Ecosyste.ms: Papers

10.1371/journal.pgen.1008984

Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model
Cited by: 16
Author(s): Huimin Na, Stefan Zdraljevic, Robyn E. Tanny, Albertha J.M. Walhout, Erik C. Andersen
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pone.0242943

Essential gene prediction using limited gene essentiality information–An integrative semi-supervised machine learning strategy
Cited by: 7
Author(s): Sutanu Nandi, Piyali Ganguli, Ram Rup Sarkar
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pone.0229146

Vegetation changes in temperate ombrotrophic peatlands over a 35 year period
Cited by: 20
Author(s): Nicolas Pinceloup, Monique Poulin, Marie‐Hélène Brice, Stéphanie Pellerin
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pcbi.1008720

Impact of between-tissue differences on pan-cancer predictions of drug sensitivity
Cited by: 4
Author(s): John P. Lloyd, Matthew B. Soellner, Sofía D. Merajver, Jun Z. Li
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0222822

Range of motion and between-measurement variation of spinal kinematics in sound horses at trot on the straight line and on the lunge
Cited by: 8
Author(s): A. M. Hardeman, Anna Byström, L. Roepstorff, J. H. Swagemakers, P. R. van Weeren, F. M. Serra Bragança
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.ppat.1009875

Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis
Cited by: 14
Author(s): Ian J. Groves, Emma L A Drane, Marco Michalski, Jack Monahan, Cinzia G. Scarpini, Stephen Smith, Giovanni Bussotti, Csilla Várnai, Stefan Schoenfelder, Peter Fraser, Anton J. Enright, Nicholas Coleman
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pgen.1008905

Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase
Cited by: 5
Author(s): Richard Silva, María Ascensión Villar-Fernández, Gerben Vader
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0237881

Identification of key odorants in honeysuckle by headspace-solid phase microextraction and solvent-assisted flavour evaporation with gas chromatography-mass spectrometry and gas chromatograph-olfactometry in combination with chemometrics
Cited by: 6
Author(s): Keran Su, Xin Zhang, Shao-Quan Liu, LiHui Jia, Benjamin Lassabliere, Kim Huey Ee, Aileen Pua, Rui Min Vivian Goh, Jingcan Sun, Bin Yu, XiaoXue Hu
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0229087

Risk factors for loneliness: The high relative importance of age versus other factors
Cited by: 59
Author(s): Bridget Shovestul, Han Jian-guo, Laura Germine, David Dodell-Feder
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0239154

Assessing the low complexity of protein sequences via the low complexity triangle
Cited by: 4
Author(s): Pablo Mier, Miguel A. Andrade‐Navarro
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.ppat.1009539

Infection with endosymbiotic Spiroplasma disrupts tsetse (Glossina fuscipes fuscipes) metabolic and reproductive homeostasis
Cited by: 8
Author(s): Jae Hak Son, Brian L. Weiss, Daniela Schneider, Kiswend-Sida Mikhailou Dera, Fabian Gstöttenmayer, Robert Opiro, Richard Echodu, Norah P. Saarman, Geoffrey M. Attardo, Maria G Onyango, Adly M. M. Abd-Alla, Serap Aksoy
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pcbi.1008807

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations
Cited by: 7
Author(s): Andreas Haahr Larsen, Lilya Tata, Laura John, Mark S. P. Sansom
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pgen.1009027

Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD
Cited by: 5
Author(s): Christian Groß, Chiara Bortoluzzi, Dick de Ridder, Hendrik‐Jan Megens, Martien A. M. Groenen, Marcel J. T. Reinders, Mirte Bosse
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pgen.1009645

An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing
Cited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0241704

Evaluating the effectiveness of a group-based resilience intervention versus psychoeducation for emergency responders in England: A randomised controlled trial
Cited by: 19
Author(s): Jennifer Wild, Shama El-Salahi, Michelle Degli Esposti, Graham R. Thew
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1008769

COMSUC: A web server for the identification of consensus molecular subtypes of cancer based on multiple methods and multi-omics data
Cited by: 1
Author(s): Song He, Xinyu Song, Xisheng Yang, Jianyang Yu, Yao Wen, Lianlian Wu, Bowei Yan, Jiannan Feng, Xiaochen Bo
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0250282

