Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: TMB

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/TMB

Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
34 versions
Latest release: over 1 year ago
36 dependent packages
28,448 downloads last month

Papers Mentioning TMB 24

Tumor mutation burden (TMB)-associated signature constructed to predict survival of lung squamous cell carcinoma patients
Cited by: 13
Author(s): Yan Duan, Yi Chen
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0231690

Limited evidence for common interannual trends in Baltic Sea summer phytoplankton biomass
Cited by: 8
Author(s): Jennifer R. Griffiths, Sirpa Lehtinen, Sanna Suikkanen, Monika Winder
Software Mentions: 6
Published: over 4 years ago

10.1186/s13073-020-00729-2

Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival
Cited by: 59
Author(s): M. C. Wood, Benjamin R. Weeder, Julianne K. David, Abhinav Nellore, Reid F. Thompson
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0197954

No-U-turn sampling for fast Bayesian inference in ADMB and TMB: Introducing the adnuts and tmbstan R packages
Cited by: 50
Author(s): Cole C. Monnahan, Kasper Kristensen
Software Mentions: 5
Published: over 6 years ago

10.1098/rsos.192146

Biological and statistical interpretation of size-at-age, mixed-effects models of growth
Cited by: 8
Author(s): Simone Vincenzi, Dušan Jeseňsek, Alain J. Crivellì
Software Mentions: 4
Published: over 4 years ago

10.1186/s12874-021-01318-6

High performance implementation of the hierarchical likelihood for generalized linear mixed models: an application to estimate the potassium reference range in massive electronic health records datasets
Cited by: 1
Author(s): Cristian Bologa, V. Shane Pankratz, Mark Unruh, Maria Roumelioti, Vallabh O. Shah, Kamran Shaffi, Soraya Arzhan, John P. Cook, Christos Argyropoulos
Software Mentions: 4
Published: over 3 years ago

10.3389/fpsyg.2020.00606

Book Review: Modern Psychometrics With R
Cited by: 0
Author(s): Alexander Robitzsch
Software Mentions: 3
Published: over 4 years ago

10.1038/srep26677

State-space models’ dirty little secrets: even simple linear Gaussian models can have estimation problems
Cited by: 103
Author(s): Marie Auger‐Méthé, Chris Field, Christoffer Moesgaard Albertsen, Andrew E. Derocher, Mark A. Lewis, Ian D. Jonsen, Joanna Mills Flemming
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0216129

Efficient estimation of generalized linear latent variable models
Cited by: 45
Author(s): Jenni Niku, Wesley Brooks, Riki Herliansyah, Francis K. C. Hui, Sara Taskinen, David I. Warton
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.29198

Quantifying the contribution of Plasmodium falciparum malaria to febrile illness amongst African children
Cited by: 34
Author(s): Ursula Dalrymple, Ewan Cameron, Samir Bhatt, Daniel J. Weiss, Sunetra Gupta, Peter W. Gething
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-017-14278-z

Positioning of aquatic animals based on time-of-arrival and random walk models using YAPS (Yet Another Positioning Solver)
Cited by: 61
Author(s): Henrik Baktoft, Karl Øystein Gjelland, Finn Økland, Uffe Høgsbro Thygesen
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-40405-z

Generalizing the first-difference correlated random walk for marine animal movement data
Cited by: 14
Author(s): Christoffer Moesgaard Albertsen
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12916-020-01876-4

