cran: tidyverse | Projects | Ecosyste.ms: Papers

10.1038/s41598-020-76683-1

Revisiting potential associations between brain morphology, fear acquisition and extinction through new data and a literature review
Cited by: 7
Author(s): Mana R. Ehlers, Janne Nold, Manuel Kuhn, Maren Klingelhöfer-Jens, Tina B. Lonsdorf
Software Mentions: 44
Published: about 4 years ago

10.12688/f1000research.22259.1

Fluent genomics with plyranges and tximeta
Cited by: 2
Author(s): Stuart Lee, Michael C. Lawrence, Michael I. Love
Software Mentions: 35
Published: almost 5 years ago

10.1038/s41598-019-54004-5

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
Cited by: 61
Author(s): Arun Gonzales Decano, Tim Downing
Software Mentions: 30
Published: almost 5 years ago

10.15252/msb.20209539

Predictive features of gene expression variation reveal mechanistic link with differential expression
Cited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago

10.3390/ani9070417

Talking to Dogs: Companion Animal-Directed Speech in a Stress Test
Cited by: 9
Author(s): Raffaela Lesch, Kurt Kotrschal, Iris Schöberl, Andrea Beetz, Judith Solomon, W. Tecumseh Fitch
Software Mentions: 25
Published: over 5 years ago

10.1038/s41598-021-96198-7

Cross-modal auditory priors drive the perception of bistable visual stimuli with reliable differences between individuals
Cited by: 2
Author(s): Zsófia Pálffy, Kinga Farkas, Gábor Csukly, Szabolcs Kéri, Bertalan Polner
Software Mentions: 25
Published: over 3 years ago

10.1038/s41598-020-74015-x

Rural–urban scaling of age, mortality, crime and property reveals a loss of expected self-similar behaviour
Cited by: 7
Author(s): Jack Sutton, Golnaz Shahtahmassebi, Haroldo V. Ribeiro, Quentin S. Hanley
Software Mentions: 24
Published: about 4 years ago

10.3389/fimmu.2021.659444

Development and Validation of a CD8+ T Cell Infiltration-Related Signature for Melanoma Patients
Cited by: 13
Author(s): Yuan Yuan, Zheng Zhu, Ying Lan, Saili Duan, Zijue Zhu, Xi Zhang, Guoyin Li, Hui Qü, Yao Feng, Hui Cai, Zewen Song
Software Mentions: 24
Published: over 3 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

10.3389/fimmu.2021.701085

A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients
Cited by: 29
Author(s): Florian Bieberich, Rodrigo Vazquez-Lombardi, Alexander Yermanos, Roy Ehling, Derek M Mason, Bastian Wagner, Edo Kapetanovic, Raphaël Brisset Di Roberto, Cédric R. Weber, Miodrag Savic, Fabian Rudolf, Sai T. Reddy
Software Mentions: 23
Published: over 3 years ago

10.1093/molbev/msaa288

Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes
Cited by: 6
Author(s): Tina Begum, Marc Robinson‐Rechavi
Software Mentions: 22
Published: about 4 years ago

10.1038/s41421-020-00226-1

Patient-derived SARS-CoV-2 mutations impact viral replication dynamics and infectivity in vitro and with clinical implications in vivo
Cited by: 68
Author(s): Hang‐Ping Yao, Xiangyun Lu, Qiong Chen, Kaijin Xu, Yu Chen, Ming-Hui Cheng, Keda Chen, Linfang Cheng, Tian-Hao Weng, Danrong Shi, Fumin Liu, Zhigang Wu, Mingjie Xie, Haibo Wu, Changzhong Jin, Min Zheng, Nanping Wu, Chao Jiang, Lanjuan Li
Software Mentions: 21
Published: about 4 years ago

10.3389/fpls.2017.00623

A Practical Guide to Visualization and Statistical Analysis of R. solanacearum Infection Data Using R
Cited by: 25
Author(s): Niklas Schandry
Software Mentions: 21
Published: over 7 years ago

10.1186/s13071-021-04851-x

Data-driven and interpretable machine-learning modeling to explore the fine-scale environmental determinants of malaria vectors biting rates in rural Burkina Faso
Cited by: 9
Author(s): Paul Taconet, Angélique Porciani, Dieudonné Diloma Soma, Karine Mouline, Frédéric Simard, Alphonsine A. Koffi, Cédric Pennetier, Roch K. Dabiré, Morgan Mangeas, Nicolas Moiroux
Software Mentions: 21
Published: over 3 years ago

