cran: knitr | Projects | Ecosyste.ms: Papers

10.1186/s12983-016-0174-9

Crown-of-thorns starfish have true image forming vision
Cited by: 19
Author(s): Ronald Petie, Anders Garm, Michael R. Hall
Software Mentions: 6
Published: about 8 years ago

10.7717/peerj.447

Mobile phones carry the personal microbiome of their owners
Cited by: 127
Author(s): James F. Meadow, Adam E. Altrichter, Jessica L. Green
Software Mentions: 5
Published: over 10 years ago

Bacterial death and TRADD-N domains help define novel apoptosis and immunity mechanisms shared by prokaryotes and metazoans
Cited by: 14
Author(s): Gurmeet Kaur, Lakshminarayan M. Iyer, A. Maxwell Burroughs, L. Aravind
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0204391

Aseptic loosening after total hip arthroplasty and the risk of cardiovascular disease: A nested case-control study
Cited by: 0
Author(s): Agata Rysinska, Olof Sköldenberg, Anne Garland, Ola Rolfson, Sara Aspberg, Thomas Eisler, Göran Garellick, Andreas M. Stark, Nils P Hailer, Max Gordon
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0186723

Association of birth weight with corneal power in early adolescence: Results from the National Health and Nutrition Examination Survey (NHANES) 1999–2008
Cited by: 20
Author(s): Achim Fieß, Alexander K. Schuster, Norbert Pfeiffer, Stefan Nickels
Software Mentions: 5
Published: about 7 years ago

10.1136/bmjopen-2019-031251

Residential area deprivation and risk of subsequent hospital admission in a British population: the EPIC-Norfolk cohort
Cited by: 7
Author(s): Robert Luben, Shabina Hayat, Anthony P. Khawaja, Nicholas J. Wareham, Paul Pharoah, Kay‐Tee Khaw
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13063-020-4093-x

Effects of the Informed Health Choices podcast on the ability of parents of primary school children in Uganda to assess the trustworthiness of claims about treatment effects: one-year follow up of a randomised trial
Cited by: 17
Author(s): Daniel Semakula, Allen Nsangi, Andrew D Oxman, Matt Oxman, Astrid Austvoll‐Dahlgren, Sarah Rosenbaum, Angela Morelli, Claire Glenton, Simon Lewin, Laetitia Nyirazinyoye, Margaret Kaseje, Iain Chalmers, Atle Fretheim, Christopher James Rose, Nelson K. Sewankambo
Software Mentions: 5
Published: almost 5 years ago

10.1128/mBio.00201-16

Status of the Archaeal and Bacterial Census: an Update
Cited by: 117
Author(s): Patrick D. Schloss, R. Girard, Thomas Martin, Joshua Edwards, J. Cameron Thrash
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.52696

Highly regulated, diversifying NTP-dependent biological conflict systems with implications for the emergence of multicellularity
Cited by: 24
Author(s): Gurmeet Kaur, A. Maxwell Burroughs, Lakshminarayan M. Iyer, L. Aravind
Software Mentions: 5
Published: over 4 years ago

10.3390/ijerph17082912

Impact of an Individualized Cognitive Training Intervention in Preschoolers from Poor Homes
Cited by: 13
Author(s): Federico Giovannetti, Marcos Luis Pietto, María Soledad Segretin, Sebastián Javier Lipina
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0210663

Late effects of total body irradiation on hematopoietic recovery and immune function in rhesus macaques
Cited by: 18
Author(s): Laura P. Hale, Gowrisankar Rajam, George M. Carlone, Chen Jiang, Kouros Owzar, Greg Dugan, David L. Caudell, Nelson J. Chao, J. Mark Cline, Thomas C. Register, Gregory D. Sempowski
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-61659-y

Short and long period growth markers of enamel formation distinguish European Pleistocene hominins
Cited by: 16
Author(s): Mario Modesto‐Mata, MC Dean, Rodrigo S. Lacruz, Timothy Bromage, Cecilia García‐Campos, Marina Martínez de Pinillos, Laura Martín‐Francés, María Martinón‐Torres, Eudald Carbonell, Juan Luís Arsuaga, José Marı́a Bermúdez de Castro
Software Mentions: 4
Published: over 4 years ago

