pypi: Harmony | 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: over 5 years ago

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
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

10.1038/s41422-020-00453-x

Establishment of intestinal organoid cultures modeling injury-associated epithelial regeneration
Cited by: 39
Author(s): Molong Qu, Liang Xiong, Yulin Lyu, Xiannian Zhang, Jie Shen, Jingyang Guan, Peiyuan Chai, Lin Zheng, Boyao Nie, Cheng Li, Jun Xu, Hongkui Deng
Software Mentions: 13
Published: almost 4 years ago

10.3389/fgene.2021.655536

Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges
Cited by: 30
Author(s): Jiajia Li, Zusen Fan, Weiling Zhao, Xiaobo Zhou
Software Mentions: 12
Published: over 3 years ago

10.1186/s13059-021-02480-2

Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction
Cited by: 16
Author(s): Wenjing Ma, Kenong Su, Hao Wu
Software Mentions: 12
Published: about 3 years ago

10.3390/cancers13122903

Integrative Transcriptomic Analysis Reveals Distinctive Molecular Traits and Novel Subtypes of Collecting Duct Carcinoma
Cited by: 6
Author(s): Chiara Gargiuli, Pierangela Sepe, Anna Tessari, Tyler Sheetz, Maurizio Colecchia, F.G.M. De Braud, Giuseppe Procopio, Marialuisa Sensi, Elena Verzoni, Matteo Dugo
Software Mentions: 11
Published: over 3 years ago

10.1093/bioinformatics/btaa201

Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
Cited by: 37
Author(s): Meenakshi Venkatasubramanian, Kashish Chetal, Daniel Schnell, Gowtham Atluri, Nathan Salomonis
Software Mentions: 10
Published: over 4 years ago

10.1038/s41422-020-00451-z

Sequential fate-switches in stem-like cells drive the tumorigenic trajectory from human neural stem cells to malignant glioma
Cited by: 38
Author(s): Xiaofei Wang, Ran Zhou, Yanzhen Xiong, Lingling Zhou, Xiang Yan, Manli Wang, Li Fan, Chuanxing Xie, Yiming Zhang, Zongyao Huang, Chaoqiong Ding, Ke Shi, Weida Li, Liu Yu, Cao Zeyi, Zhenning Zhang, Shengtao Zhou, Chong Chen, Yan Zhang, Lu Chen, Yuan Wang
Software Mentions: 10
Published: almost 4 years ago

10.3389/fonc.2020.00973

Impact of Data Preprocessing on Integrative Matrix Factorization of Single Cell Data
Cited by: 8
Author(s): Lauren Hsu, Aedín C. Culhane
Software Mentions: 10
Published: over 4 years ago

10.20900/immunometab20210022

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models
Cited by: 21
Author(s): Austin C. Conklin, Hitoo Nishi, Florencia Schlamp, Tiit Örd, Kadri Õunap, Minna U. Kaikkonen, Edward A. Fisher, Casey E. Romanoski
Software Mentions: 9
Published: over 3 years ago

10.3390/biomedicines9040368

Single-Cell RNA Sequencing in Parkinson’s Disease
Cited by: 13
Author(s): Shi-Xun Ma, Su Bin Lim
Software Mentions: 9
Published: over 3 years ago

10.3389/fonc.2021.709210

Single-Cell Transcriptomics Reveals the Complexity of the Tumor Microenvironment of Treatment-Naive Osteosarcoma
Cited by: 45
Author(s): Yun Liu, Wei Feng, Yan Dai, Mengying Bao, Zhenchao Yuan, Mingwei He, Zhaojie Qin, Shijie Liao, Jun He, Qian Huang, Zhenyuan Yu, Yanyu Zeng, Binqian Guo, Rong Huang, Rongliang Yang, Yonghua Jiang, Jinling Liao, Zengming Xiao, Xinli Zhan, Chengsen Lin, Jiake Xu, Yu Ye, Jie Ma, Qingjun Wei, Zengnan Mo
Software Mentions: 9
Published: over 3 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: over 4 years ago

10.1186/s13059-020-02008-0

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Cited by: 24
Author(s): Wenbao Yu, Yasin Uzun, Qin Zhu, Changya Chen, Kai Tan
Software Mentions: 9
Published: over 4 years ago

10.1016/j.molcel.2018.11.006

Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains
Cited by: 117
Author(s): Jean-Philippe Lambert, S. Picaud, Takao Fujisawa, Huayun Hou, P. Savitsky, Liis Uusküla-Reimand, Gagan D. Gupta, Hala Abdouni, Zhen‐Yuan Lin, Monika Tucholska, James D.R. Knight, Beatriz Gonzalez-Badillo, Nicole St‐Denis, Joseph A. Newman, Manuel Stucki, Laurence Pelletier, Nuno Bandeira, Michael D. Wilson, P. Filippakopoulos, Anne‐Claude Gingras
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41598-020-71315-0

Characterisation of the novel spontaneously immortalized and invasively growing human skin keratinocyte line HaSKpw
Cited by: 8
Author(s): Elizabeth Pavez Loriè, Nicola Stricker, Beata Patrycja Plitta-Michalak, I-Peng Chen, Beate Volkmer, Rüdiger Greinert, Anna Jauch, Petra Boukamp, Alexander Rapp
Software Mentions: 9
Published: about 4 years ago