10.1016/j.xcrm.2020.100096

Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago

10.3389/fimmu.2021.632333

Immunological Feature and Transcriptional Signaling of Ly6C Monocyte Subsets From Transcriptome Analysis in Control and Hyperhomocysteinemic Mice
Cited by: 7
Author(s): Panpan Yang, Lu Liu, Lili Sun, Fang Pu, Nathaniel W. Snyder, Jason Saredy, Yong Ji, Wen Shen, Xuebin Qin, Qinghua Wu, Xiaofeng Yang, Hong Wang
Software Mentions: 21
Published: over 3 years ago

10.15252/msb.20199247

<scp>STAT</scp> 3 ‐dependent analysis reveals <scp>PDK</scp> 4 as independent predictor of recurrence in prostate cancer
Cited by: 34
Author(s): Monika Oberhuber, Matteo Pecoraro, Mate Rusz, Georg Oberhuber, Maritta Wieselberg, Peter Haslinger, Elisabeth Gurnhofer, Michaela Schlederer, Tanja Limberger, Sabine Lagger, Jan Pěnčík, Petra Kodajova, Sandra Högler, Georg Stockmaier, Sandra Grund-Gröschke, Fritz Aberger, Marco Bolis, Jean-Philippe Theurillat, Robert Wiebringhaus, Theresa R. Weiss, Andrea Haitel, Marc Brehme, Wolfgang Wadsak, Johannes Griss, Thomas Mohr, Alexandra Hofer, Anton Jäger, Jürgen Pollheimer, Gerda Egger, Gunda Koellensperger, Matthias Mann, Brigitte Hantusch, Lukas Kenner
Software Mentions: 21
Published: over 4 years ago

10.1016/j.xcrm.2020.100128

The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer
Cited by: 32
Author(s): Derek J. Essegian, Rimpi Khurana, Vasileios Stathias, Stephan C. Schürer
Software Mentions: 21
Published: about 4 years ago

10.12688/f1000research.18456.1

A step-by-step guide to analyzing CAGE data using R/Bioconductor
Cited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago

10.1155/2020/5418364

A Nomogram Based on Radiomics with Mammography Texture Analysis for the Prognostic Prediction in Patients with Triple-Negative Breast Cancer
Cited by: 9
Author(s): Xian Jiang, Xiuhe Zou, Jing Sun, Aiping Zheng, Chao Su
Software Mentions: 20
Published: about 4 years ago

10.1016/j.cub.2020.12.047

A sex-specific switch between visual and olfactory inputs underlies adaptive sex differences in behavior
Cited by: 32
Author(s): Tetsuya Nojima, Annika Rings, Annette D. Allen, Nils Otto, Thomas A. Verschut, Jean‐Christophe Billeter, Megan C Neville, Stephen F. Goodwin
Software Mentions: 19
Published: over 3 years ago

10.1155/2021/6613151

Genomic and Transcriptome Analysis to Identify the Role of the mTOR Pathway in Kidney Renal Clear Cell Carcinoma and Its Potential Therapeutic Significance
Cited by: 6
Author(s): Xiangyu Che, Xiaochen Qi, Yingkun Xu, Qifei Wang, Guangzhen Wu
Software Mentions: 19
Published: over 3 years ago

10.1186/s12866-021-02282-3

Associations between the gut microbiome and metabolome in early life
Cited by: 14
Author(s): Quang P. Nguyen, Margaret R. Karagas, Juliette C. Madan, Erika Dade, Thomas J. Palys, Hilary G. Morrison, Wimal Pathmasiri, Susan McRitche, Susan Sumner, H. Robert Frost, Anne G. Hoen
Software Mentions: 19
Published: about 3 years ago

10.1093/molbev/msaa311

A Two-Locus System with Strong Epistasis Underlies Rapid Parasite-Mediated Evolution of Host Resistance
Cited by: 15
Author(s): Camille Ameline, Yann Bourgeois, Felix Vögtli, Eevi Savola, Jason P. Andras, Jan Engelstädter, Dieter Ebert
Software Mentions: 19
Published: almost 4 years ago

10.1007/s10734-020-00674-4

Lights, camera, active! appreciation of active learning predicts positive attitudes towards lecture capture
Cited by: 6
Author(s): Emily Nordmann, Anne L. Clark, Elliott Spaeth, Jill R D MacKay
Software Mentions: 18
Published: almost 4 years ago

