pypi: stats | Projects | Ecosyste.ms: Papers

10.3897/BDJ.9.e71378

Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank
Cited by: 2
Author(s): Reginald H.F. Young, Rekkab Gill, Daniel Gillis, Robert Hanner
Software Mentions: 11
Published: about 3 years ago

10.2196/jmir.9710

Internet-Based Cognitive Behavioral Therapy for Symptoms of Depression and Anxiety Among Patients With a Recent Myocardial Infarction: The U-CARE Heart Randomized Controlled Trial
Cited by: 66
Author(s): Fredrika Norlund, Emma Wallin, Erik Olsson, John Wallert, Gunilla Burell, Louise von Essén, Claes Held
Software Mentions: 11
Published: over 6 years ago

10.1186/s12918-018-0662-y

Integrating node embeddings and biological annotations for genes to predict disease-gene associations
Cited by: 27
Author(s): Sezin Kircali Ata, Le Ou-Yang, Yuan Fang, Chee-Keong Kwoh, Min Wu, Xiaoli Li
Software Mentions: 11
Published: almost 6 years ago

10.1186/s40168-020-00805-0

Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed
Cited by: 80
Author(s): Hyun Kim, Kiseok Keith Lee, Jongbum Jeon, William Harris, Yong-Hwan Lee
Software Mentions: 11
Published: almost 5 years ago

10.1038/s41598-020-60329-3

Neuroestrogen synthesis modifies neural representations of learned song without altering vocal imitation in developing songbirds
Cited by: 11
Author(s): Daniel M. Vahaba, Amelia Hecsh, Luke Remage‐Healey
Software Mentions: 11
Published: over 4 years ago

10.1371/journal.pntd.0009321

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature
Cited by: 15
Author(s): Camila Farias Amorim, Fernanda O. Novais, Ba Tiep Nguyen, Maurício T. Nascimento, Jamile Lago, Alexsandro S. Lago, Lucas P. Carvalho, Daniel P. Beiting, Phillip Scott
Software Mentions: 11
Published: over 3 years ago

10.1007/s11306-016-1090-x

Discovery of A-type procyanidin dimers in yellow raspberries by untargeted metabolomics and correlation based data analysis
Cited by: 6
Author(s): Elisabete Carvalho, Pietro Franceschi, Antje Feller, Lorena Herrera, L. Palmieri, Panagiotis Arapitsas, Samantha Riccadonna, Stefan Martens
Software Mentions: 11
Published: over 8 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago

10.1016/j.mex.2018.07.003

A practical method to control spatiotemporal confounding in environmental impact studies
Cited by: 4
Author(s): Rezvan Hatami
Software Mentions: 11
Published: almost 7 years ago

10.1186/s12862-021-01786-w

Phenology-mediated effects of phenotype on the probability of social polygyny and its fitness consequences in a migratory passerine
Cited by: 6
Author(s): David Cañal, Lotte Schlicht, Simone Santoro, Carlos Camacho, Jesús Martínez‐Padilla, Jaime Potti
Software Mentions: 11
Published: over 3 years ago

10.1128/mSystems.00316-20

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
Cited by: 8
Author(s): Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
Software Mentions: 11
Published: about 4 years ago

10.1186/s12935-021-01795-1

Identification and development of a novel invasion-related gene signature for prognosis prediction in colon adenocarcinoma
Cited by: 15
Author(s): Jiahua Liu, Chunhui Jiang, Chunjie Xu, Dongyang Wang, Ya Shen, Ye Liu, Lei Gu
Software Mentions: 11
Published: almost 4 years ago

10.1534/g3.120.401270

Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans’ Gene Expression Data
Cited by: 7
Author(s): Michael Cary, Katie Podshivalova, Cynthia Kenyon
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pone.0242331

Ocean warming affected faunal dynamics of benthic invertebrate assemblages across the Toarcian Oceanic Anoxic Event in the Iberian Basin (Spain)
Cited by: 4
Author(s): Veronica Piazza, Clemens V. Ullmann, Martin Aberhan
Software Mentions: 11
Published: almost 4 years ago

10.1002/ece3.6044

Variation of chemical compounds in wild Heliconiini reveals ecological factors involved in the evolution of chemical defenses in mimetic butterflies
Cited by: 21
Author(s): Ombeline Sculfort, Érika Cristina Pinheiro de Castro, Krzysztof M. Kozak, Søren Bak, Marianne Élias, Bastien Nay, Violaine Llaurens
Software Mentions: 11
Published: almost 5 years ago

