Ecosyste.ms: Papers

10.1371/journal.pcbi.1007721

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries
Cited by: 24
Author(s): Cedoljub Bundalovic-Torma, Gregory B. Whitfield, Lindsey S. Marmont, P. Lynne Howell, John Parkinson
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0257305

Effects of blood urea nitrogen independent of the estimated glomerular filtration rate on the development of anemia in non-dialysis chronic kidney disease: The results of the KNOW-CKD study
Cited by: 4
Author(s): Hyo Jin Kim, Tae Eun Kim, Miyeun Han, Yongin Yi, Jong Cheol Jeong, Ho Jun Chin, Sang Heon Song, Joongyub Lee, Kyu‐Beck Lee, Suah Sung, Seung Hyeok Han, Eun Young Seong, Curie Ahn, Kook‐Hwan Oh, Dong‐Wan Chae
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0258515

How does individualised physiotherapy work for people with low back pain? A Bayesian Network analysis using randomised controlled trial data
Cited by: 3
Author(s): Bernard X. W. Liew, Jon Ford, Marco Scutari, Andrew J. Hahne
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1008730

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks
Cited by: 5
Author(s): Pablo Rodríguez-Mier, Nathalie Poupin, Carlo De Blasio, Laurent Le Cam, Fabien Jourdan
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0243936

A prospective study to explore the relationship between MTHFR C677T genotype, physiological folate levels, and postpartum psychopathology in at-risk women
Cited by: 4
Author(s): Emily Morris, Catriona Hippman, Arianne Albert, Caitlin Slomp, Angela Inglis, Prescilla Carrion, Rolan Batallones, Heather Andrighetti, Colin Ross, Roger Dyer, William G. Honer, Jehannine Austin
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008648

A kinesin Klp10A mediates cell cycle-dependent shuttling of Piwi between nucleus and nuage
Cited by: 3
Author(s): Zsolt Venkei, Charlotte P Choi, Suhua Feng, Cuie Chen, Steven E. Jacobsen, John K. Kim, Yukiko Yamashita
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008646

PEtab—Interoperable specification of parameter estimation problems in systems biology
Cited by: 50
Author(s): Leonard Schmiester, Yannik Schälte, Frank Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang G. Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0239345

Prestige and homophily predict network structure for social learning of medicinal plant knowledge
Cited by: 6
Author(s): Matthew O. Bond, Orou G. Gaoue
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0237373

Do dogs eavesdrop on human interactions in a helping situation?
Cited by: 4
Author(s): Hoi-Lam Jim, Sarah Marshall-Pescini, Friederike Range
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0243684

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)
Cited by: 19
Author(s): Roger Brown, Lindsey Moore, Amir Mani, Sonal Patel, Irene Salinas
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008792

Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development
Cited by: 8
Author(s): Tanzeen Yusuff, Matthew Jensen, Sneha Yennawar, Lucilla Pizzo, S. Karthikeyan, Dagny J. Gould, Avik Sarker, Erika Gedvilaite, Yurika Matsui, Janani Iyer, Zhi Chun Lai, Santhosh Girirajan
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pmed.1003188

Ambient air pollution and cause-specific risk of hospital admission in China: A nationwide time-series study
Cited by: 91
Author(s): Jianfeng Gu, Ying Shi, Yifang Zhu, Ning Chen, Haibo Wang, Zongjiu Zhang, Ting Chen
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008503

Simple models including energy and spike constraints reproduce complex activity patterns and metabolic disruptions
Cited by: 8
Author(s): Tanguy Fardet, Anna Levina
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0231718

Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish
Cited by: 20
Author(s): Sayaka Takahashi, Masato Sakata, Toshifumi Minamoto, Reiji Masuda
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008794

Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti
Cited by: 10
Author(s): Laura B. Dickson, Sarah H. Merkling, Mathieu Gautier, Amine Ghozlane, Davy Jiolle, Christophe Paupy, Diégo Ayala, Isabelle Moltini-Conclois, Albin Fontaine, Louis Lambrechts
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0252691

Industrialization as a source of heavy metals and antibiotics which can enhance the antibiotic resistance in wastewater, sewage sludge and river water
Cited by: 42
Author(s): Jakub Hubeny, Monika Harnisz, Ewa Korzeniewska, Martyna Buta, W. Zieliński, Damian Rolbiecki, Joanna Giebułtowicz, Grzegorz Nałęcz‐Jawecki, Grażyna Płaza
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008324

