Ecosyste.ms: Papers

10.1371/journal.pgen.1009679

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease
Cited by: 16
Author(s): Enrique Audain, Anna Wilsdon, Jeroen Breckpot, Jose M. G. Izarzugaza, Tomas Fitzgerald, Anne‐Karin Kahlert, Alejandro Sifrim, Florian Wünnemann, Yasset Perez‐Riverol, Hashim Abdul‐Khaliq, Mads Bak, Anne S. Bassett, Woodrow Benson, Felix Berger, Ingo Daehnert, Koenraad Devriendt, Sven Dittrich, Piers E.F. Daubeney, Vidu Garg, Karl Hackmann, Kirstin Hoff, Philipp Hofmann, Gregor Dombrowsky, Thomas Pickardt, Ulrike Bauer, Bernard Keavney, Sabine Klaassen, Hans‐Heiner Kramer, Christian R. Marshall, Dianna M. Milewicz, Scott A. LeMaire, Joseph S. Coselli, Michael E. Mitchell, Aoy Tomita‐Mitchell, Siddharth K. Prakash, Karl Stamm, Alexandre F.R. Stewart, Candice K. Silversides, Reiner Siebert, Brigitte Stiller, Jill A. Rosenfeld, Inga Vater, Alex V. Postma, Almuth Caliebe, J. David Brook, Grégor Andelfinger, Matthew E. Hurles, Bernard Thienpont, Lars Allan Larsen, Marc‐Phillip Hitz
Software Mentions: 3
Published: over 3 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.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.pgen.1009761

The CovR regulatory network drives the evolution of Group B Streptococcus virulence
Cited by: 11
Author(s): Maria-Vittoria Mazzuoli, Maëlle Daunesse, Hugo Varet, Isabelle Rosinski‐Chupin, Rachel Legendre, Odile Sismeiro, Myriam Gominet, P.A. Kaminski, Philippe Glaser, Claudia Chica, Patrick Trieu-Cuot, Arnaud Firon
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0223294

Distinctive tasks of different cyanobacteria and associated bacteria in carbon as well as nitrogen fixation and cycling in a late stage Baltic Sea bloom
Cited by: 13
Author(s): Falk Eigemann, Angela Vogts, Maren Voß, Luca Zoccarato, Heide N. Schulz-Vogt
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1008861

Adaptive evolution among cytoplasmic piRNA proteins leads to decreased genomic auto-immunity
Cited by: 12
Author(s): Luyang Wang, Daniel A. Barbash, Erin S. Kelleher
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0242071

Cultural variation in young children’s social motivation for peer collaboration and its relation to the ontogeny of Theory of Mind
Cited by: 6
Author(s): Roman Stengelin, Robert Hepach, Daniel B. M. Haun
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1009021

Evaluation of polygenic prediction methodology within a reference-standardized framework
Cited by: 84
Author(s): Oliver Pain, Kylie P. Glanville, Saskia P. Hagenaars, Saskia Selzam, Anna E. Fürtjes, Héléna A. Gaspar, Jonathan R. I. Coleman, Kaili Rimfeld, Gerome Breen, Robert Plomin, Lasse Folkersen, Cathryn M. Lewis
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009087

Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing
Cited by: 9
Author(s): Kashyap Chhatbar, Justyna Cholewa-Waclaw, Ruth Shah, Adrian Bird, Guido Sanguinetti
Software Mentions: 3
Published: about 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.0221828

Dietary inulin alters the gut microbiome, enhances systemic metabolism and reduces neuroinflammation in an APOE4 mouse model
Cited by: 73
Author(s): Jared D. Hoffman, Lucille M. Yanckello, George E. Chlipala, Tyler C. Hammond, Scott McCulloch, Ishita Parikh, Sydney Sun, Josh M. Morganti, Stefan J. Green, Ai-Ling Lin
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0252954

Perinatal exposure to a human relevant mixture of persistent organic pollutants: Effects on mammary gland development, ovarian folliculogenesis and liver in CD-1 mice
Cited by: 3
Author(s): Silje Modahl Johanson, Erik Ropstad, Gunn Charlotte Østby, Mona Aleksandersen, Galia Zamaratskaia, Gudrun Seeberg Boge, Ruth Halsne, Cathrine Trangerud, Jan Ludvig Lyche, Hanne Friis Berntsen, Karin Elisabeth Zimmer, Steven Verhaegen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008922

