Ecosyste.ms: Papers

10.1186/s13059-020-1929-3

From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis
Cited by: 231
Author(s): Feng Yan, David Powell, David Curtis, Nicholas C. Wong
Software Mentions: 21
Published: almost 5 years ago

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

10.15252/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

10.15252/msb.20209438

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

10.1016/j.cell.2020.12.016

Spatiotemporal analysis of human intestinal development at single-cell resolution
Cited by: 215
Author(s): David Fawkner-Corbett, Agne Antanaviciute, Kaushal Parikh, Marta Jagielowicz, Ana Sousa Gerós, Tarun Gupta, Neil Ashley, Doran Khamis, Darren J. Fowler, Edward Morrissey, Christine M. Cunningham, Johnson Prv., Hashem Koohy, Alison Simmons
Software Mentions: 18
Published: almost 4 years ago

10.1186/s13059-020-02104-1

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Cited by: 57
Author(s): Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo
Software Mentions: 17
Published: over 4 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

10.12688/f1000research.16198.2

scClustViz – Single-cell RNAseq cluster assessment and visualization
Cited by: 25
Author(s): Brendan T. Innes, Gary D. Bader
Software Mentions: 16
Published: over 5 years ago

10.3389/fgene.2016.00163

Single-Cell Transcriptomics Bioinformatics and Computational Challenges
Cited by: 101
Author(s): Olivier Poirion, Xun Zhu, Travers Ching, Lana X. Garmire
Software Mentions: 15
Published: about 8 years ago

10.1186/s13059-020-02116-x

Integrative analyses of single-cell transcriptome and regulome using MAESTRO
Cited by: 107
Author(s): Chenfei Wang, Dongqing Sun, Xin Huang, Changxin Wan, Ziyi Li, Ya Han, Qian Qin, Jingyu Fan, Xintao Qiu, Yingtian Xie, Clifford A. Meyer, Myles Brown, Ming Tang, Henry W. Long, Tao Liu, X. Shirley Liu
Software Mentions: 15
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

10.1007/s00401-021-02343-x

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases
Cited by: 23
Author(s): Rahel Feleke, Regina H. Reynolds, Amy M. Smith, Bension S. Tilley, Sarah A. Gagliano Taliun, John Hardy, Paul M. Matthews, Steve Gentleman, David R. Owen, Michael R. Johnson, Prashant K. Srivastava, Mina Ryten
Software Mentions: 14
Published: over 3 years ago

10.1002/1873-3468.12684

Computational approaches for interpreting sc <scp>RNA</scp> ‐seq data
Cited by: 111
Author(s): Raghd Rostom, Valentine Svensson, Sarah A. Teichmann, Gozde Kar
Software Mentions: 14
Published: over 7 years ago

10.3389/fgene.2019.00317

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis
Cited by: 549
Author(s): Geng Chen, Baitang Ning, Tieliu Shi
Software Mentions: 13
Published: over 5 years ago

10.1186/s13059-017-1305-0

Splatter: simulation of single-cell RNA sequencing data
Cited by: 575
Author(s): Luke Zappia, Belinda Phipson, Alicia Oshlack
Software Mentions: 13
Published: about 7 years ago

10.1186/s13059-020-02071-7

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data
Cited by: 56
Author(s): Ralph Patrick, David T. Humphreys, Vaibhao Janbandhu, Alicia Oshlack, Joshua W. K. Ho, Richard P. Harvey, Kitty Lo
Software Mentions: 13
Published: over 4 years ago

10.3389/fonc.2021.639013

Single-Cell Transcriptome Analysis Identifies Ligand–Receptor Pairs Associated With BCP-ALL Prognosis
Cited by: 3
Author(s): Liang Wu, Mingming Jiang, Ping Yu, Jianfeng Li, Wen Ouyang, Chong Feng, Wei Zhao, Yuting Dai, Jinyan Huang
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

10.3390/ijms21010167

RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
Cited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: almost 5 years ago