10.1002/cam4.3394

Second primary breast cancer after unilateral mastectomy alone or with contralateral prophylactic mastectomy
Cited by: 3
Author(s): Shailesh Agarwal, Lisa M. Pappas, Cindy B. Matsen, Jayant P. Agarwal
Software Mentions: 4
Published: about 4 years ago

10.1002/ece3.3041

An evaluation of semi‐automated methods for collecting ecosystem‐level data in temperate marine systems
Cited by: 8
Author(s): Kingsley J. Griffin, Luke H. Hedge, Manuel González‐Rivero, Ove Hoegh‐Guldberg, Emma L. Johnston
Software Mentions: 4
Published: over 7 years ago

10.1186/2049-2618-2-7

Bacterial communities on classroom surfaces vary with human contact
Cited by: 121
Author(s): James F. Meadow, Adam E. Altrichter, Steven W. Kembel, Maxwell Moriyama, Timothy K. O’Connor, A. M. Womack, Glen Brown, Jessica L. Green, B. J. M. Bohannan
Software Mentions: 4
Published: over 10 years ago

10.3390/v13010063

Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts
Cited by: 45
Author(s): Lakshminarayan M. Iyer, Vivek Anantharaman, Arunkumar Krishnan, A. Maxwell Burroughs, L. Aravind
Software Mentions: 4
Published: almost 4 years ago

10.1155/2016/7512360

A Prospective Observational Cohort Study on Orthopaedic and Anaesthetic Registrars Performing Femoral Nerve Block on Patients with an Acute Hip Fracture
Cited by: 1
Author(s): Åsa Thelaus, Tobias Pettersson, Max Gordon, Ferid Krupić, Olof Sköldenberg
Software Mentions: 4
Published: almost 9 years ago

10.1136/bmjopen-2020-042115

Sociodemographic and lifestyle predictors of incident hospital admissions with multimorbidity in a general population, 1999–2019: the EPIC-Norfolk cohort
Cited by: 7
Author(s): Robert Luben, Shabina Hayat, Nicholas J. Wareham, Paul Pharoah, Kay‐Tee Khaw
Software Mentions: 4
Published: about 4 years ago

10.1186/s12936-018-2203-y

Insecticide resistance evolution with mixtures and sequences: a model-based explanation
Cited by: 31
Author(s): Andy South, Ian M. Hastings
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12877-020-01573-0

Usual physical activity and subsequent hospital usage over 20 years in a general population: the EPIC-Norfolk cohort
Cited by: 10
Author(s): Robert Luben, Shabina Hayat, Nicholas J. Wareham, Paul D.P. Pharoah, Kay‐Tee Khaw
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-14-266

Characterization of differential transcript abundance through time during Nematostella vectensis development
Cited by: 73
Author(s): Rebecca R. Helm, Stefan Siebert, Sarah Tulin, Joel Smith, Casey W. Dunn
Software Mentions: 4
Published: almost 12 years ago

10.3389/fpsyg.2016.01079

Thou Shalt Be Reproducible! A Technology Perspective
Cited by: 4
Author(s): Patrick Mair
Software Mentions: 3
Published: over 8 years ago

10.1186/s12920-015-0095-z

OncoRep: an n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
Cited by: 11
Author(s): Tobias Meißner, Kathleen Fisch, Louis Gioia, Andrew I. Su
Software Mentions: 3
Published: over 9 years ago

10.3389/fgene.2019.01028

The Effect of Gut Microbiome Composition on Human Immune Responses: An Exploration of Interference by Helminth Infections
Cited by: 23
Author(s): Ivonne Martin, Maria M. M. Kaisar, Aprilianto E. Wiria, Firdaus Hamid, Yenny Djuardi, Erliyani Sartono, Bruce A. Rosa, Makedonka Mitreva, Taniawati Supali, Jeanine J. Houwing-Duistermaat, Maria Yazdanbakhsh, Linda J. Wammes
Software Mentions: 3
Published: about 5 years ago

