cran: fastcluster | Projects | Ecosyste.ms: Papers

10.3389/fmolb.2020.570702

Prognostic Prediction Using a Stemness Index-Related Signature in a Cohort of Gastric Cancer
Cited by: 27
Author(s): Xiaowei Chen, Dawei Zhang, Fei Jiang, Yan Shen, Xin Li, Xin Hu, Pingmin Wei, Xiaobing Shen
Software Mentions: 24
Published: about 4 years ago

10.1186/s13072-016-0095-z

EpiMINE, a computational program for mining epigenomic data
Cited by: 11
Author(s): Sri Ganesh Jammula, Diego Pasini
Software Mentions: 23
Published: about 8 years ago

10.1038/s41598-020-78469-x

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Cited by: 14
Author(s): Jacob Cardenas, Uthra Balaji, Jin Gu
Software Mentions: 23
Published: almost 4 years ago

10.3390/genes11030257

mRNAsi Index: Machine Learning in Mining Lung Adenocarcinoma Stem Cell Biomarkers
Cited by: 61
Author(s): Yitong Zhang, Joseph T. Tseng, I-Chia Lien, Fenglan Li, Wei Wu, Hui Li
Software Mentions: 20
Published: over 4 years ago

10.1186/s12861-018-0163-7

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells
Cited by: 4
Author(s): Anna Mantsoki, Guillaume Devailly, Anagha Joshi
Software Mentions: 13
Published: over 6 years ago

10.1186/s12711-021-00614-5

Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs
Cited by: 8
Author(s): Fany Blanc, Tatiana Maroilley, Manuel Revilla, Gaëtan Lemonnier, Jean Jacques Leplat, Yvon Billon, Laure Ravon, Olivier Bouchez, Jean Pierre Bidanel, Bertrand Bed’Hom, Marie-Hélène Pinard-van Der Laan, Jordi Estellé, Claire Rogel‐Gaillard
Software Mentions: 10
Published: over 3 years ago

10.2196/24887

Clustering of Unhealthy Behaviors: Protocol for a Multiple Behavior Analysis of Data From the Canadian Longitudinal Study on Aging
Cited by: 2
Author(s): Zack van Allen, Simon L. Bacon, Paquito Bernard, Heather Brown, Sophie Desroches, Monika Kastner, Kim Lavoie, Marta M. Marques, Nicola McCleary, Sharon E. Straus, Taljaard Monica, Kednapa Thavorn, Jennifer R Tomasone, Justin Presseau
Software Mentions: 9
Published: over 3 years ago

10.3390/v12111268

VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses
Cited by: 242
Author(s): Cristina Moraru, Arvind Varsani, Andrew M. Kropinski
Software Mentions: 9
Published: almost 4 years ago

10.3389/fnbeh.2019.00036

Prolonged Bat Call Exposure Induces a Broad Transcriptional Response in the Male Fall Armyworm (Spodoptera frugiperda; Lepidoptera: Noctuidae) Brain
Cited by: 13
Author(s): Scott D Cinel, Steven J. Taylor
Software Mentions: 9
Published: over 5 years ago

10.3389/fpls.2018.01673

Genetic and Pathogenicity Diversity of Aphanomyces euteiches Populations From Pea-Growing Regions in France
Cited by: 19
Author(s): Anne Quillévéré‐Hamard, Gwenola Le Roy, Anne Moussart, Alain Baranger, Didier Andrivon, Marie‐Laure Pilet‐Nayel, Christophe Le May
Software Mentions: 9
Published: almost 6 years ago

10.7554/eLife.31035

Phenotype inference in an Escherichia coli strain panel
Cited by: 36
Author(s): Marco Galardini, Alexandra Koumoutsi, Lucía Herrera-Domínguez, Juan Antonio Cordero Varela, Anja Telzerow, Omar Wagih, Morgane Wartel, Olivier Clermont, Erick Denamur, Athanasios Typas, Pedro Beltrão
Software Mentions: 8
Published: almost 7 years ago

