdie Lü, Li Qiu, Guangshuai Jia, Rong Guo, Qibin Leng
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.61276

Single-cell transcriptomics of the Drosophila wing disc reveals instructive epithelium-to-myoblast interactions
Cited by: 36
Author(s): Nicholas J. Everetts, Melanie I. Worley, Riku Yasutomi, Nir Yosef, Iswar K. Hariharan
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.46349

Single-cell sequencing of neonatal uterus reveals an Misr2+ endometrial progenitor indispensable for fertility
Cited by: 32
Author(s): Hatice D. Saatcioglu, Mariko Kano, Heiko Horn, Lihua Zhang, Wesley Samore, Nicholas Nagykery, Marie Charlotte Meinsohn, Minsuk Hyun, Rana Suliman, Joy Poulo, Jennifer Y.J. Hsu, Caitlin R. Sacha, Dan Wang, Guangping Gao, Kasper Lage, Esther Oliva, Mary E. Sabatini, Patricia K. Donahoe, David Pépin
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.53072

Defining the role of pulmonary endothelial cell heterogeneity in the response to acute lung injury
Cited by: 128
Author(s): Terren K. Niethamer, Collin T. Stabler, John P. Leach, Jarod A. Zepp, Michael Morley, Apoorva Babu, Shanshan Zhou, Edward E Morrisey
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.56450

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks
Cited by: 13
Author(s): Kelsey H. Elliott, Marc E. Rothenberg, Joseph Salomone, Praneet Chaturvedi, Preston A Schultz, Sai Keshavan Balchand, Jeffrey D Servetas, Aimée Zúñiga, Rolf Zeller, Brian Gebelein, Matthew T. Weirauch, Kevin A. Peterson, Samantha A. Brugmann
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.57779

Bimodal function of chromatin remodeler Hmga1 in neural crest induction and Wnt-dependent emigration
Cited by: 17
Author(s): Shashank Gandhi, Erica J. Hutchins, Krystyna Maruszko, Jong H Park, Matt Thomson, Marianne E. Bronner
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.59465

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors
Cited by: 58
Author(s): Laura Crowley, Francesco Cambuli, Luis Aparicio, Maho Shibata, Brian D. Robinson, Shouhong Xuan, Weiping Li, Hanina Hibshoosh, Massimo Loda, Raúl Rabadán, Michael M. Shen
Software Mentions: 2
Published: about 4 years ago

10.7554/eLife.64906

In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system
Cited by: 15
Author(s): Lori Glenwinkel, Seth R. Taylor, Kasper Langebeck-Jensen, Leonel Pereira, Molly Reilly, Manasa Basavaraju, Ibnul Rafi, Eviatar Yemini, Roger Pocock, Nenad Šestan, Marc Hammarlund, David M. Miller, Oliver Hobert
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.20487

Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states
Cited by: 40
Author(s): Sumin Jang, Sandeep Choubey, Leon Furchtgott, Ling Nan Zou, Adele M. Doyle, Vilas Menon, Ethan Loew, Anne Rachel Krostag, Refugio A. Martinez, Linda Madisen, Boaz P. Levi, Sharad Ramanathan
Software Mentions: 2
Published: over 7 years ago

10.18632/aging.203406

Autophagic flux in cancer cells at the invasive front in the tumor-stroma border
Cited by: 6
Author(s): Fei Yan, Xuexi Zhang, Rongying Tan, Mingchen Li, Zengtuan Xiao, Hao Wang, Zhenfa Zhang, Zhenyi Ma, Liu Zhe
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.55523

A single-cell transcriptomic and anatomic atlas of mouse dorsal raphe Pet1 neurons
Cited by: 66
Author(s): Benjamin W. Okaty, Nikita Sturrock, Yasmin Escobedo Lozoya, YoonJeung Chang, Rebecca A. Senft, Krissy A Lyon, Olga V. Alekseyenko, Susan M. Dymecki
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.67776

Single-cell transcriptome analysis defines heterogeneity of the murine pancreatic ductal tree
Cited by: 20
Author(s): Audrey M. Hendley, Rao Av, Laura Leonhardt, Sudipta Ashe, Jennifer A. Smith, Simone Giacometti, Xianlu L. Peng, Honglin Jiang, David I. Berrios, Mathias Pawlak, Lucia Y Li, Jonghyun Lee, Eric A. Collisson, Mark S. Anderson, Gabriela K. Fragiadakis, Jen Jen Yeh, Chun Jimmie Ye, Grace Kim, Valerie M. Weaver, Matthias Hebrok
Software Mentions: 2
Published: over 3 years ago

