cran: Canopy | Projects | Ecosyste.ms: Papers

10.1099/mgen.0.000409

Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses
Cited by: 64
Author(s): Ana Elena Pérez‐Cobas, Laura Gómez-Valero, Carmen Buchrieser
Software Mentions: 14
Published: over 4 years ago

10.1186/s40679-016-0031-0

Analyzing microtomography data with Python and the scikit-image library
Cited by: 22
Author(s): Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
Software Mentions: 14
Published: about 8 years ago

10.3389/fmed.2021.640515

Performance of Different Diagnostic PD-L1 Clones in Head and Neck Squamous Cell Carcinoma
Cited by: 13
Author(s): Julika Ribbat‐Idel, Frederick A. Dressler, Rosemarie Krupar, Christian Watermann, F. Paulsen, Patrick Kuppler, Luise Klapper, Anne Offermann, Barbara Wollenberg, Dirk Rades, Simon Laban, Markus Reischl, Karl‐Ludwig Bruchhage, Christian Idel, Sven Perner
Software Mentions: 9
Published: over 3 years ago

10.1016/j.ymeth.2015.07.012

Construction of an instant structured illumination microscope
Cited by: 30
Author(s): Alistair Curd, Alexa Cleasby, Katarzyna Makowska, Andrew G. York, Hari Shroff, Michelle Peckham
Software Mentions: 8
Published: about 9 years ago

10.1186/s40168-016-0154-5

Recovering complete and draft population genomes from metagenome datasets
Cited by: 195
Author(s): Naseer Sangwan, Fangfang Xia, Jack A. Gilbert
Software Mentions: 7
Published: almost 9 years ago

10.1099/mgen.0.000212

Metagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures
Cited by: 19
Author(s): Luc Cornet, Amandine Bertrand, Marc Hanikenne, Emmanuelle Javaux, Annick Wilmotte, Denis Baurain
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btaa672

A statistical approach for tracking clonal dynamics in cancer using longitudinal next-generation sequencing data
Cited by: 6
Author(s): Dimitrios V Vavoulis, Anthony Cutts, Jenny C. Taylor, Anna Schuh
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0239966

Analysis of mutational and proteomic heterogeneity of gastric cancer suggests an effective pipeline to monitor post-treatment tumor burden using circulating tumor DNA
Cited by: 2
Author(s): Noriyuki Sasaki, Takeshi Iwaya, Tadatoshi Chiba, Masashi Fujita, Ju Zhang, Fumitaka Endo, Mizunori Yaegashi, Tsuyoshi Hachiya, Ryo Sugimoto, Tamotsu Sugai, Doris R. Siwak, Lance A. Liotta, Yiling Lu, Gordon B. Mills, Hidewaki Nakagawa, Satoshi Nishizuka
Software Mentions: 4
Published: about 4 years ago

10.1016/j.csbj.2016.11.005

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
Cited by: 102
Author(s): Karel Sedlář, Kristyna Kupkova, Ivo Provazník
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13073-019-0643-9

Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time
Cited by: 8
Author(s): Paul Little, Danyu Lin, Wei Sun
Software Mentions: 4
Published: over 5 years ago

10.1098/rsos.160203

Foot pressure distributions during walking in African elephants (Loxodonta africana)
Cited by: 25
Author(s): Olga Panagiotopoulou, Todd C. Pataky, Madeleine Day, Michael C. Hensman, Sean Hensman, John R. Hutchinson, Christofer J. Clemente
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-020-59006-2

Power and pitfalls of computational methods for inferring clone phylogenies and mutation orders from bulk sequencing data
Cited by: 19
Author(s): Sayaka Miura, Tracy Vu, Jiamin Deng, Tiffany Buturla, Olumide Oladeinde, Joongdae Choi, Sudhir Kumar
Software Mentions: 4
Published: almost 5 years ago

10.18632/oncotarget.26352

Genomic characterization of metastatic ultra-hypermutated interdigitating dendritic cell sarcoma through rapid research autopsy
Cited by: 6
Author(s): Hui-Zi Chen, Russell Bonneville, Lianbo Yu, Michele R. Wing, Julie W. Reeser, Melanie A. Krook, Jharna Miya, Eric Samorodnitsky, Amy M. Smith, Dorrelyn M. Martin, Thuy Dao, Qishan Guo, David A. Liebner, Aharon G. Freud, Patricia Allenby, Sameek Roychowdhury
Software Mentions: 4
Published: almost 6 years ago

10.1002/cjp2.219

<scp>MYC</scp> amplifications are common events in childhood osteosarcoma
Cited by: 10
Author(s): Solange De Noon, Jannat Ijaz, Tim Coorens, Fernanda Amary, Hongtao Ye, Anna Strobl, Iben Lyskjær, Adrienne M. Flanagan, Sam Behjati
Software Mentions: 4
Published: over 3 years ago