10.1186/s13059-019-1795-z

A comparison of automatic cell identification methods for single-cell RNA sequencing data
Cited by: 361
Author(s): Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders, Ahmed Mahfouz
Software Mentions: 12
Published: about 5 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

10.1186/s13059-019-1766-4

scAlign: a tool for alignment, integration, and rare cell identification from scRNA-seq data
Cited by: 74
Author(s): Nelson Johansen, Gerald Quon
Software Mentions: 12
Published: over 5 years ago

10.1038/s41598-021-86396-8

Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
Cited by: 15
Author(s): Miriam I. Brandt, Florence Pradillon, Blandine Trouche, Nicolas Henry, Cathy Liautard‐Haag, Marie-Anne Cambon-Bonavita, Valérie Cueff-Gauchard, Patrick Wincker, Caroline Belser, Julie Poulain, Sophie Arnaud‐Haond, Daniela Zeppilli
Software Mentions: 11
Published: over 3 years ago

10.15252/emmm.201911900

Epigenetic gene expression links heart failure to memory impairment
Cited by: 13
Author(s): Rezaul Islam, Dawid Lbik, M. Sadman Sakib, Raoul Maximilian Hofmann, Tea Berulava, Martí Jiménez Mausbach, Julia Cha, Maria Amélia Azevêdo Goldberg, Elerdashvili Vakhtang, Christian Schiffmann, Anke Zieseniß, Dörthe M. Katschinski, Farahnaz Sananbenesi, Karl Toischer, André Fischer
Software Mentions: 11
Published: almost 4 years ago

10.1186/s13059-019-1716-1

A practical guide to methods controlling false discoveries in computational biology
Cited by: 178
Author(s): Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm, Stephanie C. Hicks
Software Mentions: 11
Published: over 5 years ago

10.1093/plankt/fbaa017

Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea
Cited by: 11
Author(s): Laura Käse, Alexandra Kraberg, Katja Metfies, Stefan Neuhaus, Pim Sprong, Bernhard M. Fuchs, Maarten Boersma, Karen Helen Wiltshire
Software Mentions: 10
Published: over 4 years ago

10.1186/s13059-016-0927-y

Design and computational analysis of single-cell RNA-sequencing experiments
Cited by: 409
Author(s): Rhonda Bacher, Christina Kendziorski
Software Mentions: 10
Published: over 8 years ago

10.3389/fgene.2021.616686

Identifying Differentially Expressed Genes of Zero Inflated Single Cell RNA Sequencing Data Using Mixed Model Score Tests
Cited by: 2
Author(s): Zhiqiang He, Yueyun Pan, Fang Shao, Hui Wang
Software Mentions: 10
Published: almost 4 years ago

10.1186/s13059-020-02083-3

DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning
Cited by: 23
Author(s): Yong He, Hao Yuan, Changbao Wu, Zhi Xie
Software Mentions: 9
Published: over 4 years ago

10.1186/s12885-021-07840-6

Cost-effectiveness of different surgical treatment approaches for early breast cancer: a retrospective matched cohort study from China
Cited by: 6
Author(s): Qing Yang, Xiaorong Zhong, Wei Zhang, Ting Luo, Ping He, Hong Zheng
Software Mentions: 9
Published: almost 4 years ago

10.1186/s13059-021-02286-2

Giotto: a toolbox for integrative analysis and visualization of spatial expression data
Cited by: 290
Author(s): Ruben Dries, Qi Zhu, Rui Dong, Chee-Huat Linus Eng, Huipeng Li, Kan Liu, Yuntian Fu, Tianxiao Zhao, Arpan Sarkar, Feng Bao, Rani E. George, Nico Pierson, Long Cai, Guo‐Cheng Yuan
Software Mentions: 9
Published: over 3 years ago