10.1186/s13046-021-01955-1

What are the applications of single-cell RNA sequencing in cancer research: a systematic review
Cited by: 28
Author(s): Lvyuan Li, Fang Xiong, Yumin Wang, Shanshan Zhang, Zhaojian Gong, Xiayu Li, Yi He, Lei Shi, Fuyan Wang, Qianjin Liao, Bo Xiang, Ming Zhou, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng, Wei Xiong, Can Guo
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1008205

Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data
Cited by: 43
Author(s): Tony Tran, Gary D. Bader
Software Mentions: 8
Published: about 4 years ago

10.1084/jem.20210615

Single cell analysis of <i>M. tuberculosis</i> phenotype and macrophage lineages in the infected lung
Cited by: 63
Author(s): Davide Pisu, Lu Huang, Vipin Narang, Monique E. Theriault, Gabrielle Lê-Bury, Bernett Lee, Agnes E Lakudzala, David Mzinza, David V. Mhango, Steven C Mitini-Nkhoma, Kondwani Jambo, Amit Singhal, Henry C. Mwandumba, David G. Russell
Software Mentions: 8
Published: over 3 years ago

10.7554/eLife.54818

A single-cell survey of Drosophila blood
Cited by: 109
Author(s): Sudhir Gopal Tattikota, Bumsik Cho, Yifang Liu, Yanhui Hu, Víctor Barrera, Michael J. Steinbaugh, Sangtae Yoon, Aram Comjean, Fangge Li, Franz Dervis, Ruei-Jiun Hung, Jin Wu Nam, Shannan Ho Sui, Jiwon Shim, Norbert Perrimon
Software Mentions: 8
Published: over 4 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: over 3 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

10.1016/j.ccell.2020.06.004

Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma
Cited by: 86
Author(s): Johannes Gojo, Bernhard Englinger, Li Jiang, Jens Martin Hübner, McKenzie Shaw, Olivia A. Hack, Sibylle Madlener, Dominik Kirchhofer, Ilon Liu, Jason W. Pyrdol, Volker Hovestadt, Emanuele Mazzola, Nathan D. Mathewson, Maria Trissal, Daniela Lötsch, Christian Dorfer, Christine Haberler, Angela Halfmann, Lisa Mayr, Andreas Peyrl, René Geyeregger, Benjamin Schwalm, Monica Mauermann, Kristian W. Pajtler, Till Milde, Marni E. Shore, Jack Geduldig, Kristine Pelton, Thomas Czech, Orr Ashenberg, Kai W. Wucherpfennig, Orit Rozenblatt-Rosen, Sanda Alexandrescu, Keith L. Ligon, Stefan M. Pfister, Aviv Regev, Irene Slavc, Walter Berger, Mario L. Suvà, Marcel Kool, Mariella G. Filbin
Software Mentions: 7
Published: over 4 years ago

10.1038/s42003-021-02440-3

Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activation
Cited by: 7
Author(s): Payal Dhar, Fahmin Basher, Zhe Ji, Lei Huang, Si Qin, Derek A. Wainwright, Jerid W. Robinson, Shaye Hagler, Jing Zhou, Sean Mackay, Jennifer D. Wu
Software Mentions: 7
Published: over 3 years ago

10.1186/s12918-016-0337-5

Quantifying differences in cell line population dynamics using CellPD
Cited by: 22
Author(s): Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond Jonckheere, David B. Agus, Shannon M. Mumenthaler, Paul Macklin
Software Mentions: 7
Published: about 8 years ago

10.21203/rs.3.rs-380803/v1

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19
Cited by: 9
Author(s): Alexandra Tsitsiklis, Beth Shoshana Zha, Ashley Byrne, Catherine DeVoe, Sophia Levan, Elze Rackaityte, Sara Sunshine, Eran Mick, Rajani Ghale, Alejandra Jauregui, Norma Neff, Aartik Sarma, Paula Hayakawa Serpa, Thomas Deiss, Amy Kistler, Sidney Carrillo, K. Mark Ansel, Aleksandra Leligdowicz, S. Christenson, Nicola L. Jones, Benjamin Wu, Spyros Darmanis, Michael A. Matthay, Susan V. Lynch, Joseph L. DeRisi, Carolyn M. Hendrickson, Kirsten N. Kangelaris, Matthew F. Krummel, Prescott G. Woodruff, David J. Erle, O. A. Rosenberg, Carolyn S. Calfee, Charles Langelier
Software Mentions: 7
Published: over 3 years ago

10.1038/s41597-021-00809-x

A multi-center cross-platform single-cell RNA sequencing reference dataset
Cited by: 14
Author(s): Xin Chen, Zujun Yang, Wanqiu Chen, Yongmei Zhao, Andrew Farmer, Bao Tran, Vyacheslav Furtak, Malcolm Moos, Wenming Xiao, Charles Wang
Software Mentions: 7
Published: almost 4 years ago