10.1038/s41421-021-00280-3

Single-cell transcriptome and TCR profiling reveal activated and expanded T cell populations in Parkinson’s disease
Cited by: 36
Author(s): Pingping Wang, Lifen Yao, Meng Luo, Wenyang Zhou, Xiyun Jin, Zhaochun Xu, Yan Shi, Yiqun Li, Chang Xu, Rui Cheng, Yan Huang, Xiaoyu Lin, Kexin Ma, Huimin Cao, Hongxin Liu, Guangfu Xue, Fangfang Han, Huan Nie, Qinghua Jiang
Software Mentions: 2
Published: over 3 years ago

10.1038/s41421-020-0168-9

Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing
Cited by: 559
Author(s): Wen Wen, Wenru Su, Hao Tang, Wenqing Le, Xiaopeng Zhang, Yingfeng Zheng, Xiuxing Liu, Lihui Xie, Jianmin Li, Jinguo Ye, Liwei Dong, Xiuliang Cui, Yushan Miao, Depeng Wang, Jie Dong, Chuan-Le Xiao, Wei Chen, Hongyang Wang
Software Mentions: 2
Published: over 4 years ago

10.1038/s41421-019-0114-x

A novel approach to remove the batch effect of single-cell data
Cited by: 31
Author(s): Feng Zhang, Yu Wu, Weidong Tian
Software Mentions: 2
Published: about 5 years ago

10.1016/j.cmet.2019.07.013

Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake
Cited by: 151
Author(s): Alice E. Adriaenssens, Emma K. Biggs, Tamana Darwish, John Tadross, Tanmay Sukthankar, Milind Girish, Joseph Polex-Wolf, Brain Y Lam, Ilona Zvetkova, Warren Pan, Davide Chiarugi, Giles S.H. Yeo, Clémence Blouet, Fiona M. Gribble, Frank Reimann
Software Mentions: 2
Published: about 5 years ago

10.1038/s41423-020-00599-z

Efficient IL-2R signaling differentially affects the stability, function, and composition of the regulatory T-cell pool
Cited by: 18
Author(s): Marc Permanyer, Berislav Bošnjak, Silke Glage, Michaela Friedrichsen, Stefan Floess, Jochen Huehn, Gwendolyn E. Patzer, Ivan Odak, Nadine Eckert, Razieh Zargari, Laura Ospina-Quintero, Hristo Georgiev, Reinhold Förster
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41421-019-0104-z

STK11 is required for the normal program of ciliated cell differentiation in airways
Cited by: 14
Author(s): Qiqi Chu, Changfu Yao, Xiangbing Qi, Barry R. Stripp, Nan Tang
Software Mentions: 2
Published: over 5 years ago

10.1186/s13619-020-00041-9

Comparison of Scanpy-based algorithms to remove the batch effect from single-cell RNA-seq data
Cited by: 4
Author(s): Jiaqi Li, Chengxuan Yu, Lifeng Ma, Jingjing Wang, Guoji Guo
Software Mentions: 2
Published: over 4 years ago

10.1016/j.celrep.2021.109542

Gli1+ progenitors mediate bone anabolic function of teriparatide via Hh and Igf signaling
Cited by: 12
Author(s): Yu Shi, Xueyang Liao, James Y. Long, Lutian Yao, Jianquan Chen, Bin Yin, Feng Lou, Guangxu He, Ling Ye, Ling Qin, Fanxin Long
Software Mentions: 2
Published: over 3 years ago

10.1038/s41421-021-00316-8

Generation of human blastocyst-like structures from pluripotent stem cells
Cited by: 65
Author(s): Yong Fan, Zheying Min, Samhan M. Alsolami, Zheng-lai Ma, E. Zhang, Wei Chen, Ke Zhong, Wendi Pei, Xiangjin Kang, Pu-Yao Zhang, Yongliang Wang, Yingying Zhang, Linfeng Zhan, Haiying Zhu, Chenrui An, Rong Li, Jie Qiao, Tao Tan, Mo Li, Yang Yu
Software Mentions: 2
Published: about 3 years ago