Mapping subnational HIV mortality in six Latin American countries with incomplete vital registration systems
Cited by: 69
Author(s): Michael A. Cork, Nathaniel J. Henry, Stefanie Watson, Andrew J. Croneberger, Mathew M. Baumann, Ian D. Letourneau, Mingyou Yang, Audrey L. Serfes, Jaffar Abbas, Nooshin Abbasi, Hedayat Abbastabar, Lucas Guimarães Abreu, Eman Abu‐Gharbieh, Basavaprabhu Achappa, Maryam Adabi, Tadele Girum Adal, Adeyinka Emmanuel Adegbosin, Victor Adekanmbi, Olatunji Adetokunboh, Marcela Agudelo-Botero, Bright Opoku Ahinkorah, Keivan Ahmadi, Muktar Beshir Ahmed, Robert Kaba Alhassan, Vahid Alipour, Amir Almasi‐Hashiani, Nelson Alvis‐Guzmán, Robert Ancuceanu, Tudorel Andrei, Davood Anvari, Muhammad Aqeel, Jalal Arabloo, Olatunde Aremu, Malke Asaad, Desta Debalkie Atnafu, Alok Atreya, Beatriz Paulina Ayala Quintanilla, Samad Azari, Darshan B. B, Atif Amin Baig, Maciej Banach, Simachew Animen Bante, Miguel A Barboza, Sanjay Basu, Neeraj Bedi, Diana Fernanda Bejarano Ramírez, Isabela M. Benseñor, Fenta Hun Y. Beyene, Yihienew Mequanint Bezabih, Akshaya Srikanth Bhagavathula, Nikha Bhardwaj, Pankaj Bhardwaj, Krittika Bhattacharyya, Zulfiqar Ahmed Bhutta, Ali Bijani, Sait Mentes Birlik, Zebenay Workneh Bitew, Somayeh Bohlouli, Archith Boloor, André R. Brunoni, Zahid A Butt, Rosario Cárdenas, Félix Carvalho, João Maurício Castaldelli-Maia, Carlos Castañeda-Orjuela, Jaykaran Charan, Souranshu Chatterjee, Vijay Kumar Chattu, Soosanna Kumary Chattu, Mohiuddin Ahsanul Kabir Chowdhury, Devasahayam Jesudas Christopher, Dinh Toi Chu, Aubrey J. Cook, Natalie Maria Cormier, Saad M A Dahlawi, Farah Daoud, Claudio Alberto Dávila-Cervantes, Nicole Davis Weaver, Fernando Pío De la Hoz, Feleke Mekonnen Demeke, Edgar Denova‐Gutiérrez, Kebede Deribe, Keshab Deuba, Samath D Dharmaratne, Govinda Prasad Dhungana, Daniel Díaz, Shirin Djalalinia, André Rodrigues Durães, Arielle Wilder Eagan, Lucas Earl, Andem Effiong, Maysaa El Sayed Zaki, Maha El Tantawi, Rajesh Elayedath, Shaimaa I El-Jaafary, Emerito Jose A Faraon, André Faro, Nazir Fattahi, Nelsensius Klau Fauk, Eduarda Fernandes, Irina Filip, Florian Fischer, Nataliya Foigt, Masoud Foroutan, Takeshi Fukumoto, Mohamed M. Gad, Tesfay B.B. Gebremariam, Ketema Bizuwork Gebremedhin, Gebreamlak Gebremedhn Gebremeskel, Hailay Abrha Gesesew, Keyghobad Ghadiri, Ahmad Ghashghaee, Syed Amir Gilani, Mahaveer Golechha, Ugo Gori, Alessandra Carvalho Goulart, Bárbara Niegia Garcia de Goulart, H. C. Gugnani, Mark D. C. Guimarães, Rafael Alves Guimarães, Hyewon Lee, Rahul Gupta, Emily Haeuser, Mohammad Rifat Haider, Teklehaimanot Gereziher Haile, Arvin Haj-Mirzaian, Arya Haj‐Mirzaian, Asif Hanif, Arief Hargono, Ninuk Hariyani, Soheil Hassanipour, Hadi Hassankhani, Khezar Hayat, Claudiu Herțeliu, Hung Chak Ho, Ramesh Holla, Mehdi Hosseinzadeh, Mowafa Househ, Bing‐Fang Hwang, Charles Ugochukwu Ibeneme, Segun Emmanuel Ibitoye, Olayinka Stephen Ilesanmi, Milena D Ilic, Irena Ilić, Usman Iqbal, Deepa Jahagirdar, Vardhmaan Jain, Mihajlo Jakovljević, Ravi Prakash Jha, Kimberly Johnson, Nitin Joseph, Farahnaz Joukar, Leila R Kalankesh, Rohol Lah Kalhor, Tanuj Kanchan, Behzad Karami Matin, André Karch, Salah Eddin Karimi, Getinet Kassahun, Gbenga A Kayode, Ali Kazemi Karyani, Maryam Keramati, Nauman Khalid, Ejaz Ahmad