10.7717/peerj.2652

Region-of-interest analyses of one-dimensional biomechanical trajectories: bridging 0D and 1D theory, augmenting statistical power
Cited by: 97
Author(s): Todd C. Pataky, Mark A. Robinson, Jos Vanrenterghem
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-020-60795-9

Biomechanical insights into the role of foot pads during locomotion in camelid species
Cited by: 10
Author(s): Christofer J. Clemente, Taylor J. M. Dick, Christopher L. Glen, Olga Panagiotopoulou
Software Mentions: 3
Published: almost 5 years ago

10.1038/srep24175

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
Cited by: 181
Author(s): Hsin-Hung Lin, Yu-Chieh Liao
Software Mentions: 3
Published: over 8 years ago

10.1038/s41416-021-01266-4

Frequent post-operative monitoring of colorectal cancer using individualised ctDNA validated by multiregional molecular profiling
Cited by: 6
Author(s): Mizunori Yaegashi, Takeshi Iwaya, Noriyuki Sasaki, Masashi Fujita, Ju Zhang, Doris R. Siwak, Tsuyoshi Hachiya, Kei Sato, Fumitaka Endo, Toshimoto Kimura, Koki Otsuka, Ryo Sugimoto, Tamotsu Sugai, Lance A. Liotta, Yiling Lu, Gordon B. Mills, Hidewaki Nakagawa, Satoshi Nishizuka
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-017-16813-4

Comprehensive statistical inference of the clonal structure of cancer from multiple biopsies
Cited by: 1
Author(s): Jie Liu, John T. Halloran, Jeffrey A. Bilmes, Riza M. Daza, Choli Lee, Elisabeth Mahen, Donna Prunkard, Chang Woo Song, Sibel Blau, Michael O. Dorschner, Vijayakrishna K. Gadi, Jay Shendure, C. Anthony Blau, William S. Noble
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-25544-z

Genomic features of renal cell carcinoma with venous tumor thrombus
Cited by: 17
Author(s): Gregor Warsow, Daniel Hübschmann, Kortine Kleinheinz, Cathleen Nientiedt, Martina Heller, Laura Van Coile, Yanis Tolstov, Lukas Trennheuser, Kathrin Wieczorek, Carine Pecqueux, Claudia Gasch, Timur H. Kuru, Joanne Nyarangi‐Dix, Gencay Hatiboglu, Doğu Teber, Sven Perner, Albrecht Stenzinger, Wilfried Roth, Boris Hadaschik, Sascha Pahernik, Dirk Jäger, Carsten Grüllich, Anette Duensing, Roland Eils, Matthias Schlesner, Holger Sültmann, Markus Hohenfellner, Stefan Duensing
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1008777

Assessing the contribution of tumor mutational phenotypes to cancer progression risk
Cited by: 1
Author(s): Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13073-021-00842-w

CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells
Cited by: 2
Author(s): Shadi Darvish Shafighi, Szymon M. Kiełbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan L. Kloet, Hendrik Veelken, Cornelis A.M. van Bergen, Ewa Szczurek
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pcbi.1005815

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data
Cited by: 8
Author(s): Theodore Roman, Lu Xie, Russell Schwartz
Software Mentions: 2
Published: about 7 years ago

10.1186/s13015-019-0155-6

Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors
Cited by: 12
Author(s): Yuanyuan Qi, Dikshant Pradhan, Mohammed El-Kebir
Software Mentions: 2
Published: over 5 years ago

10.1186/s12891-016-1271-9

Effects of two neuromuscular training programs on running biomechanics with load carriage: a study protocol for a randomised controlled trial
Cited by: 7
Author(s): Bernard X. W. Liew, Susan Morris, Justin W L Keogh, B. Appleby, Kevin Netto
Software Mentions: 2
Published: about 8 years ago

10.1186/s12920-018-0457-4

A graph-based algorithm for estimating clonal haplotypes of tumor sample from sequencing data
Cited by: 4
Author(s): Yixuan Wang, Xuanping Zhang, Shuai Ding, Yushui Geng, Jianye Liu, Zhongmeng Zhao, Rong Zhang, Xiao Xiao, Jiayin Wang
Software Mentions: 2
Published: almost 6 years ago

10.1038/srep24030

Diminution of the gut resistome after a gut microbiota-targeted dietary intervention in obese children
Cited by: 32
Author(s): Guojun Wu, Chenhong Zhang, Jing Wang, Feng Zhang, Ruirui Wang, Jian Shen, Linghua Wang, Xiaoyan Pang, Xiaojun Zhang, Liping Zhao, Menghui Zhang
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.1165