10.1016/j.celrep.2020.108093

Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells
Cited by: 47
Author(s): Jiyung Shin, Markus Schröder, Francisco Caiado, Stacia K. Wyman, Nicolas Bray, Matteo Bordi, Mark Dewitt, Jonathan T. Vu, Won‐Tae Kim, Dirk Hockemeyer, Markus G. Manz, Jacob E. Corn
Software Mentions: 2
Published: about 4 years ago

10.1016/j.xcrm.2021.100381

Dual targeting of lymphocyte homing and retention through α4β7 and αEβ7 inhibition in inflammatory bowel disease
Cited by: 20
Author(s): Bingbing Dai, Jason A. Hackney, Ryan Ichikawa, Allen Nguyen, Justin Elstrott, Luz D. Orozco, Kan Sun, Zora Modrušan, Alvin Gogineni, Alexis Scherl, John Gubatan, Aida Habtezion, Monika Deswal, Ma Somsouk, William A. Faubion, Akiko Chai, Zaineb Sharafali, Azra Hassanali, Young S. Oh, Swati Tole, Jacqueline McBride, Mary E. Keir, Tangsheng Yi
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.57571

Activity-dependent tuning of intrinsic excitability in mouse and human neurogliaform cells
Cited by: 26
Author(s): Ramesh Chittajallu, Kurt Auville, Vivek Mahadevan, Mandy Lai, Steven Hunt, Daniela Calvigioni, Kenneth A. Pelkey, Kareem A. Zaghloul, Chris J McBain
Software Mentions: 2
Published: over 4 years ago

10.1038/s41422-020-0354-1

Immunity-and-matrix-regulatory cells derived from human embryonic stem cells safely and effectively treat mouse lung injury and fibrosis
Cited by: 49
Author(s): Jun Wu, Dingyun Song, Zhongwen Li, Baojie Guo, Yani Xiao, Wenjing Liu, Liping Liang, Chunjing Feng, Tingting Gao, Yanxia Chen, Ying Li, Zai Wang, Jianyan Wen, Shengnan Yang, Peipei Li, Lei Wang, Yukai Wang, Liang Peng, Glyn Stacey, Zheng Hu, Guihai Feng, Wei Li, Yan Huo, Ronghua Jin, Ng Shyh‐Chang, Qi Zhou, Liu Wang, Baoyang Hu, Huaping Dai, Jie Hao
Software Mentions: 2
Published: over 4 years ago

10.1038/s41422-021-00523-8

A cohort autopsy study defines COVID-19 systemic pathogenesis
Cited by: 83
Author(s): Yao Xiao, Tao Luo, Shaojun Yu, Zhi Cheng He, Rui Tang, Pei Pei Zhang, Jun Cai, Xiang Zhou, Dong Jiang, Xiao Chun Fei, Xue Quan Huang, Lei Zhao, Heng Zhang, Hai Wu, Yong Ren, Zhen Hua Liu, Hua Rong Zhang, Cong Chen, Wen Fu, Heng Li, Xinyu Xia, Rong Chen, Yan Wang, Xin Dong Liu, Chang Lin Yin, Ze Xuan Yan, Juan Wang, Rui Jiang, Tai Sheng Li, Wei Qin Li, Chao‐Fu Wang, Yan Ding, Qing Mao, Ding Yu Zhang, Shuyang Zhang, Yi Ping, Xiu Wu Bian
Software Mentions: 2
Published: over 3 years ago

10.1038/s41419-021-03795-5

p63 suppresses the ability of pregnancy-identified mammary epithelial cells (PIMECs) to drive HER2-positive breast cancer
Cited by: 4
Author(s): Christopher Eyermann, Jinyu Li, Evguenia M. Alexandrova
Software Mentions: 2
Published: over 3 years ago

10.1038/s41422-021-00514-9

Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines
Cited by: 109
Author(s): Yunlong Cao, Ayijiang Yisimayi, Yali Bai, Weijin Huang, Xiaofeng Li, Zhiying Zhang, Tianjiao Yuan, Ran An, Jing Wang, Tianhe Xiao, Shuo Du, Wenping Ma, Liyang Song, Yongzheng Li, Xiang Li, Weiliang Song, Jiajing Wu, Shuo Liu, Xuemei Li, Yonghong Zhang, Bin Su, Xuesong Guo, Yu‐Sheng Wei, Chuanping Gao, Nana Zhang, Yifei Zhang, Yang Dou, Xiaoyu Xu, Rui Shi, Lan Bai, Ronghua Jin, Yingmin Ma, Cheng‐Feng Qin, Youchun Wang, Yingmei Feng, Junyu Xiao, X. Sunney Xie
Software Mentions: 2
Published: over 3 years ago

