Ecosyste.ms: Papers

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/s13059-020-1926-6

Eleven grand challenges in single-cell data science
Cited by: 646
Author(s): David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan‐Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M Keizer, Indu Khatri, Szymon M. Kiełbasa, Jan Korbel, Alexey M Kozlov, Tzu Hao Kuo, Boudewijn P. F. Lelieveldt, Ion Măndoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Łukasz Rączkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alexander Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
Software Mentions: 11
Published: almost 5 years ago

10.1186/s12864-018-4673-2

Ginkgo biloba’s footprint of dynamic Pleistocene history dates back only 390,000 years ago
Cited by: 29
Author(s): Nora Hohmann, Eva M. Wolf, Philippe Rigault, Wenbin Zhou, Markus Kiefer, Yunpeng Zhao, Chengxin Fu, Marcus A. Koch
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pcbi.1008012

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data
Cited by: 24
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 5
Published: over 4 years ago

10.3389/fgene.2020.505441

SCCNV: A Software Tool for Identifying Copy Number Variation From Single-Cell Whole-Genome Sequencing
Cited by: 5
Author(s): Xiao Dong, Lei Zhang, Xiaoxiao Hao, Tao Wang, Jan Vijg
Software Mentions: 5
Published: about 4 years ago

10.1186/s13073-021-00889-9

Single-cell sequencing of the small and AT-skewed genome of malaria parasites
Cited by: 4
Author(s): Shiwei Liu, Adam C Huckaby, Audrey C. Brown, Christopher C. Moore, Ian Burbulis, Michael J. McConnell, Jennifer L. Guler
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-02119-8

Methods for copy number aberration detection from single-cell DNA-sequencing data
Cited by: 63
Author(s): Xian Mallory, Mohammadamin Edrisi, Nicholas E. Navin, Luay Nakhleh
Software Mentions: 4
Published: over 4 years ago

10.1093/bioinformatics/bty517

iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data
Cited by: 19
Author(s): Mitulkumar V. Patel
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-016-0971-7

Single-cell sequencing reveals karyotype heterogeneity in murine and human malignancies
Cited by: 156
Author(s): Björn Bakker, Aaron Taudt, Mirjam E. Belderbos, David Porubský, Diana C.J. Spierings, Tristan de Jong, Nancy Halsema, Hinke G. Kazemier, Karina Hoekstra-Wakker, Allan Bradley, Eveline S.J.M. de Bont, Anke van den Berg, Victor Guryev, Peter M Lansdorp, Maria Colomé-Tatché, Floris Foijer
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.21615

TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24− cancer cells
Cited by: 33
Author(s): Debjani Pal, Anja Pertot, Nitin H. Shirole, Zhan Yao, Naishitha Anaparthy, Tyler Garvin, Hilary Cox, Kenneth Chang, Fred Rollins, Jude Kendall, Leyla Edwards, Vijay A Singh, Gary C. Stone, Michael C. Schatz, James Hicks, Gregory J. Hannon, Raffaella Sordella
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-019-2842-1

Aneuvis: web-based exploration of numerical chromosomal variation in single cells
Cited by: 1
Author(s): Daniel G. Piqué, Grasiella Andriani, Elaine C. Maggi, Stephanie M. Zimmerman, John M. Greally, Cristina Montagna, Jessica C. Mar
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-021-04277-3

PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity
Cited by: 1
Author(s): Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra, Gianvito Urgese
Software Mentions: 2
Published: over 3 years ago

10.1186/s12915-021-01056-7

Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation
Cited by: 6
Author(s): Jimi L. Rosenkrantz, Jessica Gaffney, Victoria H. J. Roberts, Lucia Carbone, Shawn L. Chavez
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-6-143

EST analysis in Ginkgo biloba: an assessment of conserved developmental regulators and gymnosperm specific genes
Cited by: 37
Author(s): Eric D. Brenner, Manpreet S. Katari, D. W. Stevenson, Stephen Rudd, Andrew W. Douglas, William C. Moss, Richard W Twigg, Suzan J Runko, Giulia M. Stellari, W. Richard McCombie, Gloria M. Coruzzi
Software Mentions: 2
Published: about 19 years ago

10.1186/s12920-020-00731-y

MetaCNV - a consensus approach to infer accurate copy numbers from low coverage data
Cited by: 2
Author(s): Stefanie Friedrich, Remus Barbulescu, Thomas Helleday, Erik L. L. Sonnhammer
Software Mentions: 2
Published: over 4 years ago