Unified inference of missense variant effects and gene constraints in the human genome
Cited by: 15
Author(s): Yi Huang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008591

The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter
Cited by: 13
Author(s): Selamawit Abi Woldemeskel, Allison K. Daitch, Laura Álvarez, Gaël Panis, Rilee Zeinert, Diego González, Erika Smith, Justine Collier, Peter Chien, Felipe Cava, Patrick H. Viollier, Erin D. Goley
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0232397

Correlation between musculoskeletal structure of the hand and primate locomotion: Morphometric and mechanical analysis in prehension using the cross- and triple-ratios
Cited by: 6
Author(s): Toshihiro Tamagawa, Torbjörn Lundh, Kenji Shigetoshi, Norihisa Nitta, Noritoshi Ushio, Toshiro Inubushi, Akihiko Shiino, Anders Karlsson, Takayuki Inoue, Yutaka Mera, Kodai Hino, Masaharu Komori, Shigehiro Morikawa, Shuji Sawajiri, Shigeyuki Naka, Satoru Honma, Tomoko Kimura, Yasuhiro Uchimura, Shunsuke Imai, Naoko Egi, Hiroki Otani, Jun Udagawa
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009008

Male-biased aganglionic megacolon in the TashT mouse model of Hirschsprung disease involves upregulation of p53 protein activity and Ddx3y gene expression
Cited by: 6
Author(s): Tatiana Cardinal, Karl-F. Bergeron, Rodolphe Soret, Ouliana Souchkova, Christophe Fauré, Amélina Guillon, Nicolas Pilon
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0237933

Defining the relationship between maternal care behavior and sensory development in Wistar rats: Auditory periphery development, eye opening and brain gene expression
Cited by: 5
Author(s): Jingyun Qiu, Preethi Singh, Geng Pan, Annalisa De Paolis, Frances A. Champagne, Jia Liu, Luís Cardoso, Adrián Rodríguez-Contreras
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009438

Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome
Cited by: 18
Author(s): Alison H. Nguyen, Doris Bachtrog
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0242200

Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis
Cited by: 17
Author(s): N. A. Zinovieva, Arsen V Dotsev, A.A. Sermyagin, Tatiana Deniskova, Alexandra Abdelmanova, В. Р. Харзинова, Johann Sölkner, Henry Reyer, Klaus Wimmers, Gottfried Brem
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1009182

Differential transcript usage in the Parkinson’s disease brain
Cited by: 12
Author(s): Fiona Dick, Gonzalo S. Nido, Guido Alves, Ole‐Bjørn Tysnes, Gry Hilde Nilsen, Christian Dölle, Charalampos Tzoulis
Software Mentions: 3
Published: about 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.1008673

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin
Cited by: 30
Author(s): Yuh Chwen G. Lee, Yuki Ogiyama, Nuno M. C. Martins, Brian J. Beliveau, David Acevedo, Chao-ting Wu, Giacomo Cavalli, Gary H. Karpen
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0230029

Dredging activity and associated sound have negligible effects on adult Atlantic sturgeon migration to spawning habitat in a large coastal river
Cited by: 8
Author(s): Matthew T. Balazik, Michael Barber, Safra Altman, Kevin J. Reine, Alan Katzenmeyer, Aaron J. Bunch, Greg C. Garman
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1009426

Machine learning approach for automatic recognition of tomato-pollinating bees based on their buzzing-sounds
Cited by: 9
Author(s): Alison Ribeiro, Nádia Félix Felipe da Silva, Fernanda Neiva Mesquita, Priscila de Cássia Souza Araújo, Thierson Couto Rosa, José Neiva Mesquita Neto
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pcbi.1007425

Computational design and interpretation of single-RNA translation experiments
Cited by: 12
Author(s): Luis U. Aguilera, William Raymond, Zachary Fox, Michael P. May, Elliot Djokic, Tatsuya Morisaki, Timothy J. Stasevich, Brian Munsky
Software Mentions: 3
Published: about 5 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.0238430

The social network of medical case managers, housing providers, and health department staff in the Ryan White HIV/AIDS Program: A Midwest case study
Cited by: 5
Author(s): Joseph S. Lightner, Jamie Shank, Ryan McBain, Tyler Prochnow
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008387