10.1016/j.gpb.2018.07.007

Deciphering Brain Complexity Using Single-cell Sequencing
Cited by: 50
Author(s): Quanhua Mu, Yiyun Chen, Jiguang Wang
Software Mentions: 7
Published: over 5 years ago

10.1038/s41392-021-00703-3

Differential immune responses in pregnant patients recovered from COVID-19
Cited by: 21
Author(s): Ge Chen, Yiming Zhang, Yaoyao Zhang, Jihui Ai, Bin Yang, Mengge Cui, Qiande Liao, Hanxiao Chen, Hualin Bai, Dashing Shang, Jing Chen, Chaoyang Sun, Haiyi Liu, Fengyuan Liu, Biming Mao, Guoqiang Sun, Lu Chen, Jing-wen Lin, Kezhen Li
Software Mentions: 7
Published: over 3 years ago

10.1016/j.stem.2020.11.015

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Cited by: 152
Author(s): Anna Maria Ranzoni, Andrea Tangherloni, Ivan Berest, Simone G. Riva, Brynelle Myers, Paulina M. Strzelecka, Jiarui Xu, Elisa Panada, Irina Mohorianu, Judith B. Zaugg, Ana Cvejic
Software Mentions: 7
Published: over 3 years ago

10.3389/fimmu.2021.626255

Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell Function
Cited by: 13
Author(s): Adam P. Cribbs, P. Filippakopoulos, Martin Philpott, Graham Wells, Henry Penn, Henrik Oerum, Viia Valge-Archer, Marc Feldmann, U. Oppermann
Software Mentions: 6
Published: over 3 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: almost 4 years ago

10.26508/lsa.202000707

Robust production of uniform human cerebral organoids from pluripotent stem cells
Cited by: 44
Author(s): Adam Sivitilli, Jessica Gosio, Bibaswan Ghoshal, Alesya Evstratova, Daniel Trcka, Parisa Ghiasi, J. Javier Hernández, Jean Martin Beaulieu, Jeffrey L. Wrana, Liliana Attisano
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1009071

CytoPy: An autonomous cytometry analysis framework
Cited by: 8
Author(s): Ross J. Burton, Raya Ahmed, Simone Cuff, Sarah Baker, Andreas Artemiou, Matthias Eberl
Software Mentions: 6
Published: over 3 years ago

10.1016/j.stem.2021.04.031

Naive stem cell blastocyst model captures human embryo lineage segregation
Cited by: 139
Author(s): Akira Yanagida, Daniel Spindlow, Jennifer Nichols, Anish Dattani, Austin Smith, Ge Guo
Software Mentions: 6
Published: over 3 years ago

10.21203/rs.3.rs-362886/v1

Maternal-Fetal Immune Responses in Pregnant Women Infected with SARS-CoV-2
Cited by: 6
Author(s): Valeria Garcia‐Flores, Roberto Romero, Yi Xu, Kevin R. Theis, Marcia Arenas-Hernández, Derek Miller, Azam Peyvandipour, José Galaz, Dustyn Levenson, Gaurav Bhatti, Meyer Gershater, Errile Pusod, David Kracht, Violetta Florova, Yaozhu Leng, Tao Li, Megan Faucett, Robert Para, Chaur‐Dong Hsu, Gary Zhang, Adi L. Tarca, Roger Piqué-Regi, Nardhy Gomez-López
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-020-02147-4

CSS: cluster similarity spectrum integration of single-cell genomics data
Cited by: 29
Author(s): Zhisong He, Agnieska Brazovskaja, Sebastian Ebert, J. Gray Camp, Barbara Treutlein
Software Mentions: 6
Published: about 4 years ago

10.3390/v13071197

Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal
Cited by: 3
Author(s): Suhui Zhao, Athe Tsibris
Software Mentions: 6
Published: over 3 years ago

10.1038/s42003-020-01476-1

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer
Cited by: 58
Author(s): Baijun Dong, Juju Miao, Yanqing Wang, Wenqin Luo, Zhongzhong Ji, Huadong Lai, Man Zhang, Xiaomu Cheng, Jinming Wang, Yuxiang Fang, Helen He Zhu, Chee Wai Chua, Liancheng Fan, Yao Zhu, Jiahua Pan, Jia Wang, Wei Xue, Wei‐Qiang Gao
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.celrep.2021.109362

Nutritional regulation of oligodendrocyte differentiation regulates perineuronal net remodeling in the median eminence
Cited by: 29
Author(s): Sara Kohnke, Sophie Buller, Danaé Nuzzaci, Katherine Ridley, Brian Lam, Helena Pivoňková, Marie A. Bentsen, Kimberly M. Alonge, Chao Zhao, John Tadross, Staffan Holmqvist, Takahiro Shimizu, Hannah A. Hathaway, Hui‐Liang Li, Wendy B. Macklin, Michael W. Schwartz, William D. Richardson, Giles S.H. Yeo, R. J. M. Franklin, Ragnhildur Thóra Káradóttir, David H. Rowitch, Clémence Blouet
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-019-1850-9