10.1002/1878-0261.12876

Circulating tumor cell detection and single‐cell analysis using an integrated workflow based on ChimeraX^®‐i120 Platform: A prospective study
Cited by: 9
Author(s): Pengxiang Wang, Yun-Fan Sun, Weixiang Jin, Jian‐Wen Cheng, Hai-Xiang Peng, Yang Xu, Kaiyu Zhou, Li-Meng Chen, Kai Huang, Sui-Yi Wu, Bo Hu, Zefan Zhang, Wei Guo, Yang Cao, Jian Zhou, Jia Fan, Xin‐Rong Yang
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0072958

Functional Metagenomic Investigations of Microbial Communities in a Shallow-Sea Hydrothermal System
Cited by: 39
Author(s): Kai Tang, Keshao Liu, Nianzhi Jiao, Yao Zhang, Chen‐Tung Arthur Chen
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0011604

Phylogenomic Analysis of Marine Roseobacters
Cited by: 22
Author(s): Kai Tang, Hongzhan Huang, Nianzhi Jiao, Cathy H. Wu
Software Mentions: 2
Published: over 14 years ago

10.3390/cancers13092229

Cell-Free DNA Analysis by Whole-Exome Sequencing for Hepatocellular Carcinoma: A Pilot Study in Thailand
Cited by: 13
Author(s): Pattapon Kunadirek, Natthaya Chuaypen, Piroon Jenjaroenpun, Thidathip Wongsurawat, Nutcha Pinjaroen, Pongserath Sirichindakul, Intawat Nookaew, Pisit Tangkijvanich
Software Mentions: 2
Published: over 3 years ago

10.1186/s40169-017-0177-y

Using single‐cell multiple omics approaches to resolve tumor heterogeneity
Cited by: 61
Author(s): Michael A. Ortega, Olivier Poirion, Xun Zhu, Sijia Huang, Thomas Wolfgruber, Robert Sebra, Lana X. Garmire
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13073-018-0537-2

Sensitivity to sequencing depth in single-cell cancer genomics
Cited by: 13
Author(s): João M. Alves, David Posada
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers13081947

A Single-Run Next-Generation Sequencing (NGS) Assay for the Simultaneous Detection of Both Gene Mutations and Large Chromosomal Abnormalities in Patients with Myelodysplastic Syndromes (MDS) and Related Myeloid Neoplasms
Cited by: 5
Author(s): Alessandro Liquori, Iván Lesende, Laura Palomo, Gayane Avetisyan, Mariam Ibáñez, Elisa González-Romero, Mireia Boluda-Navarro, Mireya Morote-Faubel, Cristian Garcia‐Ruiz, Cristina Martínez-Valiente, Marta Santiago-Balsera, Inés Gómez-Seguí, Alejandra Sanjuán-Pla, Miguel Á. Sanz, Guillermo Sanz, Françesc Solé, Esperanza Such, José Cervera
Software Mentions: 1
Published: over 3 years ago

10.1093/synbio/ysw001

<i>Synthetic Biology</i>: fostering the cyber-biological revolution
Cited by: 22
Author(s): Jean Peccoud
Software Mentions: 1
Published: almost 9 years ago

10.1002/ece3.11

Life-history traits maintain the genomic integrity of sympatric species of the spruce budworm (<i>Choristoneura fumiferana</i>) group on an isolated forest island
Cited by: 12
Author(s): Lisa M. Lumley, Felix A. H. Sperling
Software Mentions: 1
Published: over 13 years ago

10.3390/mi11070645

Comparison of Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) in Limited DNA Sequencing Based on Tube and Droplet
Cited by: 17
Author(s): Xiaoxiang Zhou, Ying Xü, Libo Zhu, Zhen Su, Xiaoming Han, Zhen Zhang, Yan Huang, Quanjun Liu
Software Mentions: 1
Published: over 4 years ago

10.1038/s41416-021-01327-8

Detection of clustered circulating tumour cells in early breast cancer
Cited by: 38
Author(s): Ilona Krol, Fabienne D. Schwab, Roberta Carbone, Mathilde Ritter, Sabrina Picocci, Marzia L. De Marni, Grazyna Stepien, G Franchi, Andrea Zanardi, Marco D. Rissoglio, A. Covelli, G. Guidi, Daniele Scarinci, Francesc Castro-Giner, Luca Mazzarella, Claudio Doglioni, Francesca Borghi, P. Milani, Christian Kurzeder, Walter Weber, Nicola Aceto
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2019.00775