AMPK regulates ESCRT-dependent microautophagy of proteasomes concomitant with proteasome storage granule assembly during glucose starvation
Cited by: 19
Author(s): Jianhui Li, Michal Breker, Morven Graham, Maya Schuldiner, Mark Hochstrasser
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1008894

AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization
Cited by: 5
Author(s): Nicolas Christophorou, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, Aurélie Chambon, Victor Solier, Daniel Vezon, Mathilde Grelon, Xiaoqi Feng, Nicolas Bouché, Christine Mézard
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0249859

Physiological and genetic characterization of heat stress effects in a common bean RIL population
Cited by: 17
Author(s): Yulieth Vargas, Víctor Manuel Mayor-Durán, Hector Fabio Buendia, Henry Alonso Ruiz-Guzman, Bodo Raatz
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0251905

Which public health interventions are effective in reducing morbidity, mortality and health inequalities from infectious diseases amongst children in low- and middle-income countries (LMICs): An umbrella review
Cited by: 7
Author(s): E Besnier, Katie Thomson, Donata Stonkute, Talal Mohammad, Nasima Akhter, Adam Todd, Magnus Rom Jensen, Astrid Kilvik, Clare Bambra
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1008965

Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss
Cited by: 18
Author(s): Kévin Huguet, Nicolas Rivard, Daniel Garneau, Jason Palanee, Vincent Burrus
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0237325

Exposure assessment of adults living near unconventional oil and natural gas development and reported health symptoms in southwest Pennsylvania, USA
Cited by: 9
Author(s): Hannah N. Blinn, Ryan M. Utz, Lydia H. Greiner, David R. Brown
Software Mentions: 3
Published: over 4 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.pone.0245252

Breast self-examination practice and its determinants among women in Ethiopia: A systematic review and meta-analysis
Cited by: 14
Author(s): Yordanos Gizachew Yeshitila, Getachew Mullu Kassa, Selamawit Gebeyehu, Peter Memiah, Melaku Desta
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0254744

The boundary-spanning mechanisms of Nobel Prize winning papers
Cited by: 18
Author(s): Yakub Sebastian, Chaomei Chen
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0229456

Repeatability of flatfish reflex impairment assessments based on video recordings
Cited by: 3
Author(s): Sven Sebastian Uhlmann, Noëlle Yochum, Bart Ampe
Software Mentions: 3
Published: almost 5 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.0220275

Geographical origin determines responses to salinity of Mediterranean caddisflies
Cited by: 4
Author(s): Mauricio J. Carter, M. Flores, Rodrigo Ramos–Jiliberto
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0224632

Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data
Cited by: 22
Author(s): Venugopal Panga, Ashwin Adrian Kallor, Arunima Nair, Shilpa Harshan, Srivatsan Raghunathan
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1009446

Critical role of the BAF chromatin remodeling complex during murine neural crest development
Cited by: 13
Author(s): Kathleen Wung Bi-Lin, Pratap Veerabrahma Seshachalam, Tran Tuoc, Anastassia Stoykova, Sujoy Ghosh, Manvendra K. Singh
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009580

Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos
Cited by: 10
Author(s): Longhua Guo, Joshua S. Bloom, Steve Sykes, Elaine Huang, Zain Kashif, Elise Pham, Katarina Ho, Ana Alcaraz, Xinshu Xiao, Sandra Duarte‐Vogel, Leonid Kruglyak
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0231942

Putting the microbiota to work: Epigenetic effects of early life antibiotic treatment are associated with immune-related pathways and reduced epithelial necrosis following Salmonella Typhimurium challenge in vitro
Cited by: 4
Author(s): Matheus O. Costa, Janelle M Fouhse, Ana Paula P. Silva, Benjamin P. Willing, John C. S. Harding
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pmed.1003346

Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: A living systematic review and meta-analysis
Cited by: 805
Author(s): D. Buitrago-Garcia, Dianne Egli-Gany, Michel Jacques Counotte, Stefanie Hossmann, Hira Imeri, Aziz Mert Ipekci, Georgia Salanti, Nicola Low
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pgen.1009318