10.1186/s13045-020-00941-y

A single-cell survey of cellular hierarchy in acute myeloid leukemia
Cited by: 39
Author(s): Jinliang Wu, Yanyu Xiao, Jie Sun, Huiyu Sun, Haide Chen, Yuanyuan Zhu, Haidong Fu, Chengxuan Yu, E Weigao, Shih‐Wei Lai, Lifeng Ma, Jiaqi Li, Lijiang Fei, Mengmeng Jiang, Jingjing Wang, Fang Ye, Renying Wang, Ziyu Zhou, Guodong Zhang, Tingyue Zhang, Qiong Ding, Zou Wang, Sheng Hao, Lizhen Liu, Weiyan Zheng, Jingsong He, Weijia Huang, Yungui Wang, Jin Xie, Tiefeng Li, Tao Cheng, Xiaoping Han, He Huang, Guoji Guo
Software Mentions: 9
Published: about 4 years ago

10.1126/sciadv.abg1921

Environmental vulnerability of the global ocean epipelagic plankton community interactome
Cited by: 47
Author(s): Samuel Chaffron, Erwan Delage, Marko Budinich, Damien Vintache, Nicolas Henry, Charlotte Nef, Mathieu Ardyna, Ahmed A. Zayed, Pedro C. Junger, Pierre E. Galand, Connie Lovejoy, Alison E. Murray, Hugo Sarmento, Tara Oceans Coordinators, Silvia G. Acinas, Marcel Babin, Daniele Iudicone, Olivier Jaillon, Eric Karsenti, Patrick Wincker, Lee Karp‐Boss, Matthew B. Sullivan, Chris Bowler, Colomban de Vargas, Damien Eveillard
Software Mentions: 9
Published: about 3 years ago

10.3389/fncel.2020.00065

Single-Cell Analysis of Neuroinflammatory Responses Following Intracranial Injection of G-Deleted Rabies Viruses
Cited by: 29
Author(s): Kee Wui Huang, Bernardo L. Sabatini
Software Mentions: 9
Published: over 4 years ago

10.1186/s13148-021-01144-z

Whole-genome methylation analysis of testicular germ cells from cryptozoospermic men points to recurrent and functionally relevant DNA methylation changes
Cited by: 9
Author(s): Sara Di Persio, Elsa Leitão, Marius Wöste, Tobias Tekath, Jann‐Frederik Cremers, Martin Dugas, Xiaolin Liao, Gerd Meyer zu Hörste, Sabine Kliesch, Sandra Laurentino, Nina Neuhaus, Bernhard Horsthemke
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

10.1016/j.devcel.2018.07.005

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development
Cited by: 184
Author(s): Sueli Marques, David van Bruggen, Darya Vanichkina, Elisa M. Floriddia, Hermany Munguba, Leif Väremo, Stefania Giacomello, Ana Mendanha Falcão, Mandy Meijer, Åsa K. Björklund, Jens Hjerling-Leffler, Ryan J. Taft, Gonçalo Castelo‐Branco
Software Mentions: 8
Published: over 6 years ago

10.1371/journal.pcbi.1006378

clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets
Cited by: 45
Author(s): Davide Risso, Liam Purvis, Russell B. Fletcher, Diya Das, John Ngai, Sandrine Dudoit, Elizabeth Purdom
Software Mentions: 8
Published: about 6 years ago

10.1038/s42003-020-1097-8

CD70 expression determines the therapeutic efficacy of expanded human regulatory T cells
Cited by: 30
Author(s): Rebeca Arroyo Hornero, Christos Georgiadis, Peng Hua, Dominik Trzupek, He L-Z., Waseem Qasim, John A. Todd, Ricardo C. Ferreira, Kathryn J. Wood, Fadi Issa, Joanna Hester
Software Mentions: 8
Published: over 4 years ago

10.3390/molecules24213987

Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency
Cited by: 19
Author(s): Taremekedzwa Allan Sanyanga, Bilal Nizami, Özlem Tastan Bishop
Software Mentions: 8
Published: about 5 years ago