The plant mobile domain proteins MAIN and MAIL1 interact with the phosphatase PP7L to regulate gene expression and silence transposable elements in Arabidopsis thaliana
Cited by: 12
Author(s): Mélody Nicolau, Nathalie Picault, Julie Descombin, Yasaman Jami‐Alahmadi, Suhua Feng, Etienne Bucher, Steven E. Jacobsen, Jean-Marc Deragon, James A. Wohlschlegel, Guillaume Moissiard
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0251565

The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum
Cited by: 7
Author(s): Kaylene R. Ballard, Anne Klein, R. Andrew Hayes, Tianfang Wang, Scott F. Cummins
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009058

A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2
Cited by: 9
Author(s): Edward M. Hill, Benjamin D. Atkins, Matthew James Keeling, Louise Dyson, Michael J. Tildesley
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008957

On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
Cited by: 15
Author(s): Edwin Rodríguez Horta, Martin Weigt
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009267

Unveiling functions of the visual cortex using task-specific deep neural networks
Cited by: 18
Author(s): Kshitij Dwivedi, Michael Bonner, Radoslaw Martin Cichy, Gemma Roig
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008304

PPM-Decay: A computational model of auditory prediction with memory decay
Cited by: 10
Author(s): Peter M. C. Harrison, Roberta Bianco, Maria Chait, Marcus T. Pearce
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1008666

Relaxed constraint and functional divergence of the progesterone receptor (PGR) in the human stem-lineage
Cited by: 7
Author(s): Mirna Marinić, Vincent J. Lynch
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008909

Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes
Cited by: 1
Author(s): Christophe Menichelli, Vincent Guitard, Rafael Miyazawa Martins, Sophie Lèbre, José-Juan Lopez-Rubio, Charles-Henri Lecellier, Laurent Bréhélin
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008681

The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2)
Cited by: 20
Author(s): Christos N. Velanis, Pumi Perera, Bennett Thomson, Erica de Leau, Shih Chieh Liang, Ben Hartwig, Alexander Förderer, Harry Thornton, Pedro Arêde, Jiawen Chen, Kimberly M. Webb, Serin Gümüs, Geert De Jaeger, Clinton A. Page, C. Nathan Hancock, Christos Spanos, Juri Rappsilber, Philipp Voigt, Franziska Turck, Frank Wellmer, Justin Goodrich
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0222232

A half-century of changes in migratory landbird numbers along coastal Massachusetts
Cited by: 3
Author(s): Matthew Kamm, Trevor L. Lloyd-Evans, Maina C. Handmaker, J. Michael Reed
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1008675

Tryptamine accumulation caused by deletion of MrMao-1 in Metarhizium genome significantly enhances insecticidal virulence
Cited by: 19
Author(s): Xiaowei Tong, Yundan Wang, Pengcheng Yang, Chengshu Wang, Le Kang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008395

Bacteria use structural imperfect mimicry to hijack the host interactome
Cited by: 5
Author(s): Natalia Sánchez de Groot, M. C. Torrent
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0228974

Parental investment and immune dynamics in sex-role reversed pipefishes
Cited by: 4
Author(s): Isabel Keller, Olivia Roth
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1007937

Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity
Cited by: 13
Author(s): Stefano Masoli, Alessandra Ottaviani, Stefano Casali, Egidio D’Angelo
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0254617

Tuna behaviour at anchored FADs inferred from Local Ecological Knowledge (LEK) of pole-and-line tuna fishers in the Maldives
Cited by: 4
Author(s): Ahmed Riyaz Jauharee, Manuela Capello, Monique Simier, Fabien Forget, M. Shiham Adam, Laurent Dagorn
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pmed.1003765

Impact of color-coded and warning nutrition labelling schemes: A systematic review and network meta-analysis
Cited by: 62
Author(s): Jieqiong Song, Mhairi K. Brown, Monique Tan, Graham A. MacGregor, Jacqui Webster, Norm R.C. Campbell, Kathy Trieu, Cliona Ní Mhurchú, Laura K. Cobb, Feng J He
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0224887