Ush regulates hemocyte-specific gene expression, fatty acid metabolism and cell cycle progression and cooperates with dNuRD to orchestrate hematopoiesis
Cited by: 10
Author(s): Jonathan Lenz, Robert Liefke, Julianne Funk, Samuel Shoup, Andrea Nist, Thorsten Stiewe, Robert A. Schulz, Yumiko Tokusumi, Lea Albert, Hartmann Raifer, Klaus Förstemann, Olalla Vázquez, Tsuyoshi Tokusumi, Nancy Fossett, Alexander Brehm
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0243772

Phenotypical antimicrobial resistance data of clinical and non-clinical Escherichia coli from poultry in Germany between 2014 and 2017
Cited by: 8
Author(s): Octavio Mesa-Varona, Heike Kaspar, Mirjam Grobbel, Bernd‐Alois Tenhagen
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008801

Dynamic genetic architecture of yeast response to environmental perturbation shed light on origin of cryptic genetic variation
Cited by: 14
Author(s): Yanjun Zan, Örjan Carlborg
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0252775

The role of state feelings of loneliness in the situational regulation of social affiliative behavior: Exploring the regulatory relations within a multilevel framework
Cited by: 5
Author(s): Andreas Reißmann, Ewelina Stollberg, Joachim Hauser, Ivo Kaunzinger, Klaus W. Lange
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0251245

Gut microbiome differences among Mexican Americans with and without type 2 diabetes mellitus
Cited by: 6
Author(s): Amanda K. Kitten, Laurajo Ryan, Grace C. Lee, Belinda T. Flores, Kelly R. Reveles
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009296

Multiscale representations of community structures in attractor neural networks
Cited by: 4
Author(s): Tatsuya Haga, Tomoki Fukai
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0236193

A genetic model of ivabradine recapitulates results from randomized clinical trials
Cited by: 3
Author(s): Marc‐André Legault, Johanna Sandoval, Sylvie Provost, Amina Barhdadi, Louis‐Philippe Lemieux Perreault, Sonia Shah, R. Thomas Lumbers, Simon de Denus, Benoît Tyl, Jean‐Claude Tardif, Marie‐Pierre Dubé
Software Mentions: 3
Published: over 4 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.0224448

Understanding allergic multimorbidity within the non-eosinophilic interactome
Cited by: 10
Author(s): Daniel Aguilar, Nathanaël Lemonnier, Gerard H. Koppelman, Erik Melén, Baldo Oliva, Mariona Pinart, Stefano Guerra, Jean Bousquet, Josep M. Antó
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0252245

Rationale and validation of a novel mobile application probing motor inhibition: Proof of concept of CALM-IT
Cited by: 1
Author(s): Elise M. Cardinale, Reut Naim, Simone P. Haller, Ramaris E. German, Christian Botz-Zapp, Jessica Bezek, David C. Jangraw, Melissa A. Brotman
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1009556

CRISPR/Cas9 modified An. gambiae carrying kdr mutation L1014F functionally validate its contribution in insecticide resistance and combined effect with metabolic enzymes
Cited by: 23
Author(s): Linda Grigoraki, Ruth Cowlishaw, Tony Nolan, Martin J. Donnelly, Gareth Lycett, Hilary Ranson
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0223341

Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma
Cited by: 29
Author(s): David Hervás‐Marín, Faatiemah Higgins, O. Sanmartín, José Antonio Löpez‐Guerrero, M. Carmen Bañó, J. Carlos Igual, Inma Quilis, Juan Sandoval
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0232846

Diversity in kinetics correlated with structure in nano body-stabilized LacY
Cited by: 3
Author(s): Atul Kumar Johri, J. Finer-Moore, И. Н. Смирнова, Vladimir N. Kasho, Els Pardon, Jan Steyaert, H. Ronald Kaback, Robert M. Stroud
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009370

Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm
Cited by: 13
Author(s): Katarzyna Dziasek, Lauriane Simon, Clément Lafon‐Placette, Benjamin Laenen, Cecilia Wärdig, Juan Santos‐González, Tanja Slotte, Claudia Köhler
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pcbi.1008379

Inferring latent temporal progression and regulatory networks from cross-sectional transcriptomic data of cancer samples
Cited by: 12
Author(s): Xiaoqiang Sun, Ji Zhang, Qing Nie
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0244107

