cran: umap | Projects | Ecosyste.ms: Papers

10.3389/fgene.2021.667936

Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections
Cited by: 9
Author(s): Matineh Rahmatbakhsh, Alla Gagarinova, Mohan Babu
Software Mentions: 21
Published: over 3 years ago

10.3390/ijms21228837

Machine Learning Identifies Robust Matrisome Markers and Regulatory Mechanisms in Cancer
Cited by: 6
Author(s): Anni Kääriäinen, Vilma Pesola, Annalena Dittmann, Juho A. J. Kontio, Jarkko Koivunen, Taina Pihlajaniemi, Valerio Izzi
Software Mentions: 18
Published: almost 4 years ago

10.1038/s41597-021-00998-5

A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression
Cited by: 4
Author(s): Michael Rohr, Jordan M. Beardsley, Sai Preethi Nakkina, Xiang Zhu, Jihad Aljabban, Dexter Hadley, Deborah A. Altomare
Software Mentions: 17
Published: over 3 years ago

10.1016/j.stem.2019.07.008

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

10.1186/s13059-019-1900-3

Benchmarking principal component analysis for large-scale single-cell RNA-sequencing
Cited by: 60
Author(s): Koki Tsuyuzaki, Hiroyuki Sato, K. Sato, Itoshi Nikaido
Software Mentions: 12
Published: almost 5 years ago

10.1186/s13059-021-02329-8

scMET: Bayesian modeling of DNA methylation heterogeneity at single-cell resolution
Cited by: 13
Author(s): Chantriolnt-Andreas Kapourani, Ricard Argelaguet, Guido Sanguinetti, Catalina A. Vallejos
Software Mentions: 11
Published: over 3 years ago

10.7554/eLife.67490

Non-linear dimensionality reduction on extracellular waveforms reveals cell type diversity in premotor cortex
Cited by: 27
Author(s): Eric Lee, Hymavathy Balasubramanian, Alexandra Tsolias, Stephanie Udochukwu Anakwe, Maria Medalla, Krishna V. Shenoy, Chandramouli Chandrasekaran
Software Mentions: 10
Published: over 3 years ago

10.1172/jci.insight.140443

Versatile workflow for cell type–resolved transcriptional and epigenetic profiles from cryopreserved human lung
Cited by: 6
Author(s): Maria Llamazares Prada, Elisa Espinet, Vedrana Mijošek, Uwe Schwartz, Pavlo Lutsik, Raluca Tamas, Mandy Richter, Annika Behrendt, Stephanie Pohl, Naja P. Benz, Thomas Muley, Arne Warth, Claus Peter Heusel, Hauke Winter, Jonathan Landry, Felix J.F. Herth, Tinne Mertens, Harry Karmouty‐Quintana, Ina Koch, Vladimı́r Beneš, Jan O. Korbel, Sebastian M. Waszak, Andreas Trumpp, David Wyatt, Heiko Stahl, Christoph Plass, Renata Z. Jurkowska
Software Mentions: 9
Published: over 3 years ago

10.3390/ijms22042214

How Are the Flower Structure and Nectar Composition of the Generalistic Orchid Neottia ovata Adapted to a Wide Range of Pollinators?
Cited by: 8
Author(s): Emilia Brzosko, Andrzej Bajguz, Magdalena Chmur, Justyna Burzyńska, Edyta Jermakowicz, Paweł Mirski, Piotr Zieliński
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.21642.2

Generalized EmbedSOM on quadtree-structured self-organizing maps
Cited by: 3
Author(s): Miroslav Kratochvíl, Abhishek Koladiya, Jiřı́ Vondrášek
Software Mentions: 8
Published: over 4 years ago

10.1093/g3journal/jkaa036

Visualizing population structure with variational autoencoders
Cited by: 44
Author(s): C. J. Battey, Gabrielle C. Coffing, Andrew D. Kern
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-020-1949-z

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
Cited by: 173
Author(s): Christian H. Holland, Jovan Tanevski, Javier Perales-Patón, Jan Gleixner, Manu P. Kumar, Elisabetta Mereu, Brian A. Joughin, Oliver Stegle, Douglas A. Lauffenburger, Holger Heyn, Bence Szalai, Julio Sáez-Rodríguez
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0236878