10.1186/s13326-017-0174-5

OpenBiodiv-O: ontology of the OpenBiodiv knowledge management system
Cited by: 40
Author(s): Viktor Senderov, Kiril Simov, Nico M. Franz, Pavel Stoev, Terry Catapano, Donat Agosti, Guido Sautter, Robert Morris, Lyubomir Penev
Software Mentions: 3
Published: almost 7 years ago

10.1136/bmjopen-2015-009461

Predicting admissions and time spent in hospital over a decade in a population-based record linkage study: the EPIC-Norfolk cohort
Cited by: 15
Author(s): Robert Luben, Shabina Hayat, Nick Wareham, Kay‐Tee Khaw
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.csbj.2021.04.044

protGear: A protein microarray data pre-processing suite
Cited by: 1
Author(s): Kennedy Mwai, Nelson Kibinge, James Tuju, Gathoni Kamuyu, Rinter Kimathi, James Mburu, Emily Chepsat, Lydia Nyamako, Timothy Chege, Irene Nkumama, Samson Kinyanjui, Eustasius Musenge, Faith Osier
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0200747

Alcohol consumption and future hospital usage: The EPIC-Norfolk prospective population study
Cited by: 2
Author(s): Robert Luben, Shabina Hayat, Angela A. Mulligan, Marleen Lentjes, Nicholas J. Wareham, Paul D.P. Pharoah, Kay‐Tee Khaw
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0125791

Analysis of Glioblastoma Patients' Plasma Revealed the Presence of MicroRNAs with a Prognostic Impact on Survival and Those of Viral Origin
Cited by: 27
Author(s): Ana Herman, Kristina Gruden, Andrej Blejec, Vid Podpečan, Helena Motaln, Primož Rožman, Matjaž Hren, Klemen Zupančič, Matija Veber, Urška Verbovšek, Tamara Lah Turnšek, Andrej Porčnik, Marjan Koršič, Miomir Knežević, Matjaž Jeras
Software Mentions: 3
Published: over 9 years ago

10.1590/1413-785220162404158362

UNCEMENTED ARTHROPLASTY AFTER HIP METASTATIC DISEASE AND MULTIPLE MYELOMA
Cited by: 2
Author(s): André Mathias Baptista, Sergio Pinheiro de Souza Meirelles, Daniel César Seguel Rebolledo, Luiz Filipe Marques Correia, Olavo Pires de Camargo
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.42512

Image content is more important than Bouma’s Law for scene metamers
Cited by: 31
Author(s): Thomas S. A. Wallis, Christina M. Funke, Alexander S. Ecker, Leon A. Gatys, Felix A. Wichmann, Matthias Bethge
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1007486

Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S.
Cited by: 106
Author(s): Nicholas G. Reich, Craig McGowan, Teresa K. Yamana, Abhinav Tushar, Evan L. Ray, Dave Osthus, Sasikiran Kandula, Logan Brooks, Willow Crawford-Crudell, Graham Casey Gibson, Evan Moore, Rebecca Silva, Matthew Biggerstaff, Michael A. Johansson, Roni Rosenfeld, Jeffrey Shaman
Software Mentions: 2
Published: about 5 years ago

10.1186/2047-217X-3-3

A data repository and analysis framework for spontaneous neural activity recordings in developing retina
Cited by: 32
Author(s): Stephen J. Eglen, Michael Weeks, Mark Jessop, Jennifer Simonotto, Thomas W. Jackson, Evelyne Sernagor
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pbio.1001745

Best Practices for Scientific Computing
Cited by: 435
Author(s): Greg Wilson, D. A. Aruliah, C. Titus Brown, Neil Chue Hong, M. Ryleigh Davis, Richard Guy, Steven H. D. Haddock, Kathryn D. Huff, Ian M. Mitchell, Mark D. Plumbley, B. M. Waugh, Ethan White, P.A. Wilson
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0239598