10.1111/eva.12935

The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors
Cited by: 9
Author(s): Brenna Callista Moreau Stanford, Danielle Jessica Clake, Matthew R. J. Morris, Sean M. Rogers
Software Mentions: 7
Published: over 4 years ago

10.7554/eLife.41627

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming
Cited by: 38
Author(s): Mirko Francesconi, Bruno Di Stefano, Clara Berenguer, Luísa de Andrés-Aguayo, Marcos Plana-Carmona, María Méndez-Lago, Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Marta Gut, Holger Heyn, Ben Liu, Thomas Graf
Software Mentions: 7
Published: over 5 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

10.1016/j.cell.2019.01.001

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Cited by: 956
Author(s): Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi, María Carmen Collado, Benjamin L. Rice, Casey DuLong, Xochitl C. Morgan, Christopher D. Golden, Christopher Quince, Curtis Huttenhower, Nicola Segata
Software Mentions: 6
Published: almost 6 years ago

10.3390/cancers12113457

Exploring the Role of Osteosarcoma-Derived Extracellular Vesicles in Pre-Metastatic Niche Formation and Metastasis in the 143-B Xenograft Mouse Osteosarcoma Model
Cited by: 19
Author(s): Alekhya Mazumdar, Joaquín Urdínez, Aleksandar Boro, Matthias Arlt, Fabian E. Egli, Barbara Niederöst, Patrick K. Jaeger, Greta Moschini, Roman Muff, Bruno Fuchs, Jess G. Snedeker, Ana Gvozdenovic
Software Mentions: 6
Published: almost 4 years ago

10.3390/nu13041340

Ileal Lactase Expression Associates with Lactase Persistence Genotypes
Cited by: 1
Author(s): Jan Krzysztof Nowak, Emilia Dybska, Marzena Dworacka, Natallia Tsikhan, Victoria Kononets, Saule Bermagambetova, Jarosław Walkowiak
Software Mentions: 6
Published: over 3 years ago

10.1093/ve/vez060

Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses
Cited by: 23
Author(s): Vincent Loiseau, Elisabeth A. Herniou, Yannis Moreau, Nicolas Lévêque, Carine Meignin, Laurent Daeffler, Brian A. Federici, Richard Cordaux, Clément Gilbert
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0222165

Advancing computational biology and bioinformatics research through open innovation competitions
Cited by: 5
Author(s): Andrea Blasco, Michael G. Endres, Rinat A. Sergeev, Anup Jonchhe, N. J. Maximilian Macaluso, Rajiv Narayan, Ted Natoli, Jin Hyun Paik, Bryan Briney, Chunlei Wu, Andrew I. Su, Aravind Subramanian, Karim R. Lakhani
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0105097

Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance
Cited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: about 10 years ago

10.1016/j.cmet.2018.07.005

A Role for p53 in the Adaptation to Glutamine Starvation through the Expression of SLC1A3
Cited by: 144
Author(s): Mylène Tajan, A. Höck, Julianna Blagih, Neil Robertson, Christiaan F. Labuschagne, Flore Kruiswijk, Timothy J. Humpton, Peter D. Adams, Karen H. Vousden
Software Mentions: 5
Published: about 6 years ago

10.7554/eLife.13546

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity
Cited by: 246
Author(s): Anjar Tri Wibowo, Claude Becker, G. Marconi, Julius Dürr, Jonathan Price, Jörg Hagmann, Ranjith Papareddy, Hadi Putra, Jorge Kageyama, Jörg Becker, Detlef Weigel, José Gutierrez-Marcos
Software Mentions: 5
Published: over 8 years ago

10.1186/s13321-014-0044-4

InCHlib – interactive cluster heatmap for web applications
Cited by: 45
Author(s): Ctibor Škuta, Petr Bartůněk, Daniel Svozil
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pcbi.1005711

Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock
Cited by: 16
Author(s): Wesley M. Botello‐Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jérôme J. Lacroix, Jijun Hao, Yang Luo
Software Mentions: 5
Published: about 7 years ago