10.1371/journal.pbio.3001296

Tapping into non-English-language science for the conservation of global biodiversity
Cited by: 79
Author(s): Tatsuya Amano, Violeta Berdejo‐Espinola, Alec P. Christie, Kate Willott, Munemitsu Akasaka, András Báldi, Anna Berthinussen, Sandro Bertolino, Andrew J. Bladon, Min Chen, Chang Yong Choi, Magda Bou Dagher Kharrat, Luís Guilherme de Oliveira, Perla Farhat, Marina Golivets, Nataly Hidalgo Aranzamendi, Kerstin Jantke, Joanna Kajzer‐Bonk, M. Çisel Kemahlı Aytekin, Igor Khorozyan, Kensuke Kito, Ko Konno, Da Li Lin, Nick A. Littlewood, Yang Liu, Yifan Liu, Matthias Claudio Loretto, Valentina Marconi, Philip A. Martin, William H. Morgan, Juan Pablo Narváez-Gómez, Pablo José Negret, Elham Nourani, José Manuel Ochoa Quintero, Nancy Ockendon, Rachel Rui Ying Oh, Silviu O. Petrovan, Ana Cláudia Piovezan-Borges, Ingrid L. Pollet, Danielle Leal Ramos, Ana L. Reboredo Segovia, A. Nayelli Rivera‐Villanueva, Ricardo Rocha, Marie Morgane Rouyer, Katherine A. Sainsbury, Richard Schuster, Dominik Schwab, Çaǧan H. Şekercioǧlu, Hae Min Seo, Gorm E. Shackelford, Yushin Shinoda, Rebecca K. Smith, Shan Dar Tao, Ming-shan Tsai, Elizabeth Tyler, Flóra Vajna, José O. Valdebenito, Svetlana Vozykova, Paweł Waryszak, Veronica Zamora‐Gutiérrez, Rafael Dudeque Zenni, Wenjun Zhou, William J. Sutherland
Software Mentions: 18
Published: about 3 years ago

10.1186/s12889-021-11267-w

Influence of chronic hepatitis C infection on the monocyte-to-platelet ratio: data analysis from the National Health and Nutrition Examination Survey (2009–2016)
Cited by: 1
Author(s): Aidan M. Nikiforuk, Mohammad Ehsanul Karim, David M. Patrick, Agatha Jassem
Software Mentions: 18
Published: over 3 years ago

10.1016/j.molcel.2021.05.023

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago

10.3389/fimmu.2021.700501

Interferon-γ-Producing CD4+ T Cells Drive Monocyte Activation in the Bone Marrow During Experimental Leishmania donovani Infection
Cited by: 6
Author(s): Audrey Romano, Najmeeyah Brown, Helen Ashwin, Johannes S. P. Doehl, Jonathan Hamp, Mohamed Osman, Nidhi Sharma Dey, Gulab Fatima Rani, Tiago Luiz Ferreira, Paul M. Kaye
Software Mentions: 18
Published: about 3 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: about 5 years ago

10.3389/fimmu.2020.01691

Leveraging Public Single-Cell and Bulk Transcriptomic Datasets to Delineate MAIT Cell Roles and Phenotypic Characteristics in Human Malignancies
Cited by: 22
Author(s): Tony Yao, Parisa Shooshtari, S. M. Mansour Haeryfar
Software Mentions: 18
Published: over 4 years ago

10.31744/einstein_journal/2020AO6127

COVID-19 information exposure in digital media and implications for employees in the health care sector: findings from an online survey
Cited by: 7
Author(s): Paulo Rodrigo Bazán, Raymundo Machado de Azevedo Neto, Julia Abou Dias, Vanessa Gil Salvatierra, Liana Guerra Sanches, Sheylla Nadjane Batista Lacerda, Edson Amaro, Elisa Harumi Kozasa, Joana Bisol Balardin
Software Mentions: 17
Published: almost 5 years ago

10.7717/peerj.9539

The importance of open science for biological assessment of aquatic environments
Cited by: 15
Author(s): Marcus W. Beck, Casey C. O’Hara, Julia S. Stewart Lowndes, Raphael D. Mazor, Susanna Theroux, David J. Gillett, Belize Lane, Gregory Gearheart
Software Mentions: 17
Published: over 4 years ago

10.1371/journal.pone.0200653

Cryopreservation of human mucosal tissues
Cited by: 13
Author(s): Sean M. Hughes, April L. Ferre, Sarah E Yandura, Cory Shetler, Chris A. R. Baker, Fernanda Calienes, Claire Levy, Rena D. Astronomo, Zhiquan Shu, Gretchen M. Lentz, Michael Fialkow, Anna C. Kirby, M. Juliana McElrath, Elizabeth Sinclair, Lisa C. Rohan, Peter L. Anderson, Barbara L. Shacklett, Charlene S. Dezzutti, Dayong Gao, Florian Hladik
Software Mentions: 17
Published: over 6 years ago

10.1186/s13059-019-1819-8

SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
Cited by: 12
Author(s): Abraham Gihawi, Ghanasyam Rallapalli, Rachel Hurst, Colin S. Cooper, Richard M. Leggett, Daniel Brewer
Software Mentions: 17
Published: about 5 years ago