How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey
Cited by: 28
Author(s): Tom E Hardwicke, Steven N. Goodman
Software Mentions: 2
Published: about 4 years ago

10.1186/1741-7015-11-220

Criteria for the use of omics-based predictors in clinical trials: explanation and elaboration
Cited by: 107
Author(s): Lisa M. McShane, Margaret M. Cavenagh, Tracy Lively, David A. Eberhard, William L. Bigbee, P. Stephen Williams, Jill P. Mesirov, Mei Yin Polley, Kelly Y. Kim, James V. Tricoli, Jeremy M. G. Taylor, Deborah J. Shuman, Richard Simon, James H. Doroshow, Barbara A. Conley
Software Mentions: 2
Published: about 11 years ago

10.3389/fvets.2018.00026

Benefit–Cost Analysis of Foot-and-Mouth Disease Vaccination at the Farm-Level in South Vietnam
Cited by: 16
Author(s): Dinh Bao Truong, Flavie Goutard, Stéphane Bertagnoli, Alexis Delabouglise, Vladimir Grosbois, Marisa Peyre
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pbio.1002303

Computing Workflows for Biologists: A Roadmap
Cited by: 32
Author(s): Ashley Shade, Tracy K. Teal
Software Mentions: 2
Published: almost 9 years ago

10.1038/sdata.2015.3

The pediatric template of brain perfusion
Cited by: 51
Author(s): Brian B. Avants, Jeffrey T. Duda, Emily Kilroy, Kate Krasileva, Kay Jann, Benjamin M. Kandel, Nicholas J. Tustison, Lirong Yan, Mayank Jog, Robert X. Smith, Yi Wang, Mirella Dapretto, Danny J.J. Wang
Software Mentions: 2
Published: almost 10 years ago

10.1016/j.dib.2020.105502

Exploring bilateral field advantage across lifespan with a visual working memory span task: Experimental data, analysis and computer simulation
Cited by: 0
Author(s): Anka Slana Ozimič, Grega Repovš
Software Mentions: 2
Published: over 4 years ago

10.1186/s13742-016-0135-4

Tools and techniques for computational reproducibility
Cited by: 118
Author(s): Stephen R. Piccolo, Michael Frampton
Software Mentions: 2
Published: over 8 years ago

10.3389/fpubh.2017.00327

Data Sharing: Convert Challenges into Opportunities
Cited by: 47
Author(s): Ana Sofia Figueiredo
Software Mentions: 2
Published: almost 7 years ago

10.3390/clinpract11030070

Peridural Anesthesia and Cancer-Related Survival after Surgery for Pancreatic Cancer—A Retrospective Cohort Study
Cited by: 3
Author(s): A. Alexander, Nadja Lehwald, Alexander Rehders, Stefanie Rabenalt, Pablo Emilio Verde, Claus Ferdinand Eisenberger, Nina Picker, Wolfram Trudo Knoefel, Peter Kienbaum
Software Mentions: 2
Published: over 3 years ago

10.1186/s13007-017-0163-9

rosettR: protocol and software for seedling area and growth analysis
Cited by: 11
Author(s): Filipa Tomé, Karel Jansseune, Bernadette Saey, Jack Grundy, Korneel Vandenbroucke, Matthew A. Hannah, Henning Redestig
Software Mentions: 2
Published: over 7 years ago

10.2478/raon-2014-0014

Identification of plasma biomarker candidates in glioblastoma using an antibody-array-based proteomic approach
Cited by: 11
Author(s): Klemen Zupančič, Andrej Blejec, Ana Herman, Matija Veber, Urška Verbovšek, Marjan Koršič, Miomir Knežević, Primož Rožman, Tamara Lah Turnšek, Kristina Gruden, Helena Motaln
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pcbi.1004961

Ten Simple Rules for Effective Statistical Practice
Cited by: 72
Author(s): Robert E. Kass, Brian Caffo, Marie Davidian, Xiao Li Meng, Bin Yu, N. Reid
Software Mentions: 1
Published: over 8 years ago