10.1016/j.stem.2019.12.005

The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty
Cited by: 144
Author(s): Jingtao Guo, Xiaolu Nie, Maria Giebler, Hana Mlčochová, Yueqi Wang, Edward J. Grow, Robin Kim, Melissa D. Tharmalingam, Gabriele Matilionyte, Cecilia Lindskog, Douglas T. Carrell, Rod T. Mitchell, Anne Goriely, James M. Hotaling, Bradley R. Cairns
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.stem.2021.01.003

Coordinated changes in cellular behavior ensure the lifelong maintenance of the hippocampal stem cell population
Cited by: 92
Author(s): Lachlan Harris, Piero Rigo, Thomas Stiehl, Zachary B. Gaber, Sophie H. L. Austin, M. Masdeu, A. Edwards, Noelia Urbán, Anna Marciniak–Czochra, François Guillemot
Software Mentions: 2
Published: over 3 years ago

10.1016/j.stem.2020.10.001

SARS-CoV-2 Infects the Brain Choroid Plexus and Disrupts the Blood-CSF Barrier in Human Brain Organoids
Cited by: 352
Author(s): Laura Pellegrini, Anna Albecka, Donna L. Mallery, Max J. Kellner, David Paul, Andrew P. Carter, Leo C. James, Madeline A. Lancaster
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.stem.2021.03.022

Commitment and oncogene-induced plasticity of human stem cell-derived pancreatic acinar and ductal organoids
Cited by: 51
Author(s): Ling Huang, Ridhdhi Desai, Daniel N. Conrad, Nayara C. Leite, Dipikaa Akshinthala, Christine Lim, Raúl González, Lakshmi Muthuswamy, Zev J. Gartner, Senthil K. Muthuswamy
Software Mentions: 2
Published: over 3 years ago

10.1016/j.stem.2021.02.025

Human naive epiblast cells possess unrestricted lineage potential
Cited by: 172
Author(s): Ge Guo, Giuliano Giuseppe Stirparo, Stanley E. Strawbridge, Daniel Spindlow, Jian Yang, James Clarke, Anish Dattani, Akira Yanagida, Meng Amy Li, Sam Myers, Buse Nurten Özel, Jennifer Nichols, Austin Smith
Software Mentions: 2
Published: over 3 years ago

10.1007/s00441-020-03249-y

Single-cell transcriptomics reveals multiple neuronal cell types in human midbrain-specific organoids
Cited by: 27
Author(s): Lisa M. Smits, Stefano Magni, Kaoru Kinugawa, Kamil Grzyb, Joachim Luginbühl, Sònia Sabaté-Soler, Silvia Bolognin, Jay W. Shin, Eiichiro Mori, Alexander Skupin, Jens Christian Schwamborn
Software Mentions: 2
Published: over 4 years ago

10.3390/cells8050503

Single Cell RNA Sequencing Identifies Subsets of Hepatic Stellate Cells and Myofibroblasts in Liver Fibrosis
Cited by: 138
Author(s): Oliver Krenkel, Jana Hundertmark, Thomas Ritz, Ralf Weiskirchen, Frank Tacke
Software Mentions: 2
Published: over 5 years ago

10.3390/cells10020241

Spermatogonia Loss Correlates with LAMA 1 Expression in Human Prepubertal Testes Stored for Fertility Preservation
Cited by: 13
Author(s): Magdalena Kurek, Elisabet Åkesson, Masahito Yoshihara, Elizabeth Oliver, Yanhua Cui, Martin Becker, João Pedro Alves-Lopes, Ragnar Bjarnason, Patrik Romerius, Mikael Sundin, Ulrika Norén Nyström, Cecilia Langenskiöld, Hartmut Vogt, Lars Henningsohn, Cecilia Petersen, Olle Söder, Jingtao Guo, Rod T Mitchell, Kirsi Jahnukainen, Jan-Bernd Stukenborg
Software Mentions: 2
Published: almost 4 years ago