Carbonate production of Micronesian reefs suppressed by thermal anomalies and Acanthaster as sea-level rises
Cited by: 8
Author(s): Robert van Woesik, Christopher William Cacciapaglia
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pmed.1003149

Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts
Cited by: 43
Author(s): Naeimeh Atabaki‐Pasdar, Mattias Ohlsson, Ana Viñuela, Francesca Frau, Hugo Pomares-Millan, Mark Haid, Angus G. Jones, E. Louise Thomas, Robert W. Koivula, Azra Kurbasic, Pascal M. Mutie, Hugo Fitipaldi, Juan Carlos Delgado Fernández, Adem Y. Dawed, G Giordano, Ian Forgie, Timothy J. McDonald, Femke Rutters, Henna Cederberg, Elizaveta Chabanova, Matilda Dale, Federico De Masi, Cecilia Engel Thomas, Kristine H. Allin, Torben Hansen, Alison Heggie, Mun Gwan Hong, Petra Elders, Gwen Kennedy, Tarja Kokkola, Helle Pedersen, Anubha Mahajan, Donna McEvoy, François Pattou, Violeta Raverdy, Ragna S. Häussler, Sapna Sharma, Henrik S. Thomsen, Jagadish Vangipurapu, Henrik Vestergaard, Leen M. ′t Hart, Jerzy Adamski, Petra B. Musholt, Søren Brage, Søren Brunak, Emmanouil T. Dermitzakis, Gary Frost, Markku Laakso, Oluf Pedersen, Martin Ridderstråle, Hartmut Ruetten, Andrew T. Hattersley, Mark Walker, Joline W.J. Beulens, Andrea Mari, Jochen M. Schwenk, Ramneek Gupta, Mark McCarthy, Ewan R. Pearson, Jimmy D. Bell, Imre Pávó, Paul W. Franks
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0257686

Measuring information flux between social media and stock prices with Transfer Entropy
Cited by: 4
Author(s): Román A. Mendoza-Urdiales, Andrés García-Medina, José Antonio Núñez Mora
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0240252

The effects of language and emotionality of stimuli on vocabulary learning
Cited by: 8
Author(s): Candice Frances, Angela de Bruin, Jon Andoni Duñabeitia
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1009710

DNA methyltransferase CHROMOMETHYLASE3 prevents ONSEN transposon silencing under heat stress
Cited by: 18
Author(s): Kohei Nozawa, Jiani Chen, Jingchao Jiang, Sarah M. Leichter, Masataka Yamada, Takamasa Suzuki, Fengquan Liu, Hidetaka Ito, Xuehua Zhong
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009321

Regulating the expression of gene drives is key to increasing their invasive potential and the mitigation of resistance
Cited by: 63
Author(s): Andrew Hammond, Xenia Karlsson, Ioanna Morianou, Kyros Kyrou, Andrea Beaghton, Matthew O. Gribble, Nace Kranjc, Roberto Galizi, Austin Burt, Andrea Crisanti, Tony Nolan
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0236684

Distinct patterns of activity in individual cortical neurons and local networks in primary somatosensory cortex of mice evoked by square-wave mechanical limb stimulation
Cited by: 2
Author(s): Mischa V Bandet, Bin Dong, Ian R. Winship
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0225064

Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth
Cited by: 14
Author(s): Qianqian Guo, Pei Qin Ng, Shanshan Shi, Diwen Fan, Jun Li, Jing Zhao, Hua Wang, Rakesh David, Parul Mittal, Quang Trung, Ralph Bock, Ming Zhao, Wenbin Zhou, Iain Searle
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0256975

Lens fluorescence and skin fluorescence in the Copenhagen Twin Cohort Eye Study: Covariates and heritability
Cited by: 0
Author(s): Jakob Bjerager, Sami Dabbah, Mohamed Belmouhand, S. P. Rothenbuehler, Birgit Sander, Michael Larsen
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1009686

A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing
Cited by: 11
Author(s): Akihiro Nita, Akinobu Matsumoto, Ronghao Tang, Chisa Shiraishi, Kazuya Ichihara, Daisuke Saito, Mikita Suyama, Tomoharu Yasuda, Gaku Tsuji, Masutaka Furue, Bunpei Katayama, Toshiyuki Ozawa, Takaho Murata, Teruki Dainichi, Kenji Kabashima, Atsushi Hatano, Masaki Matsumoto, Keiichi I. Nakayama
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008190

Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes
Cited by: 5
Author(s): Quirine A. ten Bosch, Joseph Wagman, Fanny Castro-Llanos, Nicole L. Achee, John P. Grieco, T. Alex Perkins
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1008197

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases
Cited by: 8
Author(s): Janani Durairaj, Elena Melillo, Harro J. Bouwmeester, Jules Beekwilder, Dick de Ridder, Aalt D. J. van Dijk
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pmed.1003777

Predictive symptoms for COVID-19 in the community: REACT-1 study of over 1 million people
Cited by: 63
Author(s): Joshua Elliott, Matthew Whitaker, Barbara Bodinier, Oliver Eales, Steven Riley, Helen Ward, Graham Cooke, Ara Darzi, Marc Chadeau‐Hyam, Paul Elliott
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1008927

Embedding optimization reveals long-lasting history dependence in neural spiking activity
Cited by: 6
Author(s): Lucas Rudelt, D Marx, Michael Wibral, Viola Priesemann
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1007829

Improving the coverage of credible sets in Bayesian genetic fine-mapping
Cited by: 30
Author(s): Anna Hutchinson, Hope Watson, Chris Wallace
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0229490

NAA and 6-BA promote accumulation of oleanolic acid by JA regulation in Achyranthes bidentata Bl
Cited by: 1
Author(s): Yanqing Liu, Li Tang, Can Wang, Jinting Li
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pmed.1003566

Dynamics of sputum conversion during effective tuberculosis treatment: A systematic review and meta-analysis
Cited by: 9
Author(s): Claire Calderwood, James P. Wilson, Katherine Fielding, Rebecca Harris, Aaron S Karat, Raoul Mansukhani, Jane Falconer, Malin Bergström, S.D. Johnson, Nicky McCreesh, Edward J M Monk, Jasantha Odayar, P. J. Scott, Sarah A. Stokes, Hannah Theodorou, David Moore
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0229661

Measuring childhood maltreatment: Psychometric properties of the Norwegian version of the Maltreatment and Abuse Chronology of Exposure (MACE) scale
Cited by: 11
Author(s): Roar Fosse, Dag Vegard Skjelstad, Inga Schalinski, Dorothea Thekkumthala, Thomas Elbert, Chris Margaret Aanondsen, Hanne Klæboe Greger, Thomas Jozefiak
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1008192

Nonlinear stimulus representations in neural circuits with approximate excitatory-inhibitory balance
Cited by: 17
Author(s): Cody Baker, Vicky Zhu, Robert Rosenbaum
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1007659

Achieving stable dynamics in neural circuits
Cited by: 14
Author(s): Leo Kozachkov, Mikael Lundqvist, Jean‐Jacques E. Slotine, Earl K. Miller
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008249

PyOIF: Computational tool for modelling of multi-cell flows in complex geometries
Cited by: 14
Author(s): Iveta Jančigová, Kristína Kovalčíková, Rudolf Weeber, Ivan Cimrák
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1009625

Light affects behavioral despair involving the clock gene Period 1
Cited by: 16
Author(s): Iwona Olejniczak, Jürgen A. Ripperger, Federica Sandrelli, Anna Schnell, Laureen Mansencal-Strittmatter, Katrin S. Wendrich, Ka Yi Hui, Andrea Brenna, Naïla Ben Fredj, Urs Albrecht
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pmed.1003436

Induction of labour at 41 weeks or expectant management until 42 weeks: A systematic review and an individual participant data meta-analysis of randomised trials
Cited by: 23
Author(s): Mårten Alkmark, Judit K. J. Keulen, Joep C. Kortekaas, Christina Bergh, Jeroen van Dillen, Ruben G. Duijnhoven, Henrik Hagberg, Ben Willem J. Mol, Mattias Molin, Joris A. M. van der Post, Sissel Saltvedt, Anna‐Karin Wikström, Ulla‐Britt Wennerholm, Esteriek de Miranda
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1009523