Khan, Gulfaraz Khan, Nuruzzaman Khan, Khaled Khatab, Neda Kianipour, Yun Jin Kim, Sezer Kısa, Adnan Kısa, Soewarta Kosen, Sindhura Lakshmi Koulmane Laxminarayana, Ai Koyanagi, Kewal Krishan, Barthélémy Kuate Defo, Ricardo Kuchenbecker, Vaman Kulkarni, Nithin Kumar, Manasi Kumar, Om Kurmi, Dian Kusuma, Carlo La Vecchia, Dharmesh Kumar Lal, Iván Landires, Savita Lasrado, Paul H. Lee, Kate E LeGrand, Bingyu Li, Shanshan Li, Xuefeng Li, Hawraz Ibrahim M. Amin, Daiane Borges Machado, Deepak Madi, Carlos Magis-Rodríguez, Déborah Carvalho Malta, Mohammad Alì Mansournia, Dilshad Manzar, Carlos Alberto Marrugo-Arnedo, Francisco Rogerlândio Martins-Melo, Seyedeh Zahra Masoumi, Benjamin K. Mayala, Carlo Eduardo Medina-Solís, Ziad A. Memish, Walter Mendoza, Ritesh G. Menezes, Tomislav Meštrović, Andreea Mirică, Babak Moazen, Yousef Mohammad, Naser Mohammad Gholi Mezerji, Abdollah Mohammadian-Hafshejani, Reza Mohammadpourhodki, Shafiu Mohammed, Ali H. Mokdad, Mohammad Ali Moni, Masoud Moradi, Yousef Moradi, Rahmatollah Moradzadeh, Paula Moraga, Amin Mou Savi Khaneghah, Ghulam Mustafa, Lillian Mwanri, Nagaraja Ravishankar, Ahamarshan Jayaraman Nagarajan, Mukhammad David Naimzada, Bruno Ramos Nascimento, Muhammad Naveed, Vinod C Nayak, Javad Nazari, Hadush Negash, Ionuţ Negoi, Samata Nepal, Georges Nguefack‐Tsague, Cuong Tat Nguyen, Huong Lan Thi Nguyen, Rajan Nikbakhsh, Jean Jacques Noubiap, Virginia Núñez-Samudio, Bogdan Oancea, Felix Akpojene Ogbo, Andrew T Olagunju, Nikita Otstavnov, Mahesh P. A, Jagadish Rao Padubidri, Seithikurippu R. Pandi‐Perumal, Ana Melisa Pardo Montaño, Urvish Patel, Shrikant Pawar, Emmanuel Peprah, Alexandre C. Pereira, Samantha Perkins, Júlia Moreira Pescarini, Khem Narayan Pokhrel, Maarten J. Postma, Faheem Hyder Pottoo, Sergio I. Prada, Liliana Preoţescu, Dimas Ria Angga Pribadi, Amir Radfar, Fakher Rahim, Mohammad Hifz Ur Rahman, Amir Masoud Rahmani, Kiana Ramezanzadeh, Juwel Rana, Chhabi Lal Ranabhat, Sowmya J Rao, Priya Rathi, Salman Rawaf, David Laith Rawaf, Reza Rawassizadeh, Vishnu Renjith, Nima Rezaei, Aziz Rezapour, Ana Isabel Ribeiro, Leonardo Roever, Enrico Rubagotti, Susan F. Rumisha, Godfrey Mutashambara Rwegerera, Rajesh Sagar, S. Mohammad Sajadi, Marwa Rashad Salem, Abdallah M. Samy, Rodrigo Sarmiento-Suárez, Brijesh Sathian, Lauren E. Schaeffer, Ione Jayce Ceola Schneider, Abdul Aziz Seidu, Feng Sha, Masood Ali Shaikh, Kio Mars Sharafi, Aziz Sheikh, Kenji Shibuya, Jae Il Shin, Diego Augusto Santos Silva, Jasvinder A Singh, Valentin Yurievich Skryabin, Anna Aleksandrovna Skryabina, Amber Sligar, Amin Soheili, Krista M. Steuben, Mu’awiyyah Babale Sufiyan, Eyayou Girma Tadesse, Ayenew Kassie, Fisaha Haile Tesfay, Rekha Thapar, Robert L. Thompson, Marcos Roberto Tovani‐Palone, Bach Xuan Tran, Gebiyaw Wudie Tsegaye, Chukwuma David Umeokonkwo, B Unnikrishnan, Yasser Vasseghian, Francesco Saverio Violante, Bay Vo, Giang Thu Vu, Yasir Waheed, Yuan‐Pang Wang, Yanzhong Wang, Paul Ward, Fissaha Tekulu Welay, Ronny Westerman, Nuwan Darshana Wickramasinghe, Sanni Yaya, Paul Yip, Naohiro Yonemoto, Chuanhua Yu, Deniz Yüce, Hasan Yusefzadeh, Maryam Zamanian, Михаил Сергеевич Застрожин, Zhi Jiang Zhang, Yunquan Zhang, Arash Ziapour, Simon I Hay, Laura Dwyer-Lindgren
Software Mentions: 1
Published: almost 4 years ago