A new formulation of compartmental epidemic modelling for arbitrary distributions of incubation and removal times
Cited by: 2
Author(s): P. Hernández, Carlos Peña, Alberto Ramos, J.J. Gómez-Cadenas
Software Mentions: 3
Published: almost 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.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.pgen.1009086

miRNA-mediated loss of m6A increases nascent translation in glioblastoma
Cited by: 20
Author(s): John P. Zepecki, David Karambizi, J. Eduardo Fajardo, Kristin M. Snyder, Charlotte Guetta-Terrier, Oliver Y. Tang, Jia-Shu Chen, Atom Sarkar, András Fiser, Steven Toms, Nikos Tapinos
Software Mentions: 3
Published: over 3 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.pone.0253934

Characterization of clopyralid resistance in lawn burweed (Soliva sessilis)
Cited by: 4
Author(s): Hossein Ghanizadeh, Fengshuo Li, Lulu He, K.C. Harrington
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pcbi.1009416

Integration, coincidence detection and resonance in networks of spiking neurons expressing Gamma oscillations and asynchronous states
Cited by: 6
Author(s): Eduarda Susin, Alain Destexhe
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1008720

Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses
Cited by: 144
Author(s): Chris Wallace
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0237461

The association of motivation with mind wandering in trait and state levels
Cited by: 5
Author(s): Toshikazu Kawagoe, Keiichi Onoda, Shûhei Yamaguchi
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009687

Reduction of Derlin activity suppresses Notch-dependent tumours in the C. elegans germ line
Cited by: 2
Author(s): Ramya Singh, Ryan B Smit, Xin Wang, Chris Wang, Hilary Racher, Dave Hansen
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pgen.1008582

Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality
Cited by: 32
Author(s): Katherine Lagree, Carol A. Woolford, Manning Y. Huang, Gemma E. May, C. Joel McManus, Norma V. Solis, Scott G. Filler, Aaron P. Mitchell
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1008949

The Paramecium histone chaperone Spt16-1 is required for Pgm endonuclease function in programmed genome rearrangements
Cited by: 11
Author(s): Augustin de Vanssay, Amandine Touzeau, Olivier Arnaiz, Andrea Frapporti, Jamie Phipps, Sandra Duharcourt
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1008941

A point mutation decouples the lipid transfer activities of microsomal triglyceride transfer protein
Cited by: 16
Author(s): Meredith H. Wilson, Sujith Rajan, Aidan Danoff, Richard White, Monica R. Hensley, Vanessa H. Quinlivan, Rosario Recacha, James H. Thierer, Frederick J. Tan, Elisabeth M Busch-Nentwich, Lloyd W. Ruddock, M. Mahmood Hussain, Steven A. Farber
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0250923

Clinical factors associated with rapid treatment of sepsis
Cited by: 1
Author(s): Xing Song, Mei Liu, Lemuel R. Waitman, Anurag Patel, Steven Q. Simpson
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0255313

Competing risk of mortality in association studies of non-fatal events
Cited by: 6
Author(s): Petra Bùžková
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0257206

Dabrafenib, idelalisib and nintedanib act as significant allosteric modulator for dengue NS3 protease
Cited by: 4
Author(s): R. V. Sriram Uday, Rajdip Misra, Annaram Harika, Sandip Dolui, Achintya Saha, Samir Kumar Pal, V. Ravichandiran, Nakul C. Maiti
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0229217

Testing gene-environment interactions for rare and/or common variants in sequencing association studies
Cited by: 4
Author(s): Zihan Zhao, Jianjun Zhang, Qiuying Sha, Hao Han
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009245

bsAS, an antisense long non-coding RNA, essential for correct wing development through regulation of blistered/DSRF isoform usage
Cited by: 5
Author(s): Sílvia Pérez-Lluch, Cecília C. Klein, Alessandra Breschi, Marina Ruiz-Romero, Amaya Abad, Emilio Palumbo, Lyazzat Bekish, Carme Arnan, Roderic Guigó
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0237829

Failure to modulate reward prediction errors in declarative learning with theta (6 Hz) frequency transcranial alternating current stimulation
Cited by: 6
Author(s): Kate Ergo, Esther De Loof, Gillian Debra, Bernhard Pastötter, Tom Verguts
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0242336

Applications of a working framework for the measurement of representative learning design in Australian football
Cited by: 13
Author(s): Peter Browne, Carl T. Woods, Alice Sweeting, Sam Robertson
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0229467