10.3390/cells10082129

Heterogeneity of Hepatic Stellate Cells in Fibrogenesis of the Liver: Insights from Single-Cell Transcriptomic Analysis in Liver Injury
Cited by: 16
Author(s): Wenjun Zhang, Simon J. Conway, Ying Liu, Paige Snider, Hanying Chen, Hongyu Gao, Yunlong Liu, Kadir Isidan, Kevin Lopez, Gonzalo Campaña, Ping Li, Burçin Ekser, Heather Francis, Weinian Shou, Chandrashekhar A. Kubal
Software Mentions: 2
Published: over 3 years ago

10.3390/cells9041045

Association Analysis of Single-Cell RNA Sequencing and Proteomics Reveals a Vital Role of Ca2+ Signaling in the Determination of Skeletal Muscle Development Potential
Cited by: 11
Author(s): Kai Qiu, Dianna Xu, Liqi Wang, Xin Zhang, Ning Jiao, Lu Gong, Jingdong Yin
Software Mentions: 2
Published: over 4 years ago

10.1186/s13578-021-00637-x

Single-cell transcriptomic analysis of endometriosis provides insights into fibroblast fates and immune cell heterogeneity
Cited by: 33
Author(s): Junyan Ma, Liqi Zhang, Hong Zhan, Yufei Mo, Zuanjie Ren, Anwen Shao, Jizhen Lin
Software Mentions: 2
Published: over 3 years ago

10.7554/eLife.65615

CD8+ T cell self-tolerance permits responsiveness but limits tissue damage
Cited by: 5
Author(s): Emily Nestor Truckenbrod, Kristina S. Burrack, Todd P. Knutson, Henrique Borges da Silva, Katharine E. Block, Stephen O’Flanagan, Katie R Stagliano, Arthur A. Hurwitz, Ross B. Fulton, Kristin R. Renkema, Stephen C. Jameson
Software Mentions: 2
Published: over 3 years ago

10.3390/cells9122646

Glycosaminoglycan Modification of Decorin Depends on MMP14 Activity and Regulates Collagen Assembly
Cited by: 10
Author(s): Alexes C. Daquinag, Zhan‐Guo Gao, Cale Fussell, Kai Sun, Mikhail G. Kolonin
Software Mentions: 2
Published: almost 4 years ago

10.1002/advs.202001019

Biphasic Regulation of Mesenchymal Genes Controls Fate Switches During Hematopoietic Differentiation of Human Pluripotent Stem Cells
Cited by: 6
Author(s): Hongtao Wang, Mengge Wang, Yao Wen, Changlu Xu, Xiaoyuan Chen, Dan Wu, Pei Su, Wen Zhou, Tao Cheng, Lihong Shi, Jiaxi Zhou
Software Mentions: 1
Published: over 4 years ago

10.1186/s40478-020-01103-4

Human cutaneous neurofibroma matrisome revealed by single-cell RNA sequencing
Cited by: 29
Author(s): Jean Philippe Brosseau, Adwait Amod Sathe, Yong Wang, Toan Bao Nguyen, Donald A. Glass, Chao Xing, Lu Q. Le
Software Mentions: 1
Published: almost 4 years ago

10.3389/fonc.2021.656564

A Cancer Cell Cluster Marked by LincRNA MEG3 Leads Pancreatic Ductal Adenocarcinoma Metastasis
Cited by: 13
Author(s): Hong Pan, Diao Huan-rong, Wen Zhong, Taifang Wang, Ping Wen, Chunli Wu
Software Mentions: 1
Published: over 3 years ago

10.3389/fonc.2021.639947

Patients With Short PFS to EGFR-TKIs Predicted Better Response to Subsequent Anti-PD-1/PD-L1 Based Immunotherapy in EGFR Common Mutation NSCLC
Cited by: 20
Author(s): Sangtian Liu, Fengying Wu, Xuefei Li, Chao Zhao, Yijun Jia, Keyi Jia, Ruoshuang Han, Meng Qiao, Wei Li, Jia Yu, Fei Zhou, Anwen Xiong, Bin Chen, Jue Fan, Shengxiang Ren
Software Mentions: 1
Published: over 3 years ago

10.1186/s12885-021-07865-x

Involvement of mutant and wild-type CYSLTR2 in the development and progression of uveal nevi and melanoma
Cited by: 13
Author(s): Rogier J. Nell, Nino Valentijn Menger, Mieke Versluis, Gregorius P M Luyten, Robert M. Verdijk, Michele C. Madigan, Martine J. Jager, Pieter A. van der Velden
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41385-020-0273-y