10.1001/jamanetworkopen.2020.37227

Trends in US Pediatric Hospital Admissions in 2020 Compared With the Decade Before the COVID-19 Pandemic
Cited by: 115
Author(s): Jonathan Pelletier, Jaskaran Rakkar, Alicia K. Au, Dana Y. Fuhrman, Robert S. B. Clark, Christopher M. Horvat
Software Mentions: 17
Published: almost 4 years ago

10.1002/eap.1898

Spatiotemporal prediction of wildfire size extremes with Bayesian finite sample maxima
Cited by: 40
Author(s): Maxwell B. Joseph, Matthew W. Rossi, Nathan Mietkiewicz, Adam L. Mahood, Megan E. Cattau, Lise A. St. Denis, R. Chelsea Nagy, Virginia Iglesias, John T. Abatzoglou, Jennifer K. Balch
Software Mentions: 17
Published: over 5 years ago

10.1016/j.cell.2019.12.013

Identification of a Master Regulator of Differentiation in Toxoplasma
Cited by: 154
Author(s): Benjamin S. Waldman, Dominic Schwarz, Marc H. Wadsworth, Jeroen P. J. Saeij, Alex K. Shalek, Sebastian Lourido
Software Mentions: 17
Published: almost 5 years ago

10.1371/journal.pone.0244876

Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes
Cited by: 12
Author(s): Moamen M. Elmassry, Sunghwan Kim, Ben Busby
Software Mentions: 16
Published: almost 4 years ago

10.1080/17453674.2020.1846956

Uncemented or cemented stems in first-time revision total hip replacement? An observational study of 867 patients including assessment of femoral bone defect size
Cited by: 7
Author(s): Yosef Tyson, Christer Hillman, Norbert Majenburg, Olof Sköldenberg, Ola Rolfson, Johan Kärrholm, Maziar Mohaddes, Nils P Hailer
Software Mentions: 16
Published: about 4 years ago

10.1186/s13059-020-02020-4

Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians
Cited by: 43
Author(s): Meagan A Rubel, Arwa Abbas, Louis J. Taylor, Andrew Jesse Connell, Ceylan Tanes, Kyle Bittinger, Valantine Ngum Ndze, Julius Y. Fonsah, Eric Ngwang, André Essiane, Charles Fokunang, Alfred K. Njamnshi, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 16
Published: over 4 years ago

10.1371/journal.pone.0231982

Rapid processing of neutral and angry expressions within ongoing facial stimulus streams: Is it all about isolated facial features?
Cited by: 2
Author(s): Antonio Schettino, Emanuele Porcu, Christopher Gundlach, Christian Keitel, Matthias Müller
Software Mentions: 16
Published: over 4 years ago

10.1038/s41419-021-03909-z

Diagnostic and prognostic potential of the proteomic profiling of serum-derived extracellular vesicles in prostate cancer
Cited by: 14
Author(s): Michele Signore, Romina Alfonsi, Giulia Federici, Simona Nanni, Antonio Addario, Lucia Bertuccini, Aurora Aiello, Anna Pace, Isabella Sperduti, Giovanni Muto, Alessandro Giacobbe, Devis Collura, Lidia Brunetto, Giuseppe Simone, Manuela Costantini, Lucio Crinò, Stefania Rossi, Claudio Tabolacci, Marco Diociaiuti, Tania Merlino, Michele Gallucci, Steno Sentinelli, Rocco Papalia, Ruggero De Maria, Dèsirèe Bonci
Software Mentions: 16
Published: over 3 years ago

10.1093/conphys/coaa131

Automated flow control of a multi-lane swimming chamber for small fishes indicates species-specific sensitivity to experimental protocols
Cited by: 3
Author(s): Björn Illing, Andrea Severati, Justin Hochen, Paul M. Boyd, Paulin Raison, Rachel Mather, Adam T. Downie, Jodie L. Rummer, Frederieke J. Kroon, Craig Humphrey
Software Mentions: 16
Published: almost 4 years ago

10.1371/journal.pgen.1008927

On the cross-population generalizability of gene expression prediction models
Cited by: 34
Author(s): Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. LeNoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux
Software Mentions: 16
Published: over 4 years ago

10.3389/fpsyg.2021.627561

Automatic Facial Expression Recognition in Standardized and Non-standardized Emotional Expressions
Cited by: 41
Author(s): Theresa Küntzler, T. Tim A. Höfling, Georg W. Alpers
Software Mentions: 16
Published: over 3 years ago

10.1371/journal.pone.0230416

The citation advantage of linking publications to research data
Cited by: 131
Author(s): Giovanni Colavizza, Iain Hrynaszkiewicz, Isla Staden, Kirstie Whitaker, Barbara McGillivray
Software Mentions: 16
Published: over 4 years ago

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: about 3 years ago

10.1111/eva.13246

Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest
Cited by: 11
Author(s): Djampa Kozlowski, Rahim Hassanaly‐Goulamhoussen, Martine Da Rocha, Georgios Koutsovoulos, Marc Bailly‐Bechet, Étienne Danchin
Software Mentions: 15
Published: over 3 years ago