A benchmark of batch-effect correction methods for single-cell RNA sequencing data
Cited by: 506
Author(s): Hoa Tran, Kok Siong Ang, Marion Chevrier, Xiaomeng Zhang, Nicole Yee Shin Lee, Michelle Goh, Jinmiao Chen
Software Mentions: 6
Published: almost 5 years ago

10.7554/eLife.61405

Cohesin mutations are synthetic lethal with stimulation of WNT signaling
Cited by: 17
Author(s): Chue Vin Chin, Jisha Antony, Sarada Ketharnathan, Anastasia Labudina, Grégory Gimenez, Kate M Parsons, Jin-Shu He, Amee J. George, Maria Michela Pallotta, Antonio Musio, Antony W. Braithwaite, Parry Guilford, Ross D. Hannan, Julia A. Horsfield
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13287-021-02354-1

Single-cell RNA sequencing of cultured human endometrial CD140b+CD146+ perivascular cells highlights the importance of in vivo microenvironment
Cited by: 11
Author(s): Dandan Cao, Rachel Chan, Ernest Hung Yu Ng, Kristina Gemzell‐Danielsson, William S.B. Yeung
Software Mentions: 6
Published: over 3 years ago

10.1038/s41392-020-00263-y

Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals
Cited by: 127
Author(s): Fan Zhang, Rui Gan, Ziqi Zhen, Xiaoli Hu, Xiang Li, Fengxia Zhou, Ying Liu, Chuangeng Chen, Shuangyu Xie, Bailing Zhang, Xiaoke Wu, Zhiwei Huang
Software Mentions: 6
Published: over 4 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

10.1161/CIRCULATIONAHA.119.039596

Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins
Cited by: 74
Author(s): Sonia Chothani, Sebastian Schäfer, Eleonora Adami, V. Sivakumar, Anissa A. Widjaja, Sarah R. Langley, Jessie Tan, Mao Wang, Nicholas M Quaife, Chee Jian Pua, G. D’Agostino, Shamini Guna Shekeran, Benjamin L. George, Si Ching Lim, Elaine Yiqun Cao, Sebastiaan van Heesch, Franziska Witte, Leanne E. Felkin, Eleni G. Christodoulou, Jinqiao Dong, Susanne Blachut, Giannino Patone, Paul J.R. Barton, Norbert Hübner, Stuart A. Cook, Owen J. L. Rackham
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pbio.3001077

Cell-level metadata are indispensable for documenting single-cell sequencing datasets
Cited by: 5
Author(s): Sidhant Puntambekar, Jay R. Hesselberth, Kent Riemondy, Rui Fu
Software Mentions: 6
Published: over 3 years ago

10.1038/s41421-020-00236-z

Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss
Cited by: 74
Author(s): Chuang Guo, Pengfei Cai, Lina Jin, Qing Sha, Qiaoni Yu, Wen Zhang, Chen Jiang, Qian Liu, Dandan Zong, Kun Li, Jingwen Fang, Fangting Lu, Yanshi Wang, Daojing Li, Jun Lin, Lü Li, Zhutian Zeng, Xianhong Tong, Haiming Wei, Kun Qu
Software Mentions: 5
Published: almost 4 years ago

10.1172/jci.insight.142501

Surfactant protein C mutation links postnatal type 2 cell dysfunction to adult disease
Cited by: 10
Author(s): Sneha Sitaraman, Emily P. Martin, Cheng-Lun Na, Shuyang Zhao, Jenna Green, Hitesh Deshmukh, Anne‐Karina T. Perl, James P. Bridges, Yan Xu, Timothy E. Weaver
Software Mentions: 5
Published: over 3 years ago

10.15252/embr.202050932

Foxm1 regulates neural progenitor fate during spinal cord regeneration
Cited by: 6
Author(s): Diane Pelzer, Lauren S. Phipps, Raphaël Thuret, Carlos J Gallardo-Dodd, Syed Murtuza Baker, Karel Dorey
Software Mentions: 5
Published: about 3 years ago

10.1093/bib/bbaa339

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test
Cited by: 9
Author(s): Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed Lein, Richard H. Scheuermann
Software Mentions: 5
Published: almost 4 years ago

10.1038/s42003-021-02201-2

Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis
Cited by: 28
Author(s): Kohei Saeki, Gregory Chang, Noriko Kanaya, Xiwei Wu, Jinhui Wang, Lauren Bernal, Desiree Ha, Susan L. Neuhausen, Shiuan Chen
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-020-02048-6

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows
Cited by: 289
Author(s): Elena Denisenko, Belinda Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, C Olivier, Rebecca K. Simmons, Ryan Lister, Alistair R.R. Forrest
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.58716

Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?
Cited by: 210
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Francesca Luca, Yi Xu, Adnan Alazizi, Yaozhu Leng, Chaur Dong Hsu, Nardhy Gomez-López
Software Mentions: 5
Published: over 4 years ago

10.3390/cancers12061393

Anti-EGFR Therapy Induces EGF Secretion by Cancer-Associated Fibroblasts to Confer Colorectal Cancer Chemoresistance
Cited by: 37
Author(s): Colleen M. Garvey, Roy Lau, Alyssa Sanchez, Ren Sun, Emma Fong, Michael E. Doche, Oscar Chen, Anthony Jusuf, Heinz‐Josef Lenz, Brent K. Larson, Shannon M. Mumenthaler
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.60225