10.1093/g3journal/jkab104

Strongyloides RNA-seq Browser: a web-based software platform for on-demand bioinformatics analyses of Strongyloides species
Cited by: 2
Author(s): Astra S. Bryant, Stephanie F. DeMarco, Elissa A. Hallem
Software Mentions: 11
Published: over 3 years ago

10.1042/BSR20210527

Construction of a prognostic model for non-small-cell lung cancer based on ferroptosis-related genes
Cited by: 10
Author(s): Ke Han, Jukun Wang, Kun Qian, Teng Zhao, Xingsheng Liu, Yi Zhang
Software Mentions: 11
Published: over 3 years ago

10.1186/s12859-017-1579-y

metaX: a flexible and comprehensive software for processing metabolomics data
Cited by: 402
Author(s): Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
Software Mentions: 11
Published: over 7 years ago

10.1186/s12859-018-2105-6

Building protein-protein interaction networks for Leishmania species through protein structural information
Cited by: 17
Author(s): Crhisllane Rafaele dos Santos Vasconcelos, Túlio de Lima Campos, Antônio Mauro Rezende
Software Mentions: 11
Published: over 6 years ago

10.3389/fonc.2021.626654

Identification of a Novel Four-Gene Signature Correlated With the Prognosis of Patients With Hepatocellular Carcinoma: A Comprehensive Analysis
Cited by: 7
Author(s): Weihua Zhu, Lixin Ru, Zhenchao Ma
Software Mentions: 11
Published: over 3 years ago

10.3389/fonc.2021.709077

Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis
Cited by: 57
Author(s): Anji Ju, Jintian Tang, Shuohua Chen, Yan Fu, Yongzhang Luo
Software Mentions: 11
Published: over 3 years ago

10.1093/bioinformatics/btv428

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
Cited by: 1,079
Author(s): Tal Galili
Software Mentions: 10
Published: over 9 years ago

10.1371/journal.pone.0190532

Space use by 4 strains of laying hens to perch, wing flap, dust bathe, stand and lie down
Cited by: 26
Author(s): Elizabeth R. Riddle, Ahmed B.A. Ali, Dennis Campbell, Janice M. Siegford
Software Mentions: 10
Published: almost 7 years ago

10.3389/fonc.2018.00659

The Role of COL5A2 in Patients With Muscle-Invasive Bladder Cancer: A Bioinformatics Analysis of Public Datasets Involving 787 Subjects and 29 Cell Lines
Cited by: 28
Author(s): Xiangyu Meng, Mingjun Shi, Zhao-Yi Zeng, Chen Chen, Tong-Zu Liu, Qiuji Wu, Shuo Li
Software Mentions: 10
Published: almost 6 years ago

10.1371/journal.pone.0228812

dLagM: An R package for distributed lag models and ARDL bounds testing
Cited by: 22
Author(s): Haydar Demirhan
Software Mentions: 10
Published: over 4 years ago

10.1038/s41598-021-91378-x

Barrier crossings and winds shape daily travel schedules and speeds of a flight generalist
Cited by: 5
Author(s): Lina López‐Ricaurte, Wouter M. G. Vansteelant, Jesús Hernández‐Pliego, Daniel García‐Silveira, Ana Bermejo-Bermejo, Susana Casado, Jacopo G. Cecere, Javier de la Puente, Fernando Garcés‐Toledano, Juan Martínez‐Dalmau, Alfredo Ortega, Beatriz Rodríguez‐Moreno, Diego Rubolini, Maurizio Sarà, Javier Bustamante
Software Mentions: 10
Published: over 3 years ago

10.3389/fmolb.2021.692530

Ferroptosis-Related Gene Signature and Patterns of Immune Infiltration Predict the Overall Survival in Patients With Lung Adenocarcinoma
Cited by: 5
Author(s): Yuxuan Wang, Weikang Chen, Minqi Zhu, Lei Xian
Software Mentions: 10
Published: over 3 years ago

10.3389/fnagi.2018.00144

Differentiating Patients at the Memory Clinic With Simple Reaction Time Variables: A Predictive Modeling Approach Using Support Vector Machines and Bayesian Optimization
Cited by: 9
Author(s): John Wallert, Eric Westman, Johnny Ulinder, Mathilde Annerstedt, Beata Terzis, Urban Ekman
Software Mentions: 10
Published: over 6 years ago