10.1128/AAC.01207-19

Mechanism-of-Action Classification of Antibiotics by Global Transcriptome Profiling
Cited by: 50
Author(s): Aubrie O’Rourke, Sinem Beyhan, Yongwook Choi, Pavel Morales, Agnes P. Chan, Josh L. Espinoza, Chris L. Dupont, Kirsten J. Meyer, Amy L. Spoering, Kim Lewis, William C. Nierman, Karen E. Nelson
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-016-2524-6

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants
Cited by: 16
Author(s): Julie Ferreira de Carvalho, Carla Oplaat, Nikolaos Pappas, Martijn F.L. Derks, Dick de Ridder, Koen J. F. Verhoeven
Software Mentions: 4
Published: over 8 years ago

10.1155/2014/986048

Advanced Heat Map and Clustering Analysis Using Heatmap3
Cited by: 187
Author(s): Shilin Zhao, Yan Guo, Quanhu Sheng, Yu Shyr
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pntd.0008279

Fine-scale population genetic structure of dengue mosquito vector, Aedes aegypti, in Metropolitan Manila, Philippines
Cited by: 18
Author(s): Thaddeus M. Carvajal, Kohei Ogishi, Sakiko Yaegeshi, Lara Fides T. Hernandez, Katherine M. Viacrusis, Howell T. Ho, Divina Amalin, Kozo Watanabe
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2020.615922

Hazelnut Pollen Phenotyping Using Label-Free Impedance Flow Cytometry
Cited by: 9
Author(s): Lorenzo Ascari, V. Cristofori, Federico Macrì, Roberto Botta, Cristian Silvestri, Tommaso De Gregorio, Eloy Suarez Huerta, Marco Di Berardino, Silvan Kaufmann, Consolata Siniscalco
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.08419

CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling
Cited by: 93
Author(s): C. Keith Cassidy, Benjamin A. Himes, Frances Joan D. Alvarez, Jun Ma, Gongpu Zhao, Juan R. Perilla, Klaus Schulten, Peijun Zhang
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0238595

Shark discards in selective and mixed-species pelagic longline fisheries
Cited by: 7
Author(s): Gareth L. Jordaan, Jorge Santos, Johan C. Groeneveld
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0166460

Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models
Cited by: 17
Author(s): Edrisse Chermak, Renato De Donato, Marc F. Lensink, Andrea Petta, Luigi Serra, Vittorio Scarano, Luigi Cavallo, Romina Oliva
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-019-49313-8

Pseudomonas spp. are key players in agricultural biogas substrate degradation
Cited by: 23
Author(s): Christian Buettner, Martin von Bergen, Nico Jehmlich, Matthias Noll
Software Mentions: 2
Published: about 5 years ago

10.1186/s12859-020-03600-8

The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
Cited by: 7
Author(s): Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva
Software Mentions: 2
Published: about 4 years ago

10.3390/genes10110906

In-Silico Molecular Binding Prediction for Human Drug Targets Using Deep Neural Multi-Task Learning
Cited by: 26
Author(s): Kyoungyeul Lee, Dongsup Kim
Software Mentions: 2
Published: almost 5 years ago

10.2807/1560-7917.ES.2019.24.13.1800124

Clonal expansion of community-associated meticillin-resistant Staphylococcus aureus (MRSA) in people who inject drugs (PWID): prevalence, risk factors and molecular epidemiology, Bristol, United Kingdom, 2012 to 2017
Cited by: 12
Author(s): Simon Packer, Bruno Pichon, Stephen Thompson, Jane Neale, J. Njoroge, Rachel Kwiatkowska, Isabel Oliver, Maggie Telfer, Michel Doumith, Camillus Buunaaisie, Ellen Heinsbroek, Noreen Hopewell-Kelly, Monica Desai, Vivian Hope, Owen Martin Williams, Angela Kearns, Matthew Hickman, Maya Gobin
Software Mentions: 2
Published: over 5 years ago

Ecosyste.ms: Papers

Projects: cran: fastcluster

Papers Mentioning fastcluster 36