RUNX1 marks a luminal castration-resistant lineage established at the onset of prostate development
Cited by: 28
Author(s): Renaud Mével, Ivana Steiner, Susan Mason, Laura C.A. Galbraith, Rahima Patel, Muhammad Zaki Hidayatullah Fadlullah, Imran Ahmad, Hing Y. Leung, Pedro Oliveira, Karen Blyth, Esther Baena, Georges Lacaud
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.63450

Temporal evolution of single-cell transcriptomes of Drosophila olfactory projection neurons
Cited by: 28
Author(s): Qijing Xie, Maria Brbić, Felix Horns, Sai Saroja Kolluru, Robert C. Jones, Jiefu Li, Anay R Reddy, Anthony Xie, Sayeh Kohani, Zhuoran Li, Colleen N. McLaughlin, Tongchao Li, Chuanyun Xu, David Vacek, David J. Luginbuhl, Jure Leskovec, Stephen R. Quake, Liqun Luo, Hongjie Li
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.62522

Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host 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: about 4 years ago

10.1128/mBio.01093-21

Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium
Cited by: 5
Author(s): Sushmita Sridhar, Sally Forrest, Derek Pickard, Claire Cormie, Emily A. Lees, Nicholas R. Thomson, Gordon Dougan, Stephen Baker
Software Mentions: 5
Published: over 3 years ago

10.1186/s40779-021-00336-1

Advances in single-cell sequencing: insights from organ transplantation
Cited by: 7
Author(s): Ying Wang, Jian‐Ye Wang, Angelika Schnieke, Konrad Fischer
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-81349-7

Inhibition of mitochondrial function by metformin increases glucose uptake, glycolysis and GDF-15 release from intestinal cells
Cited by: 46
Author(s): Ming Yang, Tamana Darwish, Pierre Larraufie, Debra Rimmington, Irène Cimino, Deborah A. Goldspink, Benjamin Jenkins, Albert Koulman, Cheryl A. Brighton, Marcella Ma, Brian Lam, Anthony P. Coll, Stephen O’Rahilly, Frank Reimann, Fiona M. Gribble
Software Mentions: 5
Published: almost 4 years ago

10.1002/ctm2.350

Landscape and dynamics of single tumor and immune cells in early and advanced‐stage lung adenocarcinoma
Cited by: 43
Author(s): Zhencong Chen, Yiwei Huang, Zhengyang Hu, Mengnan Zhao, Ming Li, Guoshu Bi, Yuansheng Zheng, Jiaqi Liang, Tao Lu, Wei Jiang, Songtao Xu, Cheng Zhan, Junjie Xi, Qun Wang, Lijie Tan
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.591754

Scaffold-Mediated Developmental Effects on Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Are Preserved After External Support Removal
Cited by: 1
Author(s): Jun Li, Jong-Kook Lee, Keiko Miwa, Yuki Kuramoto, Kiyoshi Masuyama, Hideki Yasutake, Satoki Tomoyama, Hiroyuki Nakanishi, Yasushi Sakata
Software Mentions: 4
Published: almost 4 years ago

10.21203/rs.3.rs-916427/v1

Functional antibody and T-cell immunity following SARS-CoV-2 infection, including by variants of concern, in patients with cancer: the CAPTURE study
Cited by: 0
Author(s): Annika Fendler, Lewis Au, Scott T.C. Shepherd, Fiona Byrne, Maddalena Cerrone, Laura Amanda Boos, Karolina Rzeniewicz, William Gordon, Benjamin Shum, Camille L. Gérard, Barry Ward, Wenyi Xie, Andreas M. Schmitt, Nalinie Joharatnam‐Hogan, Georgina H. Cornish, Martin Pulé, Leila Mekkaoui, Kevin W. Ng, Eleanor Carlyle, Kim Edmonds, Lyra Del Rosario, Sarah Sarker, Karla Lingard, Mary Mangwende, Lucy Holt, Hamid Ahmod, Richard Stone, Camila Gomes, Helen Flynn, Ana Água-Doce, Philip Hobson, Simon Caidan, Michael Howell, Mary Wu, Robert Goldstone, Margaret Crawford, Laura Cubitt, Harshil Patel, Mike Gavrielides, Emma Nye, Ambrosius P. Snijders, James I. MacRae, Jérôme Nicod, Firza Alexander Gronthoud, Robyn Shea, Christina Messiou, David Cunningham, Ian Chau, Naureen Starling, Nicholas Turner, Liam Welsh, Nicholas van As, Robin L. Jones, Joanne Droney, Susana Banerjee, Kate Tatham, Shaman Jhanji, Mary O’Brien, Olivia Curtis, Kevin J. Harrington, Shreerang A. Bhide, Jessica Bazin, Anna Robinson, Clemency Stephenson, Tim Slattery, Yasir Khan, Zayd Tippu, Isla Leslie, Spyridon Gennatas, Alicia Okines, Alison Reid, Kate Young, Andrew J.S. Furness, Lisa Pickering, Sonia Gandhi, Steve Gamblin, Charles Swanton, Emma Nicholson, Sacheen Kumar, Nadia Yousaf, Katalin A. Wilkinson, Anthony J. Swerdlow, Ruth Harvey, George Kassiotis, James Larkin, Robert J. Wilkinson, Samra Turajlic
Software Mentions: 4
Published: about 3 years ago