10.1186/s12864-019-6181-4

Dynamic transcriptome sequencing and analysis during early development in the bighead carp (Hypophthalmichthys nobilis)
Cited by: 12
Author(s): Jianjun Fu, Wenbin Zhu, Lanmei Wang, Ming Luo, Fei Song, Zaijie Dong
Software Mentions: 10
Published: about 5 years ago

10.1371/journal.pgen.1003209

Centromere-Like Regions in the Budding Yeast Genome
Cited by: 36
Author(s): Philippe Lefrançois, Raymond K. Auerbach, Christopher M. Yellman, G. Shirleen Roeder, M Snyder
Software Mentions: 10
Published: almost 12 years ago

10.1038/s41598-021-88702-w

Shorter headed dogs, visually cooperative breeds, younger and playful dogs form eye contact faster with an unfamiliar human
Cited by: 23
Author(s): Zsófia Bognár, Dóra Szabó, Alexandra Deés, Enikő Kubinyi
Software Mentions: 10
Published: over 3 years ago

10.1371/journal.pcbi.1007803

Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE
Cited by: 9
Author(s): Lisa-Katrin Turnhoff, Ali Hadizadeh Esfahani, Andreas Schuppert
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pgen.1008458

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Cited by: 23
Author(s): Jessica A. Lee, Siavash Riazi, Shahla Nemati, Jannell V. Bazurto, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
Software Mentions: 10
Published: about 5 years ago

10.1186/s42523-020-00039-3

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata
Cited by: 20
Author(s): H. Pieter J. van Veelen, Joana Falcão Salles, Kevin D. Matson, Marco van der Velde, B. Irene Tieleman
Software Mentions: 10
Published: over 4 years ago

10.1186/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 3 years ago

10.1186/s13059-020-02245-3

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts
Cited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 10
Published: almost 4 years ago

10.1242/dev.169474

An integrated transcriptional analysis of the developing human retina
Cited by: 67
Author(s): Carla Mellough, R. Bauer, Joseph Collin, Birthe Dorgau, Darin Zerti, David Dolan, Carl M. Jones, Osagie Izuogu, Min Yu, Dean Hallam, Jannetta S. Steyn, Kathryn White, David Steel, Mauro Santibanez‐Koref, David Elliott, Michael S. Jackson, Susan Lindsay, Sushma Nagaraja Grellscheid, Majlinda Lako
Software Mentions: 10
Published: almost 6 years ago

10.18632/aging.202174

Periodontitis in elderly patients with type 2 diabetes mellitus: impact on gut microbiota and systemic inflammation
Cited by: 18
Author(s): Jinyou Li, Haifeng Lü, Hengchao Wu, Shunmei Huang, Lufang Chen, Qifeng Gui, Wenjing Zhou, Yichen Yang, Yue Wu, Hua Zhang, Qin Zhang, Yunmei Yang
Software Mentions: 10
Published: almost 4 years ago

10.1186/s40246-019-0226-2

Size matters: how sample size affects the reproducibility and specificity of gene set analysis
Cited by: 28
Author(s): Farhad Maleki, Katie Ovens, Ian McQuillan, Anthony Kusalik
Software Mentions: 10
Published: about 5 years ago

10.3389/fpls.2020.00136

The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato
Cited by: 17
Author(s): Araceli Lamelas, Damaris Desgarennes, Daniel López-Lima, Luc Villain, Alexandro Alonso-Sánchez, Alejandro Artacho, Amparo Latorre, Andrés Moya, Gloria Carrión
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pone.0215142

Mathematical modeling for the prediction of cerebral white matter lesions based on clinical examination data
Cited by: 7
Author(s): Yuya Shinkawa, Takashi Yoshida, Yohei Onaka, Makoto Ichinose, Kazuo Ishii
Software Mentions: 10
Published: over 5 years ago

10.1128/mSystems.00541-20

Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinis
Cited by: 17
Author(s): Luis A. Ibarra-Juárez, Maureen Burton, Peter H. W. Biedermann, Luisa F. Cruz, Damaris Desgarennes, Enrique Ibarra-Laclette, Amparo Latorre, Alexandro Alonso-Sánchez, Emanuel Villafán, Greta Hanako-Rosas, Loredana Lopez, Mirna Vázquez-Rosas-Landa, Gloria Carrión, Daniel Carrillo, Andrés Moya, Araceli Lamelas
Software Mentions: 10
Published: about 4 years ago