IL-17 production by tissue-resident MAIT cells is locally induced in children with pneumonia
Cited by: 53
Author(s): Bingtai Lu, Ming Liu, Jun Wang, Huifeng Fan, Diyuan Yang, Li Zhang, Xiaoqiong Gu, Junli Nie, Zhenjun Chen, Alexandra J. Corbett, Michael J Zhan, Shengbo Zhang, Vanessa L. Bryant, Andrew M. Lew, James McCluskey, Hai‐Bin Luo, Jun Cui, Yuxia Zhang, Yifan Zhan, Gen Liu
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-021-92521-4

Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals
Cited by: 26
Author(s): Swapnil Mahajan, Vasumathi Kode, Keshav Bhojak, Karunakaran Coral, Kayla Lee, Malini Manoharan, Athulya Ramesh, Sudheendra Hv, Ankita Srivastava, Rekha Sathian, Tahira Khan, Prasanna Kumar, Ravi Gupta, Papia Chakraborty, Amitabha Chaudhuri
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-93330-5

Cellular basis of omentum activation and expansion revealed by single-cell RNA sequencing using a parabiosis model
Cited by: 3
Author(s): Kazuhiko Ishigaki, Keiki Kumano, Kyohei Fujita, Hikaru Ueno
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-93743-2

Discovery of potential imaging and therapeutic targets for severe inflammation in COVID-19 patients
Cited by: 7
Author(s): Hyun-Jong Lee, Jeongbin Park, Hyung Jun Im, Kwon Joong Na, Hongyoon Choi
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-94588-5

Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99
Cited by: 17
Author(s): Jonas Mattisson, Marcus Danielsson, Maria Hammond, Hanna Davies, Caroline J. Gallant, Jessica Nordlund, Amanda Raine, Malin Edén, Lena Kilander, Martin Ingelsson, Jan P. Dumanski, Jonatan Halvardson, Lars A. Forsberg
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-95041-3

In vitro monitoring of HTR2A-positive neurons derived from human-induced pluripotent stem cells
Cited by: 2
Author(s): Kento Nakai, Tohru Shiga, Rika Yasuhara, Avijite Kumer Sarkar, Yuka Abe, Sumiko Nakamura, Yurie Hoashi, Koichi Kotani, Shoji Tatsumoto, Hiromasa Ishikawa, Yasuhiro Go, Tomio Inoue, Kenji Mishima, Wado Akamatsu, Kazuyoshi Baba
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-94816-y

Glutamic acid promotes hair growth in mice
Cited by: 11
Author(s): Carlos Poblete Jara, Beatriz de Andrade Berti, Nelson F. Mendes, Daiane F. Engel, Ariane Maria Zanesco, Gabriela Freitas Pereira de Souza, Renan de Medeiros Bezerra, Júlia de Toledo Bagatin, Silvya Stuchi Maria-Engler, Joseane Morari, William H. Velander, Lı́cio A. Velloso, Eliana P. Araújo
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-95215-z

Transcriptome profile of goat folliculogenesis reveals the interaction of oocyte and granulosa cell in correlation with different fertility population
Cited by: 2
Author(s): Li Shen, Jun-Jie Wang, Hongfu Zhang, Dongxue Ma, Minghui Zhao, Na Li, Yuhao Men, Yuan Zhang, Huimin Chu, Chuzhao Lei, Wei Shen, Othman El-Mahdy Othman, Yong Zhao, Min Liu
Software Mentions: 1
Published: over 3 years ago

10.3389/fonc.2021.694331

Intratumor Heterogeneity of MIF Expression Correlates With Extramedullary Involvement of Multiple Myeloma
Cited by: 2
Author(s): Jianguo Xu, Nanhui Yu, Pan Zhao, Fangfang Wang, Jingcao Huang, Yushan Cui, Hong Ding, Yiqin Yang, Yuhan Gao, Ling Pan, Hong Chang, Yuzhang Wu, Bing Xiang, Yuping Gong, Shuai Xiao, Li Hou, Liping Xie, Ting Niu, Ting Liu, Li Zhang, Weiping Liu, Wenyan Zhang, Ying Qu, Wei Lin, Yimin Zhu, Sha Zhao, Yuhuan Zheng
Software Mentions: 1
Published: over 3 years ago