10.15252/msb.202110232

Single‐cell analyses reveal SARS‐CoV‐2 interference with intrinsic immune response in the human gut
Cited by: 64
Author(s): Sergio Triana, Camila Metz-Zumaran, C. Ramı́rez, Carmon Kee, Patricio Doldan, Mohammed Shahraz, Daniel Schraivogel, Andreas R. Gschwind, Ashwini Kumar Sharma, Lars M. Steinmetz, Carl Herrmann, Theodore Alexandrov, Steeve Boulant, Megan L. Stanifer
Software Mentions: 8
Published: over 3 years ago

10.3389/fnins.2018.00031

Exploring the Complexity of Cortical Development Using Single-Cell Transcriptomics
Cited by: 12
Author(s): Hyobin Jeong, Vijay Tiwari
Software Mentions: 8
Published: almost 7 years ago

10.1186/s13073-021-00866-2

Genetic and non-genetic factors affecting the expression of COVID-19-relevant genes in the large airway epithelium
Cited by: 21
Author(s): Silva Kasela, Victor E. Ortega, Molly Martorella, Suresh Garudadri, Jennifer Nguyen, Elizabeth J. Ampleford, Anu Pasanen, Srilaxmi Nerella, Kristina L. Buschur, Igor Barjaktarević, R. Graham Barr, Eugene R. Bleecker, Russell P. Bowler, Alejandro P. Comellas, Christopher B. Cooper, David Couper, Gerard J. Criner, Jeffrey L. Curtis, MeiLan K. Han, Nadia N. Hansel, Eric A. Hoffman, Robert J. Kaner, Jerry A. Krishnan, Fernando J. Martínez, Merry-Lynn McDonald, Deborah A. Meyers, Robert Paine, Stephen P. Peters, Mario Castro, Loren C. Denlinger, Serpil C. Erzurum, John V. Fahy, Elliot Israel, Nizar N. Jarjour, Bruce D. Levy, Xingnan Li, Wendy C. Moore, Sally E. Wenzel, Joe Zein, Charles Langelier, Prescott G. Woodruff, Tuuli Lappalainen, Stephanie A. Christenson
Software Mentions: 8
Published: over 3 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

10.3389/fmicb.2019.02736

Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding
Cited by: 14
Author(s): Simona Armeli Minicante, Roberta Piredda, Grazia Marina Quero, Stefania Finotto, Fabrizio Bernardi Aubry, Mauro Bastianini, Alessandra Pugnetti, Adriana Zingone
Software Mentions: 8
Published: almost 5 years ago

10.1186/s12859-020-03641-z

A rank-based marker selection method for high throughput scRNA-seq data
Cited by: 23
Author(s): Alexander Vargo, Anna C. Gilbert
Software Mentions: 8
Published: about 4 years ago

10.7554/eLife.56980

m6A RNA methylation impacts fate choices during skin morphogenesis
Cited by: 18
Author(s): Linghe Xi, Thomas Carroll, Irina Matos, Ji‐Dung Luo, Lisa Polak, H. Amalia Pasolli, Samie R. Jaffrey, Elaine Fuchs
Software Mentions: 8
Published: about 4 years ago

10.3389/fgene.2019.01331

Reproducibility of Methods to Detect Differentially Expressed Genes from Single-Cell RNA Sequencing
Cited by: 50
Author(s): Tian Mou, Wenjiang Deng, Fengyun Gu, Yudi Pawitan, Trung Nghia Vu
Software Mentions: 8
Published: almost 5 years ago

10.7554/eLife.38519

Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetes
Cited by: 106
Author(s): Diego Balboa, Jonna Saarimäki-Vire, Daniel Borshagovski, Mantas Survila, Päivi Lindholm, Emilia Galli, Solja Eurola, Jarkko Ustinov, Heli Grym, Hanna Huopio, Juha Partanen, Kirmo Wartiovaara, Timo Otonkoski
Software Mentions: 8
Published: about 6 years ago