10.1002/embj.201386825

Key regulators control distinct transcriptional programmes in blood progenitor and mast cells
Cited by: 48
Author(s): Fernando J. Calero-Nieto, Felicia Ng, Nicola K. Wilson, Rebecca Hannah, Victoria Moignard, Ana Leal-Cervantes, Isabel Jimenez-Madrid, Evangelia Diamanti, Lorenz Wernisch, Berthold Göttgens
Software Mentions: 10
Published: over 10 years ago

10.3389/fonc.2020.526577

Patient Stratification of Clear Cell Renal Cell Carcinoma Using the Global Transcription Factor Activity Landscape Derived From RNA-Seq Data
Cited by: 7
Author(s): Yanyan Zhu, Shundong Cang, Bowang Chen, Ye Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
Software Mentions: 10
Published: almost 4 years ago

10.15252/msb.20209522

Neural G0: a quiescent‐like state found in neuroepithelial‐derived cells and glioma
Cited by: 19
Author(s): Samantha O'Connor, Heather Feldman, Sonali Arora, Pia Hoellerbauer, Chad M. Toledo, Philip Corrin, Lucas Carter, Megan Kufeld, Hamid Bolouri, Ryan Basom, Jeffrey J. Delrow, José L. McFaline-Figueroa, Cole Trapnell, Steven M. Pollard, Anoop P. Patel, Patrick J. Paddison, Christopher Plaisier
Software Mentions: 10
Published: over 3 years ago

10.1128/mSphere.00334-20

Extreme Viral Partitioning in a Marine-Derived High Arctic Lake
Cited by: 13
Author(s): Myriam Labbé, Catherine Girard, Warwick F. Vincent, Alexander I. Culley
Software Mentions: 10
Published: over 4 years ago

10.7717/peerj.11903

Taxonomic and functional diversity of benthic macrofauna associated with rhodolith beds in SE Brazil
Cited by: 10
Author(s): Patricia Sarcinelli Stelzer, Ana Carolina de Azevedo Mazzuco, L.E. de O. Gomes, João Luiz Martins, Sérgio A. Netto, Ângelo F. Bernardino
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2021.657508

Land-Use System and Forest Floor Explain Prokaryotic Metacommunity Structuring and Spatial Turnover in Amazonian Forest-to-Pasture Conversion Areas
Cited by: 3
Author(s): Fernando Igne Rocha, Thiago Gonçalves Ribeiro, Marcelo Antoniol Fontes, Stefan Schwab, Márcia Reed Rodrigues Coelho, J. F. Lumbreras, P. E. F. da Motta, W. G. Teixeira, James R. Cole, Ana Carolina Borsanelli, Iveraldo S. Dutra, Adina Howe, Aline Pacobahyba de Oliveira, Ederson da Conceição Jesus
Software Mentions: 10
Published: over 3 years ago

10.3389/fmicb.2020.01190

Genetic Organization of the aprX-lipA2 Operon Affects the Proteolytic Potential of Pseudomonas Species in Milk
Cited by: 14
Author(s): Christopher Maier, Christopher Huptas, Mario von Neubeck, Stephen W. Scherer, Mareike Wenning, Genia Lücking
Software Mentions: 10
Published: over 4 years ago

10.7554/eLife.65088

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Cited by: 604
Author(s): Francesco Beghini, Lauren J. McIver, Aitor Blanco-Míguez, Léonard Dubois, Francesco Asnicar, Sagun Maharjan, Ana Mailyan, Paolo Manghi, Matthias Scholz, Andrew Maltez Thomas, Mireia Vallès-Colomer, George Weingart, Yancong Zhang, Moreno Zolfo, Curtis Huttenhower, Eric A. Franzosa, Nicola Segata
Software Mentions: 10
Published: over 3 years ago

10.1038/s41598-019-48986-5

Assessing Susceptibility of Debris Flow in Southwest China Using Gradient Boosting Machine
Cited by: 36
Author(s): Baofeng Di, Hanyue Zhang, Yongyao Liu, Jierui Li, Ningsheng Chen, Constantine A. Stamatopoulos, Yuzhou Luo, Yu Zhan
Software Mentions: 10
Published: about 5 years ago

10.7717/peerj.7907

motoRneuron: an open-source R toolbox for time-domain motor unit analyses
Cited by: 0
Author(s): Andrew J. Tweedell, Matthew S. Tenan
Software Mentions: 10
Published: almost 5 years ago