10.2196/24889

A Novel Machine Learning Framework for Comparison of Viral COVID-19–Related Sina Weibo and Twitter Posts: Workflow Development and Content Analysis
Cited by: 7
Author(s): Shi Chen, Lina Zhou, Yunya Song, Qian Xu, Ping Wang, Kanlun Wang, Yaorong Ge, Daniel Janies
Software Mentions: 15
Published: almost 4 years ago

10.1371/journal.pone.0219892

Quantification and isolation of Bacillus subtilis spores using cell sorting and automated gating
Cited by: 18
Author(s): Marianna Karava, Felix Bracharz, Johannes Kabisch
Software Mentions: 15
Published: over 5 years ago

10.3390/cells8111321

Transcriptional Regulation of Autophagy Genes via Stage-Specific Activation of CEBPB and PPARG during Adipogenesis: A Systematic Study Using Public Gene Expression and Transcription Factor Binding Datasets
Cited by: 16
Author(s): Mahmoud Ahmed, Trang Huyen Lai, Jin Seok Hwang, Sahib Zada, Trang Minh Pham, Deok Ryong Kim
Software Mentions: 15
Published: about 5 years ago

10.3390/cells10061292

Effect of Differences in the Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background
Cited by: 1
Author(s): Axel Künstner, Rédouane Aherrahrou, Misa Hirose, Petra Bruse, Saleh M. Ibrahim, Hauke Busch, Jeanette Erdmann, Zouhair Aherrahrou
Software Mentions: 15
Published: over 3 years ago

10.3389/fimmu.2021.668391

A Transcriptional Signature of PDGF-DD Activated Natural Killer Cells Predicts More Favorable Prognosis in Low-Grade Glioma
Cited by: 21
Author(s): Yuhan Sun, Alexander James Sedgwick, Yaseelan Palarasah, Stefano Mangiola, Alexander D. Barrow
Software Mentions: 15
Published: about 3 years ago

10.1038/s41598-021-87843-2

Bodily ownership and agency sensations in a natural state
Cited by: 1
Author(s): Souta Hidaka, Kyoshiro Sasaki, Toshikazu Kawagoe, Nobuyuki Asai, Wataru Teramoto
Software Mentions: 15
Published: over 3 years ago

10.3389/fchem.2021.734132

The “DOLPHINS” Project: A Low-Cost Real-Time Multivariate Process Control From Large Sensor Arrays Providing Sparse Binary Data
Cited by: 1
Author(s): Eugenio Alladio, Marcello Baricco, Vincenzo Leogrande, Renato Pagliari, Fabio Pozzi, Paolo Foglio, Marco Vincenti
Software Mentions: 15
Published: about 3 years ago

10.1186/s12866-019-1598-0

Characterization of Salmonella Dublin isolated from bovine and human hosts
Cited by: 35
Author(s): Narayan Paudyal, Hang Pan, Mohammed Elbediwi, Xiao Hua Zhou, Xianqi Peng, Xiaoliang Li, Weihuan Fang, Min Yue
Software Mentions: 15
Published: about 5 years ago

10.1007/s00204-021-03031-1

Functional alterations by a subgroup of neonicotinoid pesticides in human dopaminergic neurons
Cited by: 26
Author(s): Dominik Loser, María G. Hinojosa, John D. Blum, Jasmin Schaefer, Markus Brüll, Ylva Johansson, Ilinca Suciu, Karin Grillberger, Timm Danker, Clemens Möller, Iain Gardner, Gerhard Ecker, Susanne Hougaard Bennekou, Anna Forsby, Udo Kraushaar, Marcel Leist
Software Mentions: 15
Published: over 3 years ago

10.3389/fpls.2021.618028

Floral UV Features of Plant Species From a Neotropical Savanna
Cited by: 6
Author(s): Priscila Tunes, Maria Gabriela Gutierrez Camargo, Elza Guimarães
Software Mentions: 15
Published: over 3 years ago

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago

10.3390/insects10100321

Evaluation of NEON Data to Model Spatio-Temporal Tick Dynamics in Florida
Cited by: 5
Author(s): Geraldine Klarenberg, Samantha M. Wisely
Software Mentions: 14
Published: about 5 years ago

10.3390/ijms20174162

SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers
Cited by: 13
Author(s): Fabia Fricke, Malwina Michalak, Uwe Warnken, Ingrid Haußer, Martina Schnölzer, Jürgen Kopitz, Johannes Gebert
Software Mentions: 14
Published: about 5 years ago