Aicardi-Goutières syndrome-associated gene SAMHD1 preserves genome integrity by preventing R-loop formation at transcription–replication conflict regions
Cited by: 25
Author(s): Kiwon Park, Jeongmin Ryoo, Heena Jeong, Minsu Kim, Sungwon Lee, Sung-Yeon Hwang, Ji-Young Ahn, Doyeon Kim, Hyungseok C. Moon, Daehyun Baek, Kwangsoo Kim, Hye Yoon Park, Kwangseog Ahn
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0223203

Unexpected predicted length variation for the coding sequence of the sleep related gene, BHLHE41 in gorilla amidst strong purifying selection across mammals
Cited by: 0
Author(s): Krishna Unadkat, Justen B. Whittall
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008104

Regional sequence expansion or collapse in heterozygous genome assemblies
Cited by: 23
Author(s): Kathryn C. Asalone, Kara M. Ryan, Maryam Yamadi, Annastelle Cohen, William G. Farmer, Deborah J. George, Claudia Joppert, Kaitlyn Kim, Madeeha Froze Mughal, Rana Said, Metin Toksoz-Exley, Evgeny Bisk, John R. Bracht
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008840

The kinase Isr1 negatively regulates hexosamine biosynthesis in S. cerevisiae
Cited by: 3
Author(s): Emma B Alme, Erica Stevenson, Nevan J. Krogan, Danielle L. Swaney, David P. Toczyski
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008266

A mesoscopic simulator to uncover heterogeneity and evolutionary dynamics in tumors
Cited by: 8
Author(s): Juan Jiménez-Sánchez, Álvaro Martínez-Rubio, Антон Попов, Julián Pérez-Beteta, Youness Azimzade, David Molina-García, Juan Belmonte-Beitia, Gabriel F. Calvo, Víctor M. Pérez‐García
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1008322

Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
Cited by: 44
Author(s): Jordan Douglas, Rong Zhang, Remco Bouckaert
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1007822

Biophysically grounded mean-field models of neural populations under electrical stimulation
Cited by: 36
Author(s): Caglar Cakan, Klaus Obermayer
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0255799

Substance use disorders and suicidality in youth: A systematic review and meta-analysis with a focus on the direction of the association
Cited by: 16
Author(s): Charlie Rioux, Anne-Sophie Huet, Natalie Castellanos‐Ryan, Laurianne Fortier, Marie-Ève Blanc, Stéphanie Hamaoui, Marie‐Claude Geoffroy, Johanne Renaud, Jean R. Séguin
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0242078

How automatic speed control based on distance affects user behaviours in telepresence robot navigation within dense conference-like environments.
Cited by: 6
Author(s): Anil Ufuk Batmaz, Jens Maiero, Ernst Kruijff, Bernhard E. Riecke, Carman Neustaedter, Wolfgang Stuerzlinger
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pmed.1003074

Association of suicidal behavior with exposure to suicide and suicide attempt: A systematic review and multilevel meta-analysis
Cited by: 42
Author(s): Nicole T. M. Hill, Jo Robinson, Jane Pirkis, Karl Andriessen, Karolina Krysińska, Amber Payne, Alexandra Boland, Alison Clarke, Allison Milner, Katrina Witt, Stephan Krohn, Amit Lampit
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0251732

Phlpp1 is induced by estrogen in osteoclasts and its loss in Ctsk-expressing cells does not protect against ovariectomy-induced bone loss
Cited by: 2
Author(s): Marcelline K. Hanson, Ismael Y. Karkache, David H. H. Molstad, Andrew Norton, Kim C. Mansky, Elizabeth W. Bradley
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008237

Graph-theoretical formulation of the generalized epitope-based vaccine design problem
Cited by: 3
Author(s): Emilio Dorigatti, Benjamin Schubert
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pmed.1003100

Metabolic risk factors and incident advanced liver disease in non-alcoholic fatty liver disease (NAFLD): A systematic review and meta-analysis of population-based observational studies
Cited by: 177
Author(s): Helen Jarvis, Dawn Craig, Robert Barker, Gemma Spiers, Daniel Stow, Quentin M. Anstee, Barbara Hanratty
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0256463

Adapting the coordination of eyes and head to differences in task and environment during fully-mobile visual exploration
Cited by: 12
Author(s): John M. Franchak, Brianna McGee, Gabrielle Blanch
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008647

A fly model establishes distinct mechanisms for synthetic CRISPR/Cas9 sex distorters
Cited by: 35
Author(s): Barbara Fasulo, Angela Meccariello, Maya Morgan, Carl Borufka, Philippos Aris Papathanos, Nikolai Windbichler
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0231415