10.1111/jcmm.16619

Systematic profiling of invasion‐related gene signature predicts prognostic features of lung adenocarcinoma
Cited by: 17
Author(s): Ping Yu, L. Tong, Yujia Song, Hui Qü, Ying Chen
Software Mentions: 10
Published: over 3 years ago

10.1038/s42003-021-02137-7

The lexicon of antimicrobial peptides: a complete set of arginine and tryptophan sequences
Cited by: 33
Author(s): Sam Clark, Thomas A. Jowitt, Lynda K. Harris, Christopher G. Knight, Curtis B. Dobson
Software Mentions: 10
Published: over 3 years ago

10.7554/eLife.18683

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development
Cited by: 185
Author(s): Felipe Mora‐Bermúdez, Farhath Badsha, Sabina Kanton, J. Gray Camp, Benjamin Vernot, Kathrin Köhler, Birger Voigt, Keisuke Okita, Tomislav Maričić, Zhisong He, Robert Lachmann, Svante Pääbo, Barbara Treutlein, Wieland B. Huttner
Software Mentions: 10
Published: about 8 years ago

10.1371/journal.pbio.2004045

A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates
Cited by: 41
Author(s): Jean-Louis Plouhinec, Sofía Medina-Ruíz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael B. Eisen, Richard M. Harland, Anne H. Monsoro-Burq
Software Mentions: 9
Published: about 7 years ago

10.1186/s13073-021-00902-1

Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer
Cited by: 16
Author(s): Corinna Keup, Vinay Suryaprakash, Siegfried Hauch, Markus Storbeck, Peter F. Hahn, Markus Sprenger-Haussels, Hans‐Christian Kolberg, Mitra Tewes, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir‐Bauer
Software Mentions: 9
Published: over 3 years ago

10.3389/fgene.2020.00817

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure
Cited by: 17
Author(s): Júber Herrera-Uribe, Haibo Li, Kristen A Byrne, Zahra F Bond, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0224186

Studying global processing in autism and attention-deficit/hyperactivity disorder with gaze movements: The example of a copying task
Cited by: 2
Author(s): Divya Seernani, Chara Ioannou, K. Damania, Kurt P. Spindler, Holger Hill, Tom Foulsham, Nikolaos Smyrnis, Stephan Bender, Christian Fleischhaker, Monica Biscaldi, Ulrich W. Ebner‐Priemer, Christoph Klein
Software Mentions: 9
Published: over 4 years ago

10.3390/jcm10194354

Application of an Exploratory Knowledge-Discovery Pipeline Based on Machine Learning to Multi-Scale OMICS Data to Characterise Myocardial Injury in a Cohort of Patients with Septic Shock: An Observational Study
Cited by: 3
Author(s): Bernardo Bollen Pinto, Vicent Ribas Ripoll, Paula Subías-Beltrán, Antoine Herpain, Cristina Barlassina, Eliandre de Oliveira, Roberta Pastorelli, Daniele Braga, Matteo Barcella, Laia Subirats, Julia Bauzá‐Martinez, Antonia Odena, Manuela Ferrario, Giuseppe Baselli, Federico Aletti, Karim Bendjelid
Software Mentions: 9
Published: about 3 years ago

10.1038/s41598-017-07880-8

Global mapping of miRNA-target interactions in cattle (Bos taurus)
Cited by: 19
Author(s): Troels K. H. Scheel, Michael J. Moore, Joseph M. Luna, Eiko Nishiuchi, John Fak, Robert B. Darnell, Charles M. Rice
Software Mentions: 9
Published: over 7 years ago

10.3390/cancers13040722

Prognostic and Predictive Value of Integrated Qualitative and Quantitative Magnetic Resonance Imaging Analysis in Glioblastoma
Cited by: 19
Author(s): Maikel Verduin, Sergey Primakov, Inge Compter, Henry C. Woodruff, Sander M. J. van Kuijk, Bram Ramaekers, Maarten te Dorsthorst, Elles G. M. Revenich, Mark ter Laan, Sjoert Pegge, Frederick J. A. Meijer, Jan Beckervordersandforth, Ernst-Jan M. Speel, Benno Küsters, Wendy W.J. de Leng, Monique M. Anten, Martijn P. G. Broen, Linda Ackermans, Olaf Schijns, Onno P.M. Teernstra, Koos E. Hovinga, Marc Vooijs, Vivianne C. G. Tjan‐Heijnen, Daniëlle Eekers, Alida A. Postma, Ann Hoeben
Software Mentions: 9
Published: almost 4 years ago