10.3390/ijerph18179227

Multivariate Analysis of Risk Factors of the COVID-19 Pandemic in the Community of Madrid, Spain
Cited by: 2
Author(s): Víctor Pérez-Segura, Raquel Caro Carretero, António Rua
Software Mentions: 14
Published: about 3 years ago

10.3390/plants10040615

Polyphenol Diversity and Antioxidant Activity of European Cistus creticus L. (Cistaceae) Compared to Six Further, Partly Sympatric Cistus Species
Cited by: 11
Author(s): Brigitte Lukas, Laura Bragagna, Katharina Starzyk, Klaudia Labedz, Klaus Stolze, Johannes Novak
Software Mentions: 14
Published: over 3 years ago

10.3390/microorganisms9061222

Salivary Microbiome Diversity in Kuwaiti Adolescents with Varied Body Mass Index—A Pilot Study
Cited by: 5
Author(s): Hend Alqaderi, Meganathan P. Ramakodi, Rasheeba Nizam, Sindhu Jacob, Sriraman Devarajan, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0248185

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis
Cited by: 15
Author(s): Laura Vega, Giovanny Herrera, Marina Muñoz, Manuel A. Patarroyo, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0249268

Outdoor cycling activity affected by COVID-19 related epidemic-control-decisions
Cited by: 38
Author(s): Anne-Maria Schweizer, Anna Leiderer, Veronika Mitterwallner, Anna Walentowitz, Gregor Mathes, Manuel J. Steinbauer
Software Mentions: 14
Published: over 3 years ago

10.7717/peerj.11880

Integrated bioinformatics analysis of the NEDD4 family reveals a prognostic value of NEDD4L in clear-cell renal cell cancer
Cited by: 6
Author(s): Hui Zhao, Junjun Zhang, Xiaoliang Fu, Dongdong Mao, Xuesen Qi, Shuai Liang, Gang Ma, Zewen Song, Ru Yang, Zhenni Guo, Binghua Tong, Meiqing Sun, Baile Zuo, Guoyin Li
Software Mentions: 14
Published: over 3 years ago

10.1186/s12889-021-11060-9

Identifying US County-level characteristics associated with high COVID-19 burden
Cited by: 9
Author(s): Daniel Li, Sheila M. Gaynor, Corbin Quick, Jarvis T. Chen, Briana Stephenson, Brent A. Coull, Xihong Lin
Software Mentions: 14
Published: over 3 years ago

10.1371/journal.pone.0248202

Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevils
Cited by: 1
Author(s): Ava Mackay-Smith, Mary Kate Dornon, R.E. Lucier, Annalisa Okimoto, Flavia Mendonca de Sousa, Marcela Silvina Rodriguero, Viviana A. Confalonieri, Analía Alicia Lanteri, Andrea S. Sequeira
Software Mentions: 14
Published: over 3 years ago

10.1186/s13148-021-01173-8

Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism
Cited by: 5
Author(s): Kristyna Kupkova, Savera J. Shetty, Rashidul Haque, William A. Petri, David T. Auble
Software Mentions: 14
Published: about 3 years ago

10.1038/s41598-021-97362-9

N6-methylandenosine-related lncRNAs play an important role in the prognosis and immune microenvironment of pancreatic ductal adenocarcinoma
Cited by: 5
Author(s): Yuhai Hu, Yiping Chen
Software Mentions: 14
Published: about 3 years ago

10.1371/journal.pone.0242060

The difference between cellulolytic ‘culturomes’ and microbiomes inhabiting two contrasting soil types
Cited by: 3
Author(s): Elizaveta V. Evdokimova, Grigory Gladkov, Natalya I. Kuzina, Е. А. Иванова, Anastasiia K. Kimeklis, Aleksei Zverev, Arina Kichko, Tatyana S. Aksenova, А. Г. Пинаев, Evgeny Andronov
Software Mentions: 14
Published: about 4 years ago

10.1007/s00204-020-02956-3

Human neuronal signaling and communication assays to assess functional neurotoxicity
Cited by: 13
Author(s): Dominik Loser, Jasmin Schaefer, Timm Danker, Clemens Möller, Markus Brüll, Ilinca Suciu, Anna‐Katharina Ückert, Stefanie Klima, Marcel Leist, Udo Kraushaar
Software Mentions: 14
Published: almost 4 years ago

10.3390/pathogens9100841

Diverse Epidemiology of Leptospira Serovars Notified in New Zealand, 1999–2017
Cited by: 12
Author(s): Shahista Nisa, David A. Wilkinson, Olivia Angelin‐Bonnet, Shevaun Paine, Karen Weber Cullen, Jackie Wight, Michael G Baker, Jackie Benschop
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: over 4 years ago