10.3389/fcvm.2021.628885

Single-Cell Transcriptome Analysis Decipher New Potential Regulation Mechanism of ACE2 and NPs Signaling Among Heart Failure Patients Infected With SARS-CoV-2
Cited by: 13
Author(s): Mengqiu Ma, Yanhua Xu, Yang Su, Sang‐Bing Ong, Xingdong Hu, Min Chai, Maojun Zhao, Hong Li, Xiaojuan Fan, Yingjie Chen, Dan Xu, Xiaojiang Xu
Software Mentions: 4
Published: over 3 years ago

10.1530/REP-20-0231

Single cell transcriptome research in human placenta
Cited by: 38
Author(s): Hui Li, Qizhao Huang, Yu Liu, Lana X. Garmire
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-80512-w

Tumor cytotoxicity and immunogenicity of a novel V-jet neon plasma source compared to the kINPen
Cited by: 21
Author(s): Lea Miebach, Eric Freund, Stefan Horn, Felix Nießner, Sanjeev Kumar Sagwal, Thomas von Woedtke, Steffen Emmert, Klaus‐Dieter Weltmann, Ramona Clemen, Anke Schmidt, Torsten Gerling, Sander Bekeschus
Software Mentions: 4
Published: almost 4 years ago

10.1002/advs.201903438

Medical Gas Plasma Jet Technology Targets Murine Melanoma in an Immunogenic Fashion
Cited by: 75
Author(s): Sander Bekeschus, Ramona Clemen, Felix Nießner, Sanjeev Kumar Sagwal, Eric Freund, Anke Schmidt
Software Mentions: 4
Published: over 4 years ago

10.3389/fimmu.2021.668045

Multi-Omics Approaches in Immunological Research
Cited by: 16
Author(s): Xiaojing Chu, Bowen Zhang, Valerie A. C. M. Koeken, Manoj Kumar Gupta, Yang Li
Software Mentions: 4
Published: over 3 years ago

10.1016/j.heliyon.2020.e03493

Efficient differentiation and purification of human induced pluripotent stem cell-derived endothelial progenitor cells and expansion with the use of inhibitors of ROCK, TGF-β, and GSK3β
Cited by: 9
Author(s): Hiromasa Aoki, Misaki Yamashita, Tadahiro Hashita, Koichi Ogami, Shin‐ichi Hoshino, Takahiro Iwao, Tamihide Matsunaga
Software Mentions: 4
Published: over 4 years ago

10.1038/s41422-020-00465-7

The m6A methylome of SARS-CoV-2 in host cells
Cited by: 87
Author(s): June Liu, Yixin Xu, Kai Li, Qing Ye, Hang Zhou, Hai Sun, Xiaoyu Li, Yu Liu, Yong Qiang Deng, Rui Ting Li, Miao Cheng, Bo He, Jia Zhou, Xiao Feng Li, Aiping Wu, Chengqi Yi, Qi Cheng
Software Mentions: 4
Published: almost 4 years ago

10.1186/s13073-021-00933-8

Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19
Cited by: 71
Author(s): John F. Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril J. Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P. Purohit, Sadhna Ahuja, Nadejda M. Tsankova, Nathalie Jetté, Gabriel E. Hoffman, Schahram Akbarian, Mary Fowkes, John F. Crary, Guo‐Cheng Yuan, Panos Roussos
Software Mentions: 4
Published: over 3 years ago

10.1038/s41416-021-01335-8

The amino acid metabolism is essential for evading physical plasma-induced tumour cell death
Cited by: 9
Author(s): Rajesh Kumar Gandhirajan, Dorothee Meyer, Sanjeev Kumar Sagwal, Klaus‐Dieter Weltmann, Thomas von Woedtke, Sander Bekeschus
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02238-2

scMC learns biological variation through the alignment of multiple single-cell genomics datasets
Cited by: 418
Author(s): Lihua Zhang, Qing Nie
Software Mentions: 4
Published: almost 4 years ago

10.1016/j.molmet.2019.03.001

Discovering metabolic disease gene interactions by correlated effects on cellular morphology
Cited by: 12
Author(s): Yang Jiao, Umer Ahmed, M.F. Michelle Sim, Andrea Bejar, Xiaolan Zhang, Mesbah Talukder, Robert H. Rice, Jason Flannick, Anna I. Podgornaia, Dermot F. Reilly, Jesse M. Engreitz, Maria Kost‐Alimova, Kate Hartland, Josep M. Mercader, Sara A. Georges, Vilas Wagh, Marija Tadin‐Strapps, John G. Doench, J. Michael Edwardson, Justin J. Rochford, Evan D. Rosen, Amit R. Majithia
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cell.2020.10.002

Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics
Cited by: 57
Author(s): Dylan Kotliar, Aaron E. Lin, James Logue, Travis Hughes, Nadine M. Khoury, Siddharth S. Raju, Marc H. Wadsworth, Han Chen, Jonathan R. Kurtz, Bonnie Dighero-Kemp, Zach B. Bjornson, Nilanjan Mukherjee, Brian Sellers, Nancy Tran, Matthew R. Bauer, Gordon Adams, Ricky Adams, John L. Rinn, Marta Melé, Stephen F. Schaffner, Garry P. Nolan, Kayla G. Barnes, Lisa E. Hensley, David R. McIlwain, Alex K. Shalek, Pardis C. Sabeti, Richard S. Bennett
Software Mentions: 4
Published: about 4 years ago

10.7554/eLife.56969

Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Cited by: 22
Author(s): Arpan C. Ghosh, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yanhui Hu, Víctor Barrera, Shannan Ho Sui, Norbert Perrimon
Software Mentions: 4
Published: about 4 years ago

10.3390/cancers13051007

A Lung Organotypic Coculture Reveals a Role for TFEB-Lysosomal Axis in the Survival of Disseminated Dormant Cancer Cells
Cited by: 5
Author(s): Manuela Zangrossi, Probir Chakravarty, Patrizia Romani, Sirio Dupont, Steven Hooper, Erik Sahai, Marco Montagner
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0180751

Increased dermal collagen bundle alignment in systemic sclerosis is associated with a cell migration signature and role of Arhgdib in directed fibroblast migration on aligned ECMs
Cited by: 14
Author(s): Lizhi Cao, Robert Lafyatis, Linda C. Burkly
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0219652

Drone-based effective counting and ageing of hippopotamus (Hippopotamus amphibius) in the Okavango Delta in Botswana
Cited by: 16
Author(s): Victoria L. Inman, Richard T. Kingsford, Michael J. Chase, Keith E. A. Leggett
Software Mentions: 4
Published: almost 5 years ago

10.7554/eLife.55851

Genetic mapping of etiologic brain cell types for obesity
Cited by: 62
Author(s): Pascal Timshel, Jonatan J Thompson, Tune H. Pers
Software Mentions: 4
Published: about 4 years ago

10.3389/fgene.2021.636743

DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data
Cited by: 21
Author(s): Floyd Maseda, Zixuan Cang, Qing Nie
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-018-31031-2

Cytochrome C oxidase Inhibition and Cold Plasma-derived Oxidants Synergize in Melanoma Cell Death Induction
Cited by: 37
Author(s): Rajesh Kumar Gandhirajan, Katrin Rödder, Yana Bodnar, Gabriella Pasqual-Melo, Steffen Emmert, Corinne E. Griguer, Klaus‐Dieter Weltmann, Sander Bekeschus
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2021.708981

deepMNN: Deep Learning-Based Single-Cell RNA Sequencing Data Batch Correction Using Mutual Nearest Neighbors
Cited by: 10
Author(s): Bin Zou, Tongda Zhang, Ruilong Zhou, Xiaoying Jiang, Huanming Yang, Xin Jin, Yong Bai
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: over 3 years ago

10.1038/s41598-018-37169-3

Physical plasma-treated saline promotes an immunogenic phenotype in CT26 colon cancer cells in vitro and in vivo
Cited by: 103
Author(s): Eric Freund, Kim Rouven Liedtke, Julia van der Linde, Hans‐Robert Metelmann, Claus–Dieter Heidecke, Lars-Ivo Partecke, Sander Bekeschus
Software Mentions: 3
Published: almost 6 years ago

10.1126/sciadv.abg3013

<i>C9orf72</i> -derived arginine-containing dipeptide repeats associate with axonal transport machinery and impede microtubule-based motility
Cited by: 51
Author(s): Laura Fumagalli, Florence L. Young, Steven Boeynaems, Mathias De Decker, Arpan R. Mehta, Ann Swijsen, Raheem Fazal, Wenting Guo, Matthieu Moisse, Jimmy Beckers, Lieselot Dedeene, Bhuvaneish T. Selvaraj, Tijs Vandoorne, Vanesa Madan, Marka van Blitterswijk, Denitza Raitcheva, Alexander McCampbell, Koen Poesen, Aaron D. Gitler, Philipp Koch, Pieter Vanden Berghe, Dietmar Rudolf Thal, Cathérine Verfaillie, Siddharthan Chandran, Ludo Van Den Bosch, Simon L. Bullock, Philip Van Damme
Software Mentions: 3
Published: over 3 years ago

10.1038/s12276-020-0422-0

Single-cell transcriptomics in cancer: computational challenges and opportunities
Cited by: 96
Author(s): Jean Fan, Kamil Slowikowski, Fan Zhang
Software Mentions: 3
Published: about 4 years ago

10.15252/emmm.201809930

A genome‐wide <scp>RNA</scp> i screen reveals essential therapeutic targets of breast cancer stem cells
Cited by: 19
Author(s): Abir Arfaoui, Claire Rioualen, Violette Azzoni, Guillaume Pinna, Pascal Finetti, Julien Wicinski, Emmanuelle Josselin, Manon Macario, Rémy Castellano, Candi Léonard-Stumpf, Anthony Bal, Abigaëlle Gros, Sylvain Lossy, Maher Kharrat, Yves Collette, François Bertucci, Daniel Birnbaum, Hayet Douik, Ghislain Bidaut, Emmanuelle Charafe‐Jauffret, Christophe Ginestier
Software Mentions: 3
Published: about 5 years ago