10.7554/eLife.62122

Mapping the endemicity and seasonality of clinical malaria for intervention targeting in Haiti using routine case data
Cited by: 6
Author(s): Ewan Cameron, Alyssa J. Young, Katherine A. Twohig, Emilie Pothin, Darlene Bhavnani, Amber Dismer, Jean Baptiste Merilien, Karen E. S. Hamre, Phoebe Meyer, Arnaud Le Menach, Justin M. Cohen, Samson Marseille, Jean Frantz Lemoine, Marc Aurèle Telfort, Michelle Chang, Kimberly Y. Won, Alaine Knipes, Eric Rogier, Punam Amratia, Daniel J. Weiss, Peter W. Gething, Katherine E. Battle
Software Mentions: 1
Published: over 3 years ago

10.1002/cam4.1372

Microsatellite instability status determined by next-generation sequencing and compared with PD-L1 and tumor mutational burden in 11,348 patients
Cited by: 324
Author(s): Ari M. Vanderwalde, David Spetzler, Nianqing Xiao, Zoran Gatalica, John L. Marshall
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12936-018-2371-9

How long do rapid diagnostic tests remain positive after anti-malarial treatment?
Cited by: 101
Author(s): Ursula Dalrymple, Rohan Arambepola, Peter W. Gething, Ewan Cameron
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1009611

Predicting population genetic change in an autocorrelated random environment: Insights from a large automated experiment
Cited by: 7
Author(s): Marie Rescan, Daphné Grulois, Enrique Ortega Aboud, Pierre de Villemereuil, Luis‐Miguel Chevin
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0140864

From Fishing to Fish Processing: Separation of Fish from Crustaceans in the Norway Lobster-Directed Multispecies Trawl Fishery Improves Seafood Quality
Cited by: 18
Author(s): Junita Diana Karlsen, Ludvig Ahm Krag, Christoffer Moesgaard Albertsen, Rikke Frandsen
Software Mentions: 1
Published: about 9 years ago

10.3390/cancers12102825

Extracellular Vesicles as Biomarkers in Cancer Immunotherapy
Cited by: 60
Author(s): Matthen Mathew, Mariam Zade, Nadia Mezghani, Romil Patel, Yu Wang, Fatemeh Momen-Heravi
Software Mentions: 1
Published: about 4 years ago

10.3389/fimmu.2020.00604

The Biogenesis, Biology, and Clinical Significance of Exosomal PD-L1 in Cancer
Cited by: 48
Author(s): Yue Tang, Ping Zhang, Yumin Wang, Jinpeng Wang, Min Su, Ying Wang, Lianqing Zhou, Jinsong Zhou, Xiong Wang, Zhaoyang Zeng, Yujuan Zhou, Shaolin Nie, Qianjin Liao
Software Mentions: 1
Published: over 4 years ago