10.1016/j.celrep.2019.01.041

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types
Cited by: 510
Author(s): Gianni Monaco, Bernett Lee, Weili Xu, Seri Mustafah, You Yi Hwang, Christophe Carré, Nicolas Burdin, Lucian Visan, Michele Ceccarelli, Michael Poidinger, Alfred Zippelius, João Pedro de Magalhães, Anis Larbi
Software Mentions: 9
Published: almost 6 years ago

10.1038/s41437-018-0059-0

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Cited by: 46
Author(s): Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
Software Mentions: 9
Published: almost 7 years ago

10.3389/fmicb.2018.02711

Land-Use Intensity Rather Than Plant Functional Identity Shapes Bacterial and Fungal Rhizosphere Communities
Cited by: 45
Author(s): Ricardo Schöps, Kezia Goldmann, Katharina Herz, Guillaume Lentendu, Ingo Schöning, Helge Bruelheide, Tesfaye Wubet, François Buscot
Software Mentions: 9
Published: about 6 years ago

10.3389/fmicb.2018.01323

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish
Cited by: 37
Author(s): Dylan Dahan, Brooke A. Jude, Regina Lamendella, Felicia Keesing, Gabriel G. Perron
Software Mentions: 9
Published: over 6 years ago

10.1186/s13073-020-00731-8

Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy
Cited by: 28
Author(s): Anna Reustle, Moreno Di Marco, Carolin Meyerhoff, Annika Nelde, Juliane S. Walz, Stefan Winter, Siahei Kandabarau, Florian Büttner, Mathias Haag, Linus Backert, Daniel J. Kowalewski, Steffen Rausch, Jörg Hennenlotter, Viktoria Stühler, Marcus Scharpf, Falko Fend, Arnulf Stenzl, Hans‐Georg Rammensee, Jens Bedke, Stefan Stevanović, Matthias Schwab, Elke Schaeffeler
Software Mentions: 9
Published: over 4 years ago

10.2196/10076

Key Elements of mHealth Interventions to Successfully Increase Physical Activity: Meta-Regression
Cited by: 56
Author(s): Lisa V. Eckerstorfer, Norbert K. Tanzer, Claudia Vogrincic-Haselbacher, Gayannée Kedia, Hilmar Brohmer, Isabelle Dinslaken, Katja Corcoran
Software Mentions: 9
Published: about 6 years ago

10.1371/journal.pone.0240462

The origins of money: Calculation of similarity indexes demonstrates the earliest development of commodity money in prehistoric Central Europe
Cited by: 11
Author(s): Maikel H.G. Kuijpers, Cătălin Nicolae Popa
Software Mentions: 9
Published: almost 4 years ago

10.3389/fmicb.2021.616956

Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean
Cited by: 9
Author(s): Liuyang Li, Laxman Pujari, Chao Wu, Dongyang Huang, Yuqiu Wei, Congcong Guo, Guicheng Zhang, Wenzhe Xu, Haijiao Liu, Xingzhou Wang, Min Wang, Jun Sun
Software Mentions: 9
Published: over 3 years ago

10.3390/cancers12051076

Tumor-Infiltrating CD8 T Cells Predict Clinical Breast Cancer Outcomes in Young Women
Cited by: 31
Author(s): Yong Won Jin, Pingzhao Hu
Software Mentions: 9
Published: over 4 years ago

10.1093/gigascience/giy083

Clustering trees: a visualization for evaluating clusterings at multiple resolutions
Cited by: 353
Author(s): Luke Zappia, Alicia Oshlack
Software Mentions: 9
Published: over 6 years ago

10.3389/fgene.2021.661988

Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma
Cited by: 12
Author(s): Xingte Chen, Lei Wang, Liang Hong, Zhiying Su, Xiaohong Zhong, Han Zhou, Xueqing Zhang, Junxin Wang, Lingdong Shao
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pbio.3001276

Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae
Cited by: 37
Author(s): Matthieu Haudiquet, Amandine Nucci, Olaya Rendueles, Eduardo P. C. Rocha
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0179337