Validation of a 16th Century Traditional Chinese Medicine Use of Ginkgo biloba as a Topical Antimicrobial
Cited by: 38
Author(s): François Chassagne, Xinyi Huang, James T. Lyles, Cassandra L. Quave
Software Mentions: 1
Published: over 5 years ago

10.1038/s41416-018-0186-7

Detection of circulating tumour cell clusters in human glioblastoma
Cited by: 92
Author(s): Ilona Krol, Francesc Castro-Giner, Martina Maurer, Sofia Gkountela, Barbara M. Szczerba, Ramona Scherrer, Niamh Coleman, Suzanne Carreira, Felix Bachmann, Stephanie Anderson, Marc Engelhardt, Heidi A. Lane, T.R. Jeffry Evans, Ruth Plummer, Rebecca Kristeleit, Juanita Lopez, Nicola Aceto
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-017-1193-3

SynthEx: a synthetic-normal-based DNA sequencing tool for copy number alteration detection and tumor heterogeneity profiling
Cited by: 25
Author(s): Grace O. Silva, Marni B. Siegel, Lisle E. Mose, Joel S. Parker, Wei Sun, Charles M. Perou, Meng-Jie Chen
Software Mentions: 1
Published: over 7 years ago

10.3897/BDJ.4.e10194

Salix transect of Europe: patterns in the most abundant chrysomelid beetle (Coleoptera: Chrysomelidae) herbivores of willow from Greece to Arctic Norway
Cited by: 4
Author(s): Roy Canty, Enrico Ruzzier, Quentin Cronk, Diana M. Percy
Software Mentions: 1
Published: about 8 years ago

10.3897/BDJ.8.e53788

Salix transect of Europe: patterns in the distribution of willow-feeding psyllids (Hemiptera: Psylloidea) from Greece to arctic Norway
Cited by: 2
Author(s): Diana M. Percy, Quentin Cronk
Software Mentions: 1
Published: over 4 years ago

10.1186/s40478-019-0873-5

Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing
Cited by: 33
Author(s): Diego Pérez‐Rodríguez, Maria Kalyva, Melissa Leija‐Salazar, Tammaryn Lashley, Maxime Tarabichi, Viorica Chelban, Steve Gentleman, Lucía Schottlaender, Hannah Franklin, George Vasmatzis, Henry Houlden, Anthony H.V. Schapira, Thomas T. Warner, Janice L. Holton, Zane Jaunmuktane, Christos Proukakis
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12885-017-3447-6

Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications
Cited by: 20
Author(s): Shonan Sho, Colin M. Court, Paul Winograd, Sang-Jun Lee, Shuang Hou, Thomas G. Graeber, Hsian‐Rong Tseng, James S. Tomlinson
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj.4786

Phytoregionalisation of the Andean páramo
Cited by: 23
Author(s): Gwendolyn Peyre, Henrik Balslev, Xavier Font
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0181163

New library construction method for single-cell genomes
Cited by: 21
Author(s): Xi Liu, A. N. Belyaev, Sandra L. Spurgeon, Xiaohui Wang, Haibiao Gong, Robert Aboukhalil, Richard A. Fekete
Software Mentions: 1
Published: over 7 years ago

10.1073/pnas.2024176118

Accurate genomic variant detection in single cells with primary template-directed amplification
Cited by: 48
Author(s): Veronica Gonzalez-Pena, Sivaraman Natarajan, Yuntao Xia, David Klein, Caroline Robert, Yakun Pang, Bridget Shaner, Kavya Annu, Daniel K. Putnam, Wenan Chen, Jon P. Connelly, Shondra M. Pruett-Miller, Xiang Chen, John Easton, Charles Gawad
Software Mentions: 1
Published: over 3 years ago

10.1038/srep37392

Vertical Magnetic Separation of Circulating Tumor Cells for Somatic Genomic-Alteration Analysis in Lung Cancer Patients
Cited by: 23
Author(s): Chang Eun Yoo, Jong-Myeon Park, Hee-Sung Moon, Je‐Gun Joung, Dae‐Soon Son, Hyo Jeong Jeon, Yeon Jeong Kim, Kwan-Young Han, Jong‐Mu Sun, Keunchil Park, Donghyun Park, Woong-Yang Park
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-019-46606-w

A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses
Cited by: 15
Author(s): Grasiella Andriani, Elaine C. Maggi, Daniel G. Piqué, Stephanie M. Zimmerman, Moonsook Lee, Wilber Quispe-Tintaya, Alexander Y. Maslov, Judith Campisi, Jan Vijg, Jessica C. Mar, Cristina Montagna
Software Mentions: 1
Published: over 5 years ago