10.1186/s40168-020-00914-w

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients
Cited by: 118
Author(s): Alfonsina D’Amato, Lorenzo Mannelli, Elena Lucarini, Angela L. Man, Gwénaëlle Le Gall, Jacopo Junio Valerio Branca, Carla Ghelardini, Amedeo Amedei, Eugenio Bertelli, Marì Regoli, Alessandra Pacini, Giulia Luciani, Pasquale Gallina, Annalisa Altera, Arjan Narbad, Massimo Gulisano, Lesley Hoyles, David Vauzour, Claudio Nicoletti
Software Mentions: 14
Published: about 4 years ago

10.1371/journal.pone.0206563

Nitrogen addition pulse has minimal effect in big sagebrush (Artemisia tridentata) communities on the Pinedale Anticline, Wyoming (USA)
Cited by: 1
Author(s): Christopher W. Beltz, Megan L. Mobley, Ingrid C. Burke
Software Mentions: 13
Published: over 5 years ago

10.3390/ijms22062790

Differential Methylation in the GSTT1 Regulatory Region in Sudden Unexplained Death and Sudden Unexpected Death in Epilepsy
Cited by: 4
Author(s): Steffan Noe Christiansen, Stine Jacobsen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Linea C Trudsø, Karsten Olsen, Jacob Tfelt-Hansen, Jytte Banner, Niels Morling
Software Mentions: 13
Published: over 3 years ago

10.1186/s13059-020-02233-7

tidybulk: an R tidy framework for modular transcriptomic data analysis
Cited by: 22
Author(s): Stefano Mangiola, Ramyar Molania, Ruining Dong, Maria A. Doyle, Anthony T. Papenfuss
Software Mentions: 13
Published: almost 4 years ago

10.3389/fimmu.2021.730346

Nasal Immunization With Small Molecule Mast Cell Activators Enhance Immunity to Co-Administered Subunit Immunogens
Cited by: 6
Author(s): Brandi T. Johnson‐Weaver, Hae Woong Choi, Hui Yang, Joshua A. Granek, Cliburn Chan, Soman N. Abraham, Herman F. Staats
Software Mentions: 13
Published: about 3 years ago

10.1371/journal.pone.0242502

Timeliness of immunisation with the pentavalent vaccine at different levels of the health care system in the Lao People’s Democratic Republic: A cross-sectional study
Cited by: 3
Author(s): Lisa Hefele, Sengdavanh Syphan, Dalouny Xayavong, Anousin Homsana, Daria Kleine, Phetsavanh Chanthavilay, Phonethipsavanh Nouanthong, Kinnaly Xaydalasouk, Outavong Phathammavong, Somxay Billamay, Anonh Xeuatvongsa, Daniel Reinharz, Antony P. Black, Claude P. Muller
Software Mentions: 13
Published: almost 4 years ago

10.3390/cancers13174311

Landscape of Bone Marrow Metastasis in Human Neuroblastoma Unraveled by Transcriptomics and Deep Multiplex Imaging
Cited by: 15
Author(s): Daria Lazic, Florian Kromp, Fikret Rifatbegovic, Peter Repiščák, Michael Kirr, Filip Mívalt, Florian Halbritter, Marie Bernkopf, Andrea Bileck, Marek Ussowicz, Inge M. Ambros, Peter F. Ambros, Christopher Gerner, Ruth Ladenstein, Christian Ostalecki, Sabine Taschner‐Mandl
Software Mentions: 13
Published: about 3 years ago

10.1371/journal.pcbi.1008896

Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities
Cited by: 8
Author(s): Gil J. B. Henriques, Simon van Vliet, Michael Doebeli
Software Mentions: 13
Published: about 3 years ago

10.3389/fimmu.2021.652677

The Contribution of Serum Complement Component 3 Levels to 90-Day Mortality in Living Donor Liver Transplantation
Cited by: 2
Author(s): Saeko Fukui, Masaaki Hidaka, Shoichi Fukui, Shimpei Morimoto, Takanobu Hara, Akihiko Soyama, Tomohiko Adachi, Hajime Matsushima, Takayuki Tanaka, Mai Fuchigami, Hiroo Hasegawa, Katsunori Yanagihara, Susumu Eguchi
Software Mentions: 13
Published: over 3 years ago

10.7554/eLife.67784

Genetic variation, environment and demography intersect to shape Arabidopsis defense metabolite variation across Europe
Cited by: 26
Author(s): Ella Katz, Jiajie Li, Benjamin Jaegle, Haim Ashkenazy, R. Shawn Abrahams, Clement Bagaza, Samuel Holden, Chris J Pires, Ruthie Angelovici, Daniel J. Kliebenstein
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pone.0253148

Enhancing monitoring of rewilding progress through wildlife tracking and remote sensing
Cited by: 1
Author(s): Julia Carolina Mata, Robert Buitenwerf, Jens‐Christian Svenning
Software Mentions: 13
Published: over 3 years ago