10.1038/s41385-019-0248-z

Single-cell RNA sequencing analysis reveals alginate oligosaccharides preventing chemotherapy-induced mucositis
Cited by: 34
Author(s): Yong Zhao, Yanni Feng, Ming Liu, Liang Chen, Qingshi Meng, Xiangfang Tang, Shukun Wang, Lei Liu, Lan Li, Wei Shen, Hongfu Zhang
Software Mentions: 1
Published: over 4 years ago

10.1016/j.stem.2020.02.008

Plasticity of Lgr5-Negative Cancer Cells Drives Metastasis in Colorectal Cancer
Cited by: 154
Author(s): Arianna Fumagalli, Koen C. Oost, Lennart Kester, Jessica Morgner, Laura Bornes, Lotte Bruens, Lisa Spaargaren, Maria Azkanaz, Tim Schelfhorst, Evelyne Beerling, Maria C. Heinz, Daniel Postrach, Daniëlle Seinstra, Anieta M. Sieuwerts, John W.M. Martens, Stefan van der Elst, Martijn v. Baalen, Debashis Bhowmick, Nienke Vrisekoop, Saskia I.J. Ellenbroek, Saskia J.E. Suijkerbuijk, Hugo J.G. Snippert, Jacco van Rheenen
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-021-94933-8

Molecular characteristics and spatial distribution of adult human corneal cell subtypes
Cited by: 25
Author(s): Ann J. Ligocki, Wen Fury, Christian Gutierrez, Christina Adler, Tao Yang, Min Ni, Yu Bai, Yi Wei, Guillermo L. Lehmann, Carmelo Romano
Software Mentions: 1
Published: over 3 years ago

10.3390/vaccines9040340

A Whole Virion Vaccine for COVID-19 Produced via a Novel Inactivation Method and Preliminary Demonstration of Efficacy in an Animal Challenge Model
Cited by: 13
Author(s): Izabela Ragan, Lindsay Hartson, Taru Dutt, Andrés Obregón-Henao, Rachel M. Maison, Paul Gordy, Amy Fox, Burton Karger, Shaun T. Cross, Marylee Kapuscinski, Sarah K. Cooper, Brendan K. Podell, Mark D. Stenglein, Richard A. Bowen, Marcela Henao-Tamayo, Raymond P. Goodrich
Software Mentions: 1
Published: over 3 years ago

10.3389/fonc.2021.659251

Single-Cell RNA-seq Identification of the Cellular Molecular Characteristics of Sporadic Bilateral Clear Cell Renal Cell Carcinoma
Cited by: 9
Author(s): Zhenyuan Yu, Wenhao Lu, Cheng Su, Yufang Lv, Yu Ye, Bingqian Guo, Deyun Liu, Haibiao Yan, Hua Mi, Tianyu Li, Qingyun Zhang, Jian Cheng, Zengnan Mo
Software Mentions: 1
Published: over 3 years ago

10.1016/j.cell.2017.11.036

Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
Cited by: 124
Author(s): Mauro Gaya, Patricia Barral, Marianne Burbage, Shweta Aggarwal, Beatriz Montaner, Andrew W. Navia, Malika Aïd, C. Kimberly Tsui, Paula Maldonado, Usha Nair, Khader Ghneim, Padraic G. Fallon, Rafick‐Pierre Sékaly, Dan H. Barouch, Alex K. Shalek, Andreas Bruckbauer, Jessica Strid, Facundo D. Batista
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41419-019-1995-1

CD24: a marker of granulosa cell subpopulation and a mediator of ovulation
Cited by: 18
Author(s): Jun-peng Dong, Zhihui Dai, Zucheng Jiang, Yi He, Liang Wang, Qiu-ying Liao, Ning Sun, Yining Wang, Shuhan Sun, Wei Lin, Wen Li, Fusheng Yang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-021-98267-3

Integration and gene co-expression network analysis of scRNA-seq transcriptomes reveal heterogeneity and key functional genes in human spermatogenesis
Cited by: 9
Author(s): Najmeh Salehi, Mohammad Hossein Karimi‐Jafari, Mehdi Totonchi, Amir Amiri-Yekta
Software Mentions: 1
Published: about 3 years ago

Projects: cran: Seurat

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