What matters to women in the postnatal period: A meta-synthesis of qualitative studies
Cited by: 89
Author(s): Kenneth William Finlayson, Nicola Crossland, Mercedes Bonet, Soo Downe
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0243336

Bioinformatic analysis linking genomic defects to chemosensitivity and mechanism of action
Cited by: 0
Author(s): David G. Covell
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009735

Chromoanagenesis from radiation-induced genome damage in Populus
Cited by: 8
Author(s): Weier Guo, Luca Comai, Isabelle Henry
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0254943

The influence of LncRNA H19 polymorphic variants on susceptibility to cancer: A systematic review and updated meta-analysis of 28 case-control studies
Cited by: 2
Author(s): Kunpeng Wang, Zheng Zhu, Yiqiu Wang, Dayuan Zong, Peng Xue, Jingyu Gu, Da Yong Lu, Chuanquan Tu
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pmed.1003368

Qualitative process evaluation from a complex systems perspective: A systematic review and framework for public health evaluators
Cited by: 45
Author(s): Elizabeth McGill, Dalya Marks, Vanessa Er, Tarra L. Penney, Mark Petticrew, Matt Egan
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0243193

From anxiety to action—Experience of threat, emotional states, reactance, and action preferences in the early days of COVID-19 self-isolation in Germany and Austria
Cited by: 17
Author(s): Stefan Reiß, Vittoria Franchina, Chiara Jutzi, Robin Willardt, Eva Jonas
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1009260

A model of resource partitioning between foraging bees based on learning
Cited by: 8
Author(s): Thibault Dubois, Cristian Pasquaretta, Andrew B. Barron, Jacques Gautrais, Mathieu Lihoreau
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008625

A homozygous missense variant in CACNB4 encoding the auxiliary calcium channel beta4 subunit causes a severe neurodevelopmental disorder and impairs channel and non-channel functions
Cited by: 15
Author(s): Pierre Costé de Bagneaux, Leonie von Elsner, Tatjana Bierhals, Marta Campiglio, Jessika Johannsen, Gerald J. Obermair, Maja Hempel, Bernhard E. Flucher, Kerstin Kutsche
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008882

Maize adaptation across temperate climates was obtained via expression of two florigen genes
Cited by: 23
Author(s): Sara Castelletti, Aude Coupel‐Ledru, Ítalo Stefanine Correia Granato, Carine Palaffre, Llorenç Cabrera‐Bosquet, Chiara Tonelli, Stéphane Nicolas, François Tardieu, Claude Welcker, Lucio Conti
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0245501

Balancing time use for children’s fitness and adiposity: Evidence to inform 24-hour guidelines for sleep, sedentary time and physical activity
Cited by: 16
Author(s): Dorothea Dumuid, Melissa Wake, David Burgner, Mark S. Tremblay, Anthony D. Okely, Ben Edwards, Terence Dwyer, Tim Olds
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0241465

What triggers online help-seeking retransmission during the COVID-19 period? Empirical evidence from Chinese social media
Cited by: 26
Author(s): Chen Luo, Yuru Li, Anfan Chen, Yulong Tang
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0237304

A fractal kinetics SI model can explain the dynamics of COVID-19 epidemics
Cited by: 13
Author(s): Kosmas Kosmidis, Panos Macheras
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0245058

Efficient association mapping from k-mers—An application in finding sex-specific sequences
Cited by: 5
Author(s): Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, Atif Rahman
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1009634

Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin
Cited by: 5
Author(s): Salini Konikkat, Michelle R. Scribner, Rory Eutsey, N. Luisa Hiller, Vaughn S. Cooper, C. Joel McManus
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009464

Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults
Cited by: 10
Author(s): Binglan Li, Yogasudha Veturi, Anurag Verma, Yuki Bradford, Eric S. Daar, Roy M. Gulick, Sharon A. Riddler, Gregory K. Robbins, Jeffrey L. Lennox, David W. Haas, Marylyn D. Ritchie
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1008719

Mechanical coupling in the nitrogenase complex
Cited by: 6
Author(s): Qi Huang, Monika Tokmina‐Lukaszewska, Lewis E. Johnson, Hayden Kallas, Bojana Ginovska, John W. Peters, Lance C. Seefeldt, Brian Bothner, Simone Raugei
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0251659