10.3389/fpls.2021.633651

Improving Wheat Yield Prediction Using Secondary Traits and High-Density Phenotyping Under Heat-Stressed Environments
Cited by: 6
Author(s): Mohammad Zillur Rahman, Jared Crain, Atena Haghighattalab, Ravi P. Singh, Jesse Poland
Software Mentions: 13
Published: about 3 years ago

10.1002/bjs5.50138

Global variation in anastomosis and end colostomy formation following left‐sided colorectal resection
Cited by: 16
Author(s): GlobalSurg Collaborative
Software Mentions: 13
Published: over 5 years ago

10.1038/s41598-021-90901-4

Characteristics of preoperative steroid profiles and glucose metabolism in patients with primary aldosteronism developing adrenal insufficiency after adrenalectomy
Cited by: 3
Author(s): Xiao Wang, Daniel A. Heinrich, Sonja Kunz, Nina Heger, Lisa Sturm, Olaf Uhl, Felix Beuschlein, Martín Reincke, Martin Bidlingmaier
Software Mentions: 13
Published: over 3 years ago

10.3389/fbioe.2021.614324

One-Time Optimization of Advanced T Cell Culture Media Using a Machine Learning Pipeline
Cited by: 9
Author(s): Paul Grzesik, Sebastian C. Warth
Software Mentions: 13
Published: over 3 years ago

10.1371/journal.pone.0250817

#MaskOn! #MaskOff! Digital polarization of mask-wearing in the United States during COVID-19
Cited by: 48
Author(s): Jun Lang, Wesley W. Erickson, Zhuo Jing–Schmidt
Software Mentions: 13
Published: over 3 years ago

10.3390/v13061184

Age and Infectious Dose Significantly Affect Disease Progression after RHDV2 Infection in Naïve Domestic Rabbits
Cited by: 13
Author(s): Robyn N. Hall, Tegan King, Tiffany W. O’Connor, Andrew J. Read, Jane Arrow, Katherine Trought, Janine A. Duckworth, M. Treuting Piper, Tanja Strive
Software Mentions: 13
Published: over 3 years ago

10.3389/fimmu.2020.620716

Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help
Cited by: 14
Author(s): Elena Merino Tejero, Danial Lashgari, Rodrigo García-Valiente, Xuefeng Gao, Fabien Crauste, Philippe A. Robert, Michael Meyer‐Hermann, María Rodríguez Martínez, S. Marieke van Ham, Jeroen E. J. Guikema, Huub Hoefsloot, Antoine H. C. van Kampen
Software Mentions: 13
Published: almost 4 years ago

10.1038/s41598-019-49160-7

Early life determinants induce sustainable changes in the gut microbiome of six-year-old children
Cited by: 27
Author(s): Silvia Gschwendtner, Hani Kang, Elisabeth Thiering, Susanne Kublik, Bärbel U. Foesel, Holger Schulz, Susanne Krauss‐Etschmann, Joachim Heinrich, Anne Schöler, Michael Schloter, Marie Standl
Software Mentions: 13
Published: about 5 years ago

10.1038/s41398-021-01596-0

Autoantibody profiles associated with clinical features in psychotic disorders
Cited by: 6
Author(s): August Jernbom Falk, Cherrie Galletly, David R. Just, Catherine Toben, Bernhard T. Baune, Scott Clark, Dennis Liu, Peter Nilsson, Anna Månberg, Klaus Oliver Schubert
Software Mentions: 13
Published: about 3 years ago

10.1371/journal.pcbi.1008991

Memes: A motif analysis environment in R using tools from the MEME Suite
Cited by: 22
Author(s): Spencer L. Nystrom, Daniel J. McKay
Software Mentions: 12
Published: about 3 years ago

10.7717/peerj.11923

Signature identification of relapse-related overall survival of early lung adenocarcinoma after radical surgery
Cited by: 2
Author(s): Peng Han, Jiaqi Yue, Kangle Kong, Shan Huang, Pei Cao, Yu Deng, Ли Фан, Bo Zhao
Software Mentions: 12
Published: over 3 years ago

10.1186/s13073-021-00869-z

Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home
Cited by: 13
Author(s): Quinten R Ducarmon, Elisabeth M. Terveer, Sam Nooij, Michelle N Bloem, Karuna E W Vendrik, Monique A. A. Caljouw, Ingrid M J G Sanders, S.M. van Dorp, M.C. Wong, Romy D. Zwittink, Ed J. Kuijper
Software Mentions: 12
Published: over 3 years ago

10.7717/peerj.5661

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia
Cited by: 17
Author(s): Camila Duarte Ritter, Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher J. Barnes, R. Henrik Nilsson, Alexandre Antonelli
Software Mentions: 12
Published: about 6 years ago

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