The acoustic repertoire and behavioural context of the vocalisations of a nocturnal dasyurid, the eastern quoll (Dasyurus viverrinus)
Cited by: 5
Author(s): Annalie Dorph, Paul G. McDonald
Software Mentions: 9
Published: over 7 years ago

10.3390/microorganisms8010038

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota
Cited by: 13
Author(s): Matteo Chialva, Stefano Ghignone, Mara Novero, Wael N. Hozzein, Luisa Lanfranco, Paola Bonfante
Software Mentions: 9
Published: almost 5 years ago

10.1371/journal.pone.0203247

Determination of essential phenotypic elements of clusters in high-dimensional entities—DEPECHE
Cited by: 9
Author(s): Axel Theorell, Yenan T. Bryceson, Jakob Theorell
Software Mentions: 9
Published: over 5 years ago

10.3389/fonc.2021.698856

A Novel Ferroptosis-Related Gene Model for Overall Survival Predictions of Bladder Urothelial Carcinoma Patients
Cited by: 9
Author(s): Min Zhang, Xin Zhang, Minghang Yu, Wei Zhang, Di Zhang, Song Zeng, Xi Wang, Xiaosong Hu
Software Mentions: 9
Published: over 3 years ago

10.3390/microorganisms9091814

Presence of Human Pathogens of the Borrelia burgdorferi sensu lato Complex Shifts the Sequence Read Abundances of Tick Microbiomes in Two German Locations
Cited by: 7
Author(s): Angeline Hoffmann, Thomas Müller, Volker Fingerle, Matthias Noll
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0084227

Automatic Context-Specific Subnetwork Discovery from Large Interaction Networks
Cited by: 10
Author(s): Ashis Saha, Aik Choon Tan, Jaewoo Kang
Software Mentions: 9
Published: almost 11 years ago

10.1186/1471-2105-16-S6-S3

Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins
Cited by: 42
Author(s): Hossam M. Ashtawy, Nihar R. Mahapatra
Software Mentions: 9
Published: over 9 years ago

10.1038/s41598-021-89496-7

Erosion of tropical bird diversity over a century is influenced by abundance, diet and subtle climatic tolerances
Cited by: 12
Author(s): Jenna R. Curtis, W. Douglas Robinson, Ghislain Rompré, Randall P. Moore, Bruce McCune
Software Mentions: 9
Published: over 3 years ago

10.3389/fninf.2021.561689

QDECR: A Flexible, Extensible Vertex-Wise Analysis Framework in R
Cited by: 13
Author(s): Sander Lamballais, Ryan L. Muetzel
Software Mentions: 9
Published: over 3 years ago

10.1186/s13040-016-0086-4

Prediction of donor splice sites using random forest with a new sequence encoding approach
Cited by: 31
Author(s): Prabina Kumar Meher, Tanmaya Kumar Sahu, Atmakuri Ramakrishna Rao
Software Mentions: 9
Published: almost 9 years ago

10.1186/s40168-018-0535-z

High-resolution ISR amplicon sequencing reveals personalized oral microbiome
Cited by: 30
Author(s): Chiranjit Mukherjee, Clifford J. Beall, Ann L. Griffen, Eugene J. Leys
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-021-96095-z

Cell survival and DNA damage repair are promoted in the human blood thanatotranscriptome shortly after death
Cited by: 1
Author(s): Laura G. Antiga, Lode Sibbens, Yasmina Abakkouy, Ronny Decorte, Wouter Van Den Bogaert, Wim Van de Voorde
Software Mentions: 9
Published: over 3 years ago

10.1038/s41598-020-74691-9

Integration of geoscience frameworks into digital pathology analysis permits quantification of microarchitectural relationships in histological landscapes
Cited by: 4
Author(s): Timothy J. Kendall, Catherine Mary Duff, A. D. Thomson, John P. Iredale
Software Mentions: 9
Published: about 4 years ago

10.1038/s41598-020-71521-w

Direct formalin fixation induces widespread transcriptomic effects in archival tissue samples
Cited by: 9
Author(s): Leah C. Wehmas, Susan Hester, Charles E. Wood
Software Mentions: 9
Published: about 4 years ago

10.1038/s41598-020-74647-z

Passive acoustic listening stations (PALS) show rapid onset of ecological effects of harmful algal blooms in real time
Cited by: 9
Author(s): Athena M. Rycyk, Reny B. Tyson Moore, Randall S. Wells, Katherine McHugh, Elizabeth J. Berens McCabe, David A. Mann
Software Mentions: 9
Published: about 4 years ago