Modeling cannabinoids from a large-scale sample of Cannabis sativa chemotypes
Cited by: 12
Author(s): Daniela Vergara, Reggie Gaudino, Thomas Blank, Brian Keegan
Software Mentions: 6
Published: about 4 years ago

10.7554/eLife.64522

Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer
Cited by: 33
Author(s): Lakshya Chauhan, Uday Ram, Kishore Hari, Mohit Kumar Jolly
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-77777-6

Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas
Cited by: 6
Author(s): Paul Tran, Lynn Tran, John Nechtman, Bruno dos Santos, Sharad Purohit, Khaled Bin Satter, Boying Dun, Ravindra Kolhe, Suash Sharma, Roni J. Bollag, Jin Xiong She
Software Mentions: 5
Published: almost 4 years ago

10.1016/j.csbj.2021.05.028

Distinguishing between PTEN clinical phenotypes through mutation analysis
Cited by: 14
Author(s): Stephanie Portelli, Lucy Barr, Alex Guimarães Cardoso de Sá, Douglas E. V. Pires, David B. Ascher
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.68967

Spatially patterned excitatory neuron subtypes and projections of the claustrum
Cited by: 17
Author(s): Sarah R. Erwin, Brianna N. Bristow, Kaitlin E Sullivan, Rennie M Kendrick, Brian A. Marriott, Lihua Wang, Jody Clements, Andrew L. Lemire, Jesse Jackson, Mark S. Cembrowski
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0256353

Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
Cited by: 6
Author(s): Claus M. Zacho, Martina Abenhus Bager, Ashot Margaryan, Peter Gravlund, Anders Galatius, Arne Redsted Rasmussen, Morten E. Allentoft
Software Mentions: 4
Published: about 3 years ago

10.1016/j.immuni.2020.06.013

An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity
Cited by: 129
Author(s): David R. Glass, Albert Tsai, John Paul Oliveria, Felix J. Hartmann, Samuel C. Kimmey, Ariel A. Calderon, Luciene Borges, Marla C. Glass, Lisa E. Wagar, Mark M. Davis, Sean C. Bendall
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0225899

Diversity of a cytokinin dehydrogenase gene in wild and cultivated barley
Cited by: 3
Author(s): Beata I. Czajkowska, Conor M. Finlay, Glynis Jones, Terence A. Brown
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-69026-7

Unveiling functional heterogeneity in breast cancer multicellular tumor spheroids through single-cell RNA-seq
Cited by: 25
Author(s): Erick Andrés Muciño-Olmos, Aarón Vázquez-Jiménez, Ugo Avila-Ponce de León, Meztli Matadamas-Guzmán, Vilma Maldonado, Tayde López-Santaella, Abrahan Hernández‐Hernández, Osbaldo Reséndis-Antonio
Software Mentions: 3
Published: over 4 years ago

10.1186/s13148-021-01163-w

Diagnosis of pulmonary nodules by DNA methylation analysis in bronchoalveolar lavage fluids
Cited by: 10
Author(s): Lei Li, Zhujia Ye, Yang Sai, Hao Yang, Jing Jin, Yingying Zhu, Jinsheng Tao, Siyu Chen, Jiehan Xu, Yanying Li, Weihe Liang, Bo Wang, Mingli Yang, Qiaoyun Huang, Zhiwei Chen, Weimin Liu, Jian‐Bing Fan, Dan Liu
Software Mentions: 3
Published: about 3 years ago

10.3390/cancers12113133

Prognostic Stratification of Bladder Cancer Patients with a MicroRNA-Based Approach
Cited by: 8
Author(s): Ilaria Cavallari, Angela Grassi, Paola Del Bianco, Alberto Aceti, Carlotta Zaborra, Evgeniya Sharova, Irene Bertazzolo, Donna M. D’Agostino, Massimo Iafrate, Vincenzo Ciminale
Software Mentions: 3
Published: about 4 years ago

10.1186/s13148-020-00937-y

Low-dose DNA demethylating therapy induces reprogramming of diverse cancer-related pathways at the single-cell level
Cited by: 8
Author(s): Hideyuki Takeshima, Yukie Yoda, Mika Wakabayashi, Naoko Hattori, Satoshi Yamashita, Toshikazu Ushijima
Software Mentions: 2
Published: about 4 years ago

Ecosyste.ms: Papers

Projects: cran: umap

Papers Mentioning umap 24