10.1128/mBio.02880-19

Cell-to-Cell Variation in Defective Virus Expression and Effects on Host Responses during Influenza Virus Infection
Cited by: 33
Author(s): Changjiang Wang, Christian V. Forst, Tsui-Wen Chou, Adam Geber, Minghui Wang, Wissam Hamou, Melissa Smith, Robert Sebra, Bin Zhang, Bin Zhou, Elodie Ghedin
Software Mentions: 7
Published: over 4 years ago

10.1242/dmm.039297

Genome-wide analysis of androgen receptor binding and transcriptomic analysis in mesenchymal subsets during prostate development
Cited by: 10
Author(s): Christopher Nash, Nadia Boufaied, Dunarel Badescu, Yu Chang Wang, Miltiadis Paliouras, Mark Trifiro, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 7
Published: over 5 years ago

10.12688/f1000research.15830.2

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

10.1128/mBio.01468-21

Lung Epithelial Signaling Mediates Early Vaccine-Induced CD4⁺T Cell Activation and<i>Mycobacterium tuberculosis</i>Control
Cited by: 9
Author(s): Shibali Das, Nancy D. Marín, Ekaterina Esaulova, Mushtaq Ahmed, Amanda Swain, Bruce A. Rosa, Makedonka Mitreva, Javier Rangel-Moreno, Mihai G. Netea, Luis B. Barreiro, Maziar Divangahi, Maxim N. Artyomov, Deepak Kaushal, Shabaana A. Khader
Software Mentions: 7
Published: about 3 years ago

10.1186/s12859-019-2599-6

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data
Cited by: 189
Author(s): Tianyu Wang, Boyang Li, Craig E. Nelson, Sheida Nabavi
Software Mentions: 7
Published: almost 6 years ago

10.1186/s12862-015-0499-6

Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Cited by: 7
Author(s): Nathaniel J. Davies, Peter Krusche, Eran Tauber, Sascha Ott
Software Mentions: 7
Published: about 9 years ago

10.1016/j.celrep.2021.109228

Replicative senescence dictates the emergence of disease-associated microglia and contributes to Aβ pathology
Cited by: 86
Author(s): Yanling Hu, Gemma Fryatt, Mohammadmersad Ghorbani, Juliane Obst, David A. Menassa, Maria Margarida, Tim A.O. Muntslag, Adrián Olmos-Alonso, Monica Guerrero-Carrasco, Daniel Thomas, Mark S. Cragg, Diego Gómez-Nicola
Software Mentions: 7
Published: over 3 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

10.3389/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/insects12050388

Designing Aedes (Diptera: Culicidae) Mosquito Traps: The Evolution of the Male Aedes Sound Trap by Iterative Evaluation
Cited by: 3
Author(s): Kyran M. Staunton, Jianyi Liu, Michael Townsend, Mark Desnoyer, Paul Howell, Jacob E. Crawford, Xiang Wang, Nigel Snoad, Thomas R. Burkot, Scott A. Ritchie
Software Mentions: 7
Published: over 3 years ago

10.1002/glia.23767

Transcriptional profiling of microglia; current state of the art and future perspectives
Cited by: 72
Author(s): Emma Gerrits, Yang Heng, Erik Boddeke, Bart J. L. Eggen
Software Mentions: 7
Published: almost 5 years ago

10.21203/rs.3.rs-438662/v1

Systems biological assessment of human immunity to BNT162b2 mRNA vaccination
Cited by: 2
Author(s): Bali Pulendran, Prabhu S. Arunachalam
Software Mentions: 7
Published: over 3 years ago

10.1186/1745-6150-9-4

A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data
Cited by: 48
Author(s): Ngoc Tam L. Tran, Chun-Hsi Huang
Software Mentions: 7
Published: almost 11 years ago