10.26508/lsa.202000658

Predicting gene regulatory networks from cell atlases
Cited by: 7
Author(s): Andreas Fønss Møller, Kedar Nath Natarajan
Software Mentions: 9
Published: about 4 years ago

10.1093/aobpla/plab016

Divergence of stem biomechanics and hydraulics between Bauhinia lianas and trees
Cited by: 6
Author(s): Xiangwu Yan, Yu Song, Fu-Chuan Wu, Shubin Zhang, Jiao‐Lin Zhang
Software Mentions: 9
Published: over 3 years ago

10.1186/s12870-019-1679-0

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
Cited by: 34
Author(s): Alejandro Sanz-Carbonell, Maria Carmen Marqués, Alexander Bustamante, Mario A. Fares, Guillermo Rodrigo, Gustavo Gómez
Software Mentions: 9
Published: almost 6 years ago

10.1038/srep40950

Unique Bacteria Community Composition and Co-occurrence in the Milk of Different Ruminants
Cited by: 21
Author(s): Zhipeng Li, André‐Denis G. Wright, Yumei Yang, Huazhe Si, Guangyu Li
Software Mentions: 9
Published: almost 8 years ago

10.1186/s12885-021-08745-0

A case-control study of a combination of single nucleotide polymorphisms and clinical parameters to predict clinically relevant toxicity associated with fluoropyrimidine and platinum-based chemotherapy in gastric cancer
Cited by: 5
Author(s): Miguel Córdova-Delgado, María Loreto Bravo, E Cumsille, Catherine M. Hill, Matías Muñoz-Medel, Mauricio P. Pinto, Ignacio N. Retamal, María A Lavanderos, Juan Francisco Miquel, María Rodríguez-Fernández, Yuwei Liao, Chi Kong Li, Alejandro Corvalán, Ricardo Armisén, Marcelo Garrido, Luis A. Quiñones, Gareth I. Owen
Software Mentions: 9
Published: about 3 years ago

10.1093/femsec/fiab097

Host species shape the community structure of culturable endophytes in fruits of wild berry species (Vaccinium myrtillus L., Empetrum nigrum L. and Vaccinium vitis-idaea L.)
Cited by: 9
Author(s): Minh-Phuong Nguyen, Kaisa Lehosmaa, Françoise Martz, Janne J. Koskimäki, Anna Maria Pirttilä, Hely Häggman
Software Mentions: 9
Published: over 3 years ago

10.1002/ece3.6335

High dispersal capacity and biogeographic breaks shape the genetic diversity of a globally distributed reef‐dwelling calcifier
Cited by: 16
Author(s): Martina Prazeres, Raphaël Morard, Thomas E. Roberts, Steve S. Doo, Jamaluddin Jompa, Christiane Schmidt, Marleen Stuhr, Willem Renema, Michal Kučera
Software Mentions: 9
Published: over 4 years ago

10.1002/ece3.6190

Friend or foe? A parasitic wasp shifts the cost/benefit ratio in a nursery pollination system impacting plant fitness
Cited by: 2
Author(s): Carmen Villacañas de Castro, Thomas S. Hoffmeister
Software Mentions: 9
Published: over 4 years ago

10.18632/aging.203379

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues
Cited by: 8
Author(s): Margarida Ferreira, Stephany Francisco, Ana Raquel Soares, Ana Nobre, Miguel Pinheiro, Andreia Reis, Sonya Neto, Ana João Rodrigues, Nuno Sousa, Gabriela Moura, Manuel A. S. Santos
Software Mentions: 9
Published: over 3 years ago

10.1155/2021/6657397

Identifying Stage II Colorectal Cancer Recurrence Associated Genes by Microarray Meta-Analysis and Building Predictive Models with Machine Learning Algorithms
Cited by: 2
Author(s): Wei Lu, Xiang Pan, Siqi Dai, Dongliang Fu, Maxwell Hwang, Yaowu Zhu, Lina Zhang, Jingsun Wei, Xianglong Kong, Jun Li, Qian Xiao, Kefeng Ding
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12915-020-00908-y

First evidence of convergent lifestyle signal in reptile skull roof microanatomy
Cited by: 11
Author(s): Roy Ebel, Johannes Müller, Till Ramm, Christy A. Hipsley, Eli Amson
Software Mentions: 9
Published: almost 4 years ago

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