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
Cited by: 1,336
Author(s): Dongwan Kang, Jeff Froula, Rob Egan, Zhong Wang
Software Mentions: 2
Published: over 9 years ago

10.3390/molecules25133037

SUSSOL—Using Artificial Intelligence for Greener Solvent Selection and Substitution
Cited by: 15
Author(s): Hannes Sels, Herwig De Smet, Jeroen Geuens
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.6881

Foot pressure distribution in White Rhinoceroses (Ceratotherium simum) during walking
Cited by: 13
Author(s): Olga Panagiotopoulou, Todd C. Pataky, John R. Hutchinson
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.35074

IgM and IgD B cell receptors differentially respond to endogenous antigens and control B cell fate
Cited by: 57
Author(s): Mark Noviski, James L. Mueller, Anne B. Satterthwaite, Lee Ann Garrett‐Sinha, Frank Brombacher, Julie Zikherman
Software Mentions: 1
Published: almost 7 years ago

10.1101/mcs.a004002

Tumor heterogeneity and acquired drug resistance in FGFR2-fusion-positive cholangiocarcinoma through rapid research autopsy
Cited by: 55
Author(s): Melanie A. Krook, Russell Bonneville, Hui-Zi Chen, Julie W. Reeser, Michele R. Wing, Dorrelyn M. Martin, Amy M. Smith, Thuy Dao, Eric Samorodnitsky, Anoosha Paruchuri, Jharna Miya, Kaitlin R. Baker, Lianbo Yu, Cynthia Timmers, Kristin Dittmar, Aharon G. Freud, Patricia Allenby, Sameek Roychowdhury
Software Mentions: 1
Published: over 5 years ago

10.3390/e20090702

Big-Data-Mining-Based Improved K-Means Algorithm for Energy Use Analysis of Coal-Fired Power Plant Units: A Case Study
Cited by: 6
Author(s): Binghan Liu, Zhong-Guang Fu, Pengkai Wang, Lu Liu, Manda Gao, Ji Liu
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2019.00008

The Impact of Heterogeneity on Single-Cell Sequencing
Cited by: 76
Author(s): Samantha L. Goldman, Matthew MacKay, Ebrahim Afshinnekoo, Ari Melnick, Shuxiu Wu, Christopher E. Mason
Software Mentions: 1
Published: almost 6 years ago

10.3389/fpsyt.2020.591979

Cannabis Legalization and Acute Harm From High Potency Cannabis Products: A Narrative Review and Recommendations for Public Health
Cited by: 36
Author(s): Justin Matheson, Bernard Le Foll
Software Mentions: 1
Published: over 4 years ago

10.3390/s19143180

AULD: Large Scale Suspicious DNS Activities Detection via Unsupervised Learning in Advanced Persistent Threats
Cited by: 10
Author(s): Guozheng Yan, Qiang Li, Dong Guo, Bing Li
Software Mentions: 1
Published: over 5 years ago

10.2196/formative.8032

Developing Digital Facilitation of Assessments in the Absence of an Interpreter: Participatory Design and Feasibility Evaluation With Allied Health Groups
Cited by: 20
Author(s): Jill Freyne, DanaKai Bradford, Courtney Pocock, David Silvera-Tawil, Karen Harrap, Sally Brinkmann
Software Mentions: 1
Published: almost 7 years ago

10.1155/2017/5482750

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees
Cited by: 3
Author(s): Ying Liang, Bo Liao, Wen Zhu
Software Mentions: 1
Published: almost 8 years ago

10.1093/bioinformatics/bty830

MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data
Cited by: 74
Author(s): Florian Plaza Oñate, Emmanuelle Le Chatelier, Mathieu Almeida, Alessandra Cervino, Franck Gauthier, Frédéric Magoulès, S. Dusko Ehrlich, Matthieu Pichaud
Software Mentions: 1
Published: over 6 years ago

10.1093/bioinformatics/bty683

MIPUP: minimum perfect unmixed phylogenies for multi-sampled tumors via branchings and ILP
Cited by: 11
Author(s): Edin Husić, Xinyue Li, Ademir Hujdurović, Miika Mehine, Roméo Rizzi, Veli Mäkinen, Martin Milanič, Alexandru I. Tomescu
Software Mentions: 1
Published: over 6 years ago

10.3390/pathogens9010009

New Species of the Genus Curvularia: C. tamilnaduensis and C. coimbatorensis from Fungal Keratitis Cases in South India
Cited by: 11
Author(s): Noémi Kiss, Mónika Homa, M. Palanisamy, A. Mythili, Krisztina Krizsán, Revathi Rajaraman, Mónika Varga, Tamás Papp, Csaba Vágvölgyi, László Kredics, Sándor Kocsubé
Software Mentions: 1
Published: about 5 years ago

Projects: cran: Canopy

Papers Mentioning Canopy 41