Characterizing and predicting person-specific, day-to-day, fluctuations in walking behavior
Cited by: 11
Author(s): Guillaume Chevance, Dario Baretta, Matti Toivo Juhani Heino, Olga Perski, Merlijn Olthof, Predrag Klasnja, Eric B. Hekler, Job G. Godino
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0236082

Microbial community dissimilarity for source tracking with application in forensic studies
Cited by: 8
Author(s): Kyle M. Carter, L. Meng, Qianwen Luo, Hongmei Jiang, Lingling An
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0236097

A novel serum miRNA-pair classifier for diagnosis of sarcoma
Cited by: 1
Author(s): Zheng Jin, Shanshan Liu, Pei‐Wen Zhu, Mengyan Tang, Yuanxin Wang, Yuan Tian, Dong Li, X. D. Zhu, Dongmei Yan, Zhifeng Zhu
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009003

Serotonergic modulation of visual neurons in Drosophila melanogaster
Cited by: 11
Author(s): Maureen M. Sampson, Katherine M. Myers Gschweng, Ben J. Hardcastle, Shivan L. Bonanno, Tyler R. Sizemore, Rebecca C. Arnold, Fuying Gao, Andrew M. Dacks, Mark A. Frye, David E. Krantz
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1008359

A first-takes-all model of centriole copy number control based on cartwheel elongation
Cited by: 1
Author(s): Marco António Dias Louro, Mónica Bettencourt-Dias, Jorge Carneiro
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0248342

A comprehensive molecular characterization of the 8q22.2 region reveals the prognostic relevance of OSR2 mRNA in muscle invasive bladder cancer
Cited by: 4
Author(s): Daniel Uysal, Karl‐Friedrich Kowalewski, Maximilian C. Kriegmair, Ralph M. Wirtz, Zoran V. Popović, Philipp Erben
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009684

An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation?
Cited by: 10
Author(s): Margot Brandt, Sarah Kim-Hellmuth, Marcello Ziosi, Alper Gokden, Aaron Wolman, Nora Lam, Yocelyn Recinos, Zharko Daniloski, John A. Morris, Veit Hornung, Johannes Schumacher, Tuuli Lappalainen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0247873

Evaluation of counting methods for monitoring populations of a cryptic alpine passerine, the rock wren (Passeriformes, Acanthisittidae, Xenicus gilviventris)
Cited by: 3
Author(s): Joanne M. Monks, Colin F. J. O’Donnell, Terry Greene, Kerry A. Weston
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0257639

Examining the impact of a community-based exercise intervention on cardiorespiratory fitness, cardiovascular health, strength, flexibility and physical activity among adults living with HIV: A three-phased intervention study
Cited by: 9
Author(s): Kelly K O’Brien, Aileen M. Davis, Soo Chan Carusone, Lisa Avery, Ada Tang, Patricia Solomon, Rachel Aubry, Mehdi Zobeiry, Ivan Ilić, Zoran Pandovski, Ahmed M. Bayoumi
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1009502

Tempo and mode in karyotype evolution revealed by a probabilistic model incorporating both chromosome number and morphology
Cited by: 14
Author(s): Kohta Yoshida, Jun Kitano
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009044

TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers
Cited by: 9
Author(s): Wenwen Min, Tsung-Hui Chang, Shihua Zhang, Xiang Wan
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0239255

Priorities for intervention of childhood stunting in northeastern Ethiopia: A matched case-control study
Cited by: 5
Author(s): Sisay Eshete Tadesse, Tefera Chane Mekonnen, Metadel Adane
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1008391

Using B cell receptor lineage structures to predict affinity
Cited by: 11
Author(s): D. Ralph, F. A. Matsen
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pntd.0008932

Genetic diversity of Trypanosoma cruzi parasites infecting dogs in southern Louisiana sheds light on parasite transmission cycles and serological diagnostic performance
Cited by: 13
Author(s): Eric Dumonteil, Ardem Elmayan, Alicia Majeau, Weihong Tu, Brandy Duhon, Preston A. Marx, Wendy Wolfson, Garry Balsamo, Claudia Herrera
Software Mentions: 3
Published: almost 4 years ago