Discovery of antitumor lectins from rainforest tree root transcriptomes
Cited by: 3
Author(s): Atip Lawanprasert, Caitlin A. Guinan, Erica A. Langford, Carly E. Hawkins, Janna N. Sloand, Howard W. Fescemyer, Matthew R. Aronson, Jacob A. Halle, James H. Marden, Scott H. Medina
Software Mentions: 3
Published: almost 5 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.0231867

Characterizing rhizome bud dormancy in Polygonatum kingianum: Development of novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis
Cited by: 4
Author(s): Yue Wang, Donovan Bailey, Shikai Yin, Xin Dong
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009215

Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae
Cited by: 12
Author(s): Joshua J. Black, Richa Sardana, Ezzeddine W. Elmir, Arlen Johnson
Software Mentions: 3
Published: almost 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.0226707

High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0234905

Top predator reveals the stability of prey community in the western subarctic Pacific
Cited by: 1
Author(s): Dongming Lin, Xinjun Chen
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0254444

Using Assessment Design Decision Framework in understanding the impact of rapid transition to remote education on student assessment in health-related colleges: A qualitative study
Cited by: 8
Author(s): Myriam Jaam, Zachariah Nazar, Daniel Rainkie, Diana Alsayed Hassan, Farhat Hussain, Salah Kassab, Abdelali Agouni
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0225684

The opportunities and risks of mobile phones for refugees’ experience: A scoping review
Cited by: 31
Author(s): Tiziana Mancini, Federica Sibilla, Dimitris Argiropoulos, Michele Rossi, Marina Everri
Software Mentions: 3
Published: almost 5 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.pgen.1008637

Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome
Cited by: 23
Author(s): Nino A. Espinas, Le Ngoc Tu, Leonardo Furci, Yasuka Shimajiri, Yoshiko Harukawa, Saori Miura, Shohei Takuno, Hidetoshi Saze
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0241497

On the treatment effect heterogeneity of antidepressants in major depression: A Bayesian meta-analysis and simulation study
Cited by: 18
Author(s): Constantin Volkmann, Alexander Volkmann, Christian Müller
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.pmed.1003027

Potential gains in life expectancy by attaining daily ambient fine particulate matter pollution standards in mainland China: A modeling study based on nationwide data
Cited by: 87
Author(s): Jinlei Qi, Zengliang Ruan, Zhengmin Qian, Peng Yin, Yin Yang, Bipin Kumar Acharya, Lijun Wang, Hualiang Lin
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1007287

DeepHiC: A generative adversarial network for enhancing Hi-C data resolution
Cited by: 48
Author(s): Huasheng Hong, Shuai Jiang, Hao Li, Guangwei Du, Yu Sun, Tao Huan, Qimin Cheng, Chenghui Zhao, Ruijiang Li, Wanying Li, Xiaoyao Yin, Yangchen Huang, Li Cheng, Hebing Chen, Xiaochen Bo
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pcbi.1008366

A Bayesian non-parametric mixed-effects model of microbial growth curves
Cited by: 8
Author(s): Peter D. Tonner, Cynthia L. Darnell, Francesca Bushell, Peter A. Lund, Amy K. Schmid, Scott C. Schmidler
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0226518

A validation of machine learning-based risk scores in the prehospital setting
Cited by: 35
Author(s): Douglas Spangler, Thomas Hermansson, David Smékal, Hans Blomberg
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0249326

An effort-based social feedback paradigm reveals aversion to popularity in socially anxious participants and increased motivation in adolescents
Cited by: 5
Author(s): Dienke J. Bos, Emily D. Barnes, Benjamin M. Silver, Eliana L. Ajodan, Elysha Clark-Whitney, Matthew A. Scult, Jonathan D. Power, Rebecca M. Jones
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0228976

Seasonal and social factors associated with spacing in a wild territorial electric fish
Cited by: 7
Author(s): Lucía Zubizarreta, Laura Quintana, Daniel Hernández, Franco Teixeira de Mello, Mariana Meerhoff, Renato Massaaki Honji, Renata Guimarães Moreira, Ana C. Silva
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1009162

Detecting behavioural changes in human movement to inform the spatial scale of interventions against COVID-19
Cited by: 18
Author(s): Hamish Gibbs, Emily Nightingale, Yang Liu, James Cheshire, León Danon, Liam Smeeth, Carl A. B. Pearson, Chris Grundy, Adam J. Kucharski, Rosalind M Eggo
Software Mentions: 3
Published: over 3 years ago