10.3389/fvets.2018.00197

Robustness of Eco-Epidemiological Capture-Recapture Parameter Estimates to Variation in Infection State Uncertainty
Cited by: 9
Author(s): Sarah Benhaiem, Lucile Marescot, Heribert Hofer, Marion L. East, Jean‐Dominique Lebreton, Stephanie Kramer‐Schadt, Olivier Giménez
Software Mentions: 1
Published: over 6 years ago

10.1186/s12963-017-0133-5

Self-reported general health, physical distress, mental distress, and activity limitation by US county, 1995-2012
Cited by: 42
Author(s): Laura Dwyer-Lindgren, Johan P. Mackenbach, Frank J. van Lenthe, Ali H. Mokdad
Software Mentions: 1
Published: over 7 years ago

10.1186/s12963-018-0171-7

Small area estimation of under-5 mortality in Bangladesh, Cameroon, Chad, Mozambique, Uganda, and Zambia using spatially misaligned data
Cited by: 10
Author(s): Laura Dwyer-Lindgren, Ellen Squires, Stephanie Teeple, Gloria Ikilezi, D. Allen Roberts, Danny V. Colombara, Sarah Katherine Allen, Stanley M. Kamande, Nicholas Graetz, Abraham D. Flaxman, Charbel El Bcheraoui, Kristjana Ásbjörnsdóttir, Gilbert Asiimwe, Ângelo Augusto, Orvalho Augusto, Baltazar Chilundo, Caroline De Schacht, Sarah Gimbel, Carol Kamya, Faith Namugaya, Felix Masiye, Cremildo Mauieia, Yodé Miangotar, Honoré Mimche, Acácio Sabonete, Haribondhu Sarma, Kenneth Sherr, Moses C. Simuyemba, Aaron Sinyangwe, Jasim Uddin, Bradley H. Wagenaar, Stephen S Lim
Software Mentions: 1
Published: over 6 years ago

10.1038/s41597-020-0406-x

The retrospective analysis of Antarctic tracking data project
Cited by: 22
Author(s): Yan Ropert‐Coudert, Anton P. Van de Putte, Ryan R Reisinger, Horst Bornemann, Jean‐Benoît Charrassin, Daniel P. Costa, Bruno Danis, Luis A. Hückstädt, Ian D. Jonsen, Mary‐Anne Lea, David R. Thompson, Leigh G. Torres, Philip N. Trathan, Simon Wotherspoon, David G. Ainley, Rachael Alderman, Virginia Andrews‐Goff, Ben J. Arthur, Grant Ballard, John L. Bengtson, Marthán N Bester, Arnoldus Schytte Blix, Lars Boehme, Charles‐André Bost, Peter L. Boveng, Jaimie Cleeland, Rochelle Constantine, Robert J. M. Crawford, Luciano Dalla Rosa, P. J. Nico de Bruyn, Karine Delord, Sébastien Descamps, Mike Double, Louise Emmerson, Michael A. Fedak, Ari S. Friedlaender, Nick Gales, Mike Goebel, Kimberly T. Goetz, Christophe Guinet, Simon Goldsworthy, Robert Harcourt, Jefferson T. Hinke, Kerstin Jerosch, Akira Kato, Knowles Kerry, Roger Kirkwood, Gerald L. Kooyman, Kit M. Kovacs, Kieran Lawton, Andrew D. Lowther, Christian Lydersen, Phil O'b. Lyver, Azwianewi B. Makhado, María Elba Isabel Márquez, Birgitte I. McDonald, Clive R. McMahon, Mônica M. C. Muelbert, Dominik Nachtsheim, Keith W. Nicholls, Erling S. Nordøy, Silvia Olmastroni, Richard A. Phillips, Pierre Pistorius, Joachim Plötz, Klemens Pütz, Norman Ratcliffe, Peter G. Ryan, Mercedes Santos, Colin Southwell, Iain J. Staniland, Akinori Takahashi, Arnaud Tarroux, Wayne Z. Trivelpiece, Ewan D. Wakefield, Henri Weimerskirch, Bárbara Wienecke, José C. Xavier, Ben Raymond, Mark A. Hindell
Software Mentions: 1
Published: almost 5 years ago