10.1126/sciimmunol.abd1554

Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19
Cited by: 627
Author(s): Jeong Seok Lee, Seong-Wan Park, Hye Won Jeong, Jin Young Ahn, Seong Jin Choi, Hoyoung Lee, Baekgyu Choi, Su Kyung Nam, Moa Sa, Ji Soo Kwon, Su Jin Jeong, Kyung-Mi Lee, Sung Ho Park, Su–Hyung Park, Jun Yong Choi, Sung-Han Kim, Inkyung Jung, Eui Cheol Shin
Software Mentions: 7
Published: over 4 years ago

10.1093/gigascience/giz087

ascend: R package for analysis of single-cell RNA-seq data
Cited by: 35
Author(s): Anne Senabouth, Samuel W. Lukowski, Jose Alquicira Hernandez, Stacey Andersen, Xin Mei, Quan Nguyen, Joseph E. Powell
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2017.00062

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods
Cited by: 92
Author(s): Alessandra Dal Molin, Giacomo Baruzzo, Barbara Di Camillo
Software Mentions: 7
Published: over 7 years ago

10.1126/sciimmunol.abg6461

SARS-CoV-2 mutations in MHC-I-restricted epitopes evade CD8 ⁺ T cell responses
Cited by: 133
Author(s): Benedikt Agerer, Maximilian Koblischke, Venugopal Gudipati, Luis Fernando Montaño-Gutierrez, Mark J. Smyth, Alexandra Popa, Jakob-Wendelin Genger, Lukas Endler, David M. Florian, Vanessa Mühlgrabner, Marianne Graninger, Stephan W. Aberle, Anna-Maria Husa, Lisa E. Shaw, Alexander Lercher, Pia Gattinger, Ricard Torralba-Gombau, Doris Trapin, Thomas Penz, Daniele Barreca, Ingrid Faé, S. Wenda, Marianna Traugott, Gernot Walder, Winfried F. Pickl, Volker Thiel, Franz Allerberger, Hannes Stockinger, Elisabeth Puchhammer‐Stöckl, Wolfgang Weninger, Gottfried Fischer, Wolfgang Hoepler, Erich Pawelka, Alexander Zoufaly, Rudolf Valenta, Christoph Bock, Wolfgang Paster, René Geyeregger, Matthias Farlik, Florian Halbritter, Johannes B. Huppa, Judith H. Aberle, Andréas Bergthaler
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-10-325

Riboswitch Detection Using Profile Hidden Markov Models
Cited by: 33
Author(s): Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, Annangarachari Krishnamachari, Supratim Sengupta
Software Mentions: 7
Published: about 15 years ago

10.7717/peerj.2888

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization
Cited by: 67
Author(s): Xun Zhu, Travers Ching, Xinghua Pan, Sherman M. Weissman, Lana X. Garmire
Software Mentions: 7
Published: almost 8 years ago

10.3389/fpls.2021.661361

Unraveling Root Development Through Single-Cell Omics and Reconstruction of Gene Regulatory Networks
Cited by: 2
Author(s): Laura Serrano-Ron, Javier Cabrera, Pablo Pérez-García, Miguel A. Moreno-Risueño
Software Mentions: 7
Published: over 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

10.1136/jitc-2020-000778

M1^hottumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer
Cited by: 75
Author(s): Eva M. Garrido-Martín, Toby Mellows, James Clarke, Anusha-Preethi Ganesan, Oliver Wood, Angelica Cazaly, Grégory Seumois, Serena Chee, Aiman Alzetani, Emma V. King, Catherine C. Hedrick, Gareth J. Thomas, Peter S. Friedmann, Christian Ottensmeier, Pandurangan Vijayanand, Tilman Sánchez-Elsner
Software Mentions: 7
Published: over 4 years ago

10.1016/j.csbj.2021.07.010

Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome
Cited by: 3
Author(s): Márton Miskei, Adrienn Horváth, Lívia Viola, L. Varga, Éva Nagy, Orsolya Feró, Zsolt Karányi, Jason Roszik, Csaba Miskey, Zoltán Ivics, Lóránt Székvölgyi
Software Mentions: 6
Published: almost 4 years ago