10.3390/e22010001

Pearle’s Hidden-Variable Model Revisited
Cited by: 6
Author(s): Richard D. Gill
Software Mentions: 1
Published: almost 5 years ago

10.1186/2049-2618-2-8

All hail reproducibility in microbiome research
Cited by: 19
Author(s): Jacques Ravel, K. Eric Wommack
Software Mentions: 1
Published: over 10 years ago

10.3389/fpsyg.2021.625153

Consistency in Motion Event Encoding Across Languages
Cited by: 5
Author(s): Guillermo Montero-Melis
Software Mentions: 1
Published: over 3 years ago

10.1098/rsos.201494

Analytic reproducibility in articles receiving open data badges at the journal <i>Psychological Science</i> : an observational study
Cited by: 26
Author(s): Tom E Hardwicke, Manuel Bohn, Kyle MacDonald, Emily Hembacher, Michèle B. Nuijten, Benjamin N. Peloquin, Benjamin deMayo, Bria Long, Erica J. Yoon, Michael C. Frank
Software Mentions: 1
Published: almost 4 years ago

10.12688/f1000research.3-36.v2

Matched molecular pair-based data sets for computer-aided medicinal chemistry
Cited by: 5
Author(s): Ye Hu, Antonio de la Vega de León, Bijun Zhang, Jürgen Bajorath
Software Mentions: 1
Published: almost 11 years ago

10.1186/s12936-017-1735-x

Integrating malaria surveillance with climate data for outbreak detection and forecasting: the EPIDEMIA system
Cited by: 27
Author(s): Christopher L. Merkord, Yi Liu, A. Mihretie, T. Gebrehiwot, Worku Awoke, Estifanos Bayabil, Geoffrey M. Henebry, Gebeyaw T. Kassa, Mastewal Lake, Michael C. Wimberly
Software Mentions: 1
Published: over 7 years ago

10.1186/s12918-016-0288-x

Where next for the reproducibility agenda in computational biology?
Cited by: 21
Author(s): Joanna Lewis, Charles E. Breeze, Jane Charlesworth, Oliver J. Maclaren, Jonathan Cooper
Software Mentions: 1
Published: over 8 years ago

10.1186/s13643-019-0975-y

Still moving toward automation of the systematic review process: a summary of discussions at the third meeting of the International Collaboration for Automation of Systematic Reviews (ICASR)
Cited by: 80
Author(s): Annette M. O’Connor, Guy Tsafnat, Stephen B. Gilbert, Kristina A. Thayer, Ian Shemilt, James Thomas, Paul Glasziou, Mary S. Wolfe
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0191821

A user-friendly tool to evaluate the effectiveness of no-take marine reserves
Cited by: 11
Author(s): Juan Carlos Villaseñor-Derbez, Caio Faro, Melaina Wright, Jael Martínez, Sean P. Fitzgerald, Stuart Fulton, María del Mar Mancha-Cisneros, Gavin McDonald, Fiorenza Micheli, Alvin Suárez, Jorge Torre, Christopher Costello
Software Mentions: 1
Published: almost 7 years ago

10.1037/xge0000739

Apathy is associated with reduced precision of prior beliefs about action outcomes.
Cited by: 15
Author(s): Frank H. Hezemans, Noham Wolpe, James B. Rowe
Software Mentions: 1
Published: about 4 years ago

10.1038/srep44377

Gut dysbiosis and neuroimmune responses to brain infection with Theiler’s murine encephalomyelitis virus
Cited by: 34
Author(s): Francisco Carrillo‐Salinas, Leyre Mestre, Míriam Mecha, Ana Feliú, Rosa del Campo, Noelia Villarrubia, Carmen Espejo, Xavier Montalbán, José C. Álvarez‐Cermeño, Luisa María Villar, Carmen Guaza
Software Mentions: 1
Published: over 7 years ago

Projects: cran: knitr

Papers Mentioning knitr 157