10.3390/antiox9040323

Gas Plasma-Treated Prostate Cancer Cells Augment Myeloid Cell Activity and Cytotoxicity
Cited by: 15
Author(s): Sander Bekeschus, Verena Ressel, Eric Freund, Nadine Gelbrich, Alexander Mustea, Matthias B. Stope
Software Mentions: 3
Published: over 4 years ago

10.1016/j.redox.2019.101423

xCT (SLC7A11) expression confers intrinsic resistance to physical plasma treatment in tumor cells
Cited by: 46
Author(s): Sander Bekeschus, Sebastian Eisenmann, Sanjeev Kumar Sagwal, Yana Bodnar, Juliane Moritz, Broder Poschkamp, Ingo Stoffels, Steffen Emmert, Muniswamy Madesh, K.‐D. Weltmann, Thomas von Woedtke, Rajesh Kumar Gandhirajan
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.ppat.1005857

Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and Phagocytes
Cited by: 47
Author(s): Sebastian Blättner, Sudip Das, Kerstin Paprotka, Ursula Eilers, Markus Krischke, Dorothee Kretschmer, Christian W. Remmele, Marcus Dittrich, Tobias Müller, Christina Sakarikou, Tobias Hertlein, Martin J. Mueller, Bruno Huettel, Richard Reinhardt, Knut Ohlsen, Thomas Rudel, Martin Fraunholz
Software Mentions: 3
Published: about 8 years ago

10.1038/s42003-021-02562-8

Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma
Cited by: 13
Author(s): Alexander Bondoc, Kathryn Glaser, Kang Jin, Charissa Lake, Stefano Cairo, James I. Geller, Gregory M. Tiao, Bruce J. Aronow
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.ppat.1009410

Macrophage-specific responses to human- and animal-adapted tubercle bacilli reveal pathogen and host factors driving multinucleated cell formation
Cited by: 18
Author(s): Christophe J. Queval, Antony Fearns, Laure Botella, Alicia Smyth, Laura Schnettger, Morgane Mitermite, Esen Wooff, Bernardo Villarreal‐Ramos, Waldo L. García-Jiménez, Tiaan Heunis, Matthias Trost, Dirk Werling, Francisco J. Salguero, Stephen V. Gordon, Maximiliano G. Gutiérrez
Software Mentions: 3
Published: over 3 years ago

10.1007/s00441-021-03483-y

Single-cell biology to decode the immune cellular composition of kidney inflammation
Cited by: 4
Author(s): Yu Zhao, Ulf Panzer, Stefan Bonn, Christian Krebs
Software Mentions: 3
Published: over 3 years ago

10.3390/cells9051144

Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice
Cited by: 18
Author(s): Anne-Marie Galow, Markus Wolfien, Paula Müller, Madeleine Bartsch, Ronald M. Brunner, Andreas Hoeflich, Olaf Wolkenhauer, Róbert Dávid, Tom Goldammer
Software Mentions: 3
Published: over 4 years ago

10.1093/gigascience/giab026

High-throughput microscopy reveals the impact of multifactorial environmental perturbations on colorectal cancer cell growth
Cited by: 6
Author(s): Chun-Te Chiang, Roy Lau, Ahmadreza Ghaffarizadeh, Matthew Brovold, Dipen Vyas, Edwin F. Juarez, Anthony Atala, David B. Agus, Shay Söker, Paul Macklin, Daniel Ruderman, Shannon M. Mumenthaler
Software Mentions: 3
Published: over 3 years ago

10.1093/braincomms/fcab105

Use of high-content imaging to quantify transduction of AAV-PHP viruses in the brain following systemic delivery
Cited by: 6
Author(s): Edward J. Smith, Pamela Farshim, Rachel Flomen, Samuel T. Jones, Sean J McAteer, Benjamin E. Deverman, Viviana Gradinaru, Gillian P. Bates
Software Mentions: 3
Published: over 3 years ago

10.1016/j.cmet.2020.05.007

Exome Sequencing Identifies Genes and Gene Sets Contributing to Severe Childhood Obesity, Linking PHIP Variants to Repressed POMC Transcription
Cited by: 32
Author(s): Gaëlle Marenne, Audrey E. Hendricks, Aliki Perdikari, Rebecca Bounds, Felicity Payne, Julia M. Keogh, Christopher J. Lelliott, Elana Henning, Saad Pathan, Sofie Ashford, Elena G. Bochukova, Vanisha Mistry, Allan Daly, Caroline Hayward, Nicholas J. Wareham, Stephen O’Rahilly, Claudia Langenberg, Eleanor Wheeler, Eleftheria Zeggini, I. Sadaf Farooqi, Inês Barroso
Software Mentions: 3
Published: over 4 years ago

Projects: pypi: Harmony

Papers Mentioning Harmony 504