10.1186/s12863-021-00983-2

Insights into 6S RNA in lactic acid bacteria (LAB)
Cited by: 1
Author(s): Pablo G. Cataldo, Paul Klemm, Marietta Thüring, Lucila Saavedra, Elvira María Hébert, Roland K. Hartmann, Marcus Lechner
Software Mentions: 6
Published: about 3 years ago

10.1128/mSystems.00329-20

Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
Cited by: 8
Author(s): Adrián López García de Lomana, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan Péricles Rodrigues Lorenzetti, Robert L. Moritz, Nitin S. Baliga
Software Mentions: 6
Published: about 4 years ago

10.1186/s13229-020-00346-1

Identification of amygdala-expressed genes associated with autism spectrum disorder
Cited by: 19
Author(s): María Jesús Presentación Herrero, Dmitry Velmeshev, David Hernandez‐Pineda, Saarthak Sethi, Shawn F. Sorrells, Payal Banerjee, Catherine Sullivan, Abha R. Gupta, Arnold R. Kriegstein, Joshua G. Corbin
Software Mentions: 6
Published: over 4 years ago

10.3390/cells8091004

Characterizing Human Cell Types and Tissue Origin Using the Benford Law
Cited by: 6
Author(s): Sne Morag, Mali Salmon‐Divon
Software Mentions: 6
Published: about 5 years ago

10.1111/gtc.12058

<scp>DROMPA</scp>: easy‐to‐handle peak calling and visualization software for the computational analysis and validation of ChIP‐seq data
Cited by: 62
Author(s): Ryuichiro Nakato, Takehiko Itoh, Katsuhiko Shirahige
Software Mentions: 6
Published: over 11 years ago

10.1016/j.celrep.2020.03.063

A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level
Cited by: 71
Author(s): Florian Mair, Jami R. Erickson, Valentin Voillet, Yannick Simoni, Timothy Bi, Aaron J. Tyznik, Jody Martin, Raphaël Gottardo, Evan W. Newell, Martin Prlic
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-017-16685-8

Identification of genes expressed in a mesenchymal subset regulating prostate organogenesis using tissue and single cell transcriptomics
Cited by: 7
Author(s): Nadia Boufaied, Christopher Nash, Annie Rochette, Anthony K. Smith, Brigid Orr, O. Cathal Grace, Yu Chang Wang, Dunarel Badescu, Jiannis Ragoussis, Axel A. Thomson
Software Mentions: 6
Published: almost 7 years ago

10.15252/msb.20209833

Single‐cell transcriptomics reveals immune response of intestinal cell types to viral infection
Cited by: 17
Author(s): Sergio Triana, Megan L. Stanifer, Camila Metz-Zumaran, Mohammed Shahraz, Markus Mukenhirn, Carmon Kee, Clara Serger, Ronald Koschny, Diana Ordoñez-Rueda, Malte Paulsen, Vladimı́r Beneš, Steeve Boulant, Theodore Alexandrov
Software Mentions: 6
Published: over 3 years ago

10.1186/1471-2164-14-720

Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines
Cited by: 36
Author(s): Joseph W. Foley, Arend Sidow
Software Mentions: 6
Published: almost 12 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

10.1038/s41598-019-40697-1

Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control
Cited by: 3
Author(s): Petar Petrov, Alexey V Sarapulov, Lél Eöry, Cristina Scielzo, Lydia Scarfò, Jacqueline Smith, David W. Burt, Pieta K. Mattila
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-019-46932-z

DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing
Cited by: 73
Author(s): Christian T. Wohnhaas, Germán Leparc, Francesc Fernández-Albert, David Kind, Florian Gantner, Coralie Viollet, Tobias Hildebrandt, Patrick Baum
Software Mentions: 6
Published: over 5 years ago

10.1093/biostatistics/kxw055

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Cited by: 112
Author(s): Aaron T. L. Lun, John C. Marioni
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.ppat.1008408

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response
Cited by: 16
Author(s): Dylan de Vries, Vasiliki Matzaraki, Olivier B. Bakker, Harm Brugge, Harm-Jan Westra, Mihai G. Netea, Lude Franke, Vinod Kumar, Monique G. P. van der Wijst
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pntd.0009061

Outcomes from international field trials with Male Aedes Sound Traps: Frequency-dependent effectiveness in capturing target species in relation to bycatch abundance
Cited by: 8
Author(s): Kyran M. Staunton, Donovan Leiva, Alvaro Cruz, Joelyn Goi, Carlos Arisqueta, Jianyi Liu, Mark Desnoyer, Paul Howell, Francia Espinosa, Azael Che-Mendoza, Stephan Karl, Jacob E. Crawford, Xiang Wang, Pablo Manrique-Saide, Nicole L. Achee, John P. Grieco, Scott A. Ritchie, Thomas R. Burkot, Nigel Snoad
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0155802

Comparison between Timelines of Transcriptional Regulation in Mammals, Birds, and Teleost Fish Somitogenesis
Cited by: 6
Author(s): Bernard Fongang, Andrzej Kudlicki
Software Mentions: 6
Published: over 8 years ago

10.1186/1752-0509-5-S2-S3

Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite
Cited by: 7
Author(s): Xi Wang, Xuegong Zhang
Software Mentions: 6
Published: almost 14 years ago

10.1371/journal.pgen.1005465

YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
Cited by: 272
Author(s): Christoph Stein, Anaïs F. Bardet, Guglielmo Roma, Sebastian Bergling, Ieuan Clay, Alexandra Ruchti, Claudia Agarinis, Tobias Schmelzle, Tewis Bouwmeester, Dirk Schübeler, Andreas Bauer
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pgen.1008037

Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast
Cited by: 24
Author(s): Kevin S. Myers, Nicholas M. Riley, Matthew E. MacGilvray, Trey K. Sato, Mick McGee, Justin Heilberger, Joshua J. Coon, Audrey P. Gasch
Software Mentions: 6
Published: over 5 years ago

10.26508/lsa.201900520

Dynamic changes in the regulatory T-cell heterogeneity and function by murine IL-2 mutein
Cited by: 11
Author(s): Daniel Lu, Hao Wu, Ian Driver, Sarah Ingersoll, Sue J. Sohn, Songli Wang, Chi-Ming Li, Hyewon Phee
Software Mentions: 6
Published: over 4 years ago

10.1093/bioinformatics/btz726

bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
Cited by: 59
Author(s): Wenhao Tang, François Bertaux, Philipp Thomas, Claire Stefanelli, Malika Saint, Samuel Marguerat, Vahid Shahrezaei
Software Mentions: 6
Published: about 5 years ago

10.3389/fnmol.2021.637143

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data
Cited by: 7
Author(s): Jordan Sicherman, Dwight F. Newton, Paul Pavlidis, Etienne Sibille, Shreejoy J. Tripathy
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007509

Clustering-independent analysis of genomic data using spectral simplicial theory
Cited by: 19
Author(s): Kiya W. Govek, Venkata S. Yamajala, Pablo G. Cámara
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pbio.3000675

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution
Cited by: 35
Author(s): Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1003671

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Cited by: 41
Author(s): Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pone.0132798

Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration
Cited by: 20
Author(s): Lulu Huang, Sagar S. Damle, Sheri Booten, Priyam Singh, Mahyar Sabripour, Jeff Hsu, Minji Jo, Melanie Katz, Andy Watt, Christopher E. Hart, Susan M. Freier, Brett P. Monia, Shuling Guo
Software Mentions: 6
Published: over 9 years ago

10.3390/plants10061039

Comparative Analysis of Re-Annotated Genes Provides Insight into Evolutionary Divergence and Expressions of Aquaporin Family in Pepper
Cited by: 2
Author(s): Yeon Mi Lee, Geun Young Chae, Min Kyung Kim, Seungill Kim
Software Mentions: 6
Published: over 3 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