Understanding interactions between risk factors, and assessing the utility of the additive and multiplicative models through simulations
Cited by: 5
Author(s): Lina-Marcela Diaz-Gallo, Boel Brynedal, Helga Westerlind, Rickard Sandberg, Daniel Ramsköld
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1009737

Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver
Cited by: 9
Author(s): Benjamin P. Flynn, Matthew T. Birnie, Yvonne M. Kershaw, Audrys G Pauža, Sohyoung Kim, Songjoon Baek, Mark F. Rogers, Alex Paterson, Diana A. Stavreva, David Murphy, Gordon L. Hager, Stafford Lightman, Becky Conway-Campbell
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0234805

Erythrocyte sedimentation rate and hemoglobin-binding protein in free-living box turtles (Terrapene spp.)
Cited by: 6
Author(s): Laura Adamovicz, Sarah J. Baker, Ethan J. Kessler, Marta Kelly, Samantha Johnson, Janet Winter, Christopher A. Phillips, Matthew C. Allender
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1009506

Comparative analysis reveals distinctive epigenetic features of the human cerebellum
Cited by: 11
Author(s): Elaine E. Guevara, William D. Hopkins, Patrick R. Hof, John J. Ely, Brenda J. Bradley, Chet C. Sherwood
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0248560

Interpreting blood GLUcose data with R package iglu
Cited by: 25
Author(s): Steven Broll, Jacek Urbanek, D. S. Buchanan, Elizabeth Chun, John Muschelli, Naresh M. Punjabi, Irina Gaynanova
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0243301

Response of oat morphologies, root exudates, and rhizosphere fungal communities to amendments in a saline-alkaline environment
Cited by: 5
Author(s): Peina Lu, Tony Yang, Lijun Li, Baoping Zhao, Jinghui Liu
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.ppat.1009280

Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Cited by: 29
Author(s): TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlöf, Jennifer A. Cundiff, Zeus Saldaña‐Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0233823

Lignin induced iron reduction by novel sp., Tolumonas lignolytic BRL6-1
Cited by: 8
Author(s): Gina Chaput, Andrew F. Billings, Lani DeDiego, Roberto Orellana, Joshua N. Adkins, Carrie Nicora, Young Mo Kim, Rosalie K. Chu, Blake A. Simmons, Kristen M. DeAngelis
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pgen.1009574

Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets
Cited by: 13
Author(s): Matthew R. Hass, Daniel Brissette, Sreeja Parameswaran, Mario Pujato, Omer Donmez, Leah C. Kottyan, Matthew T. Weirauch, Raphael Kopan
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0241128

Kin recognition: Neurogenomic response to mate choice and sib mating avoidance in a parasitic wasp
Cited by: 0
Author(s): Aurore Gallot, Sandrine Sauzet, Emmanuel Desouhant
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1008372

Reduction in social learning and increased policy uncertainty about harmful intent is associated with pre-existing paranoid beliefs: Evidence from modelling a modified serial dictator game
Cited by: 13
Author(s): Joseph M Barnby, Vaughan Bell, Mitul A. Mehta, Michael Moutoussis
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0238497

Signatures of somatic mutations and gene expression from p16INK4A positive head and neck squamous cell carcinomas (HNSCC)
Cited by: 2
Author(s): Nabil F. Saba, Ashok R. Dinasarapu, Kelly R. Magliocca, Bhakti Dwivedi, Sandra Seby, Zhaohui S. Qin, Mihir R. Patel, Christopher C. Griffith, Xu Wang, Mark W. El‐Deiry, Conor E. Steuer, Jeanne Kowalski, Dong M. Shin, Michael E. Zwick, Zhuo Georgia Chen
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0219807

Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm
Cited by: 12
Author(s): Korin Eckstrom, John W. Barlow
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pone.0219874

Decision-making flexibility in New Caledonian crows, young children and adult humans in a multi-dimensional tool-use task
Cited by: 7
Author(s): Rachael Miller, Romana Gruber, Anna Frohnwieser, Martina Schiestl, Sarah A. Jelbert, Russell D. Gray, Markus Boeckle, Alexander Taylor, Nicola S. Clayton
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0249944

Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity
Cited by: 16
Author(s): Yu-Chi Chiu, Shih‐Wei Lee, Chen‐Wuing Liu, Rebecca Chou-Jui Lin, Yung‐Chia Huang, Tsuo-Hung Lan, Lawrence Shih Hsin Wu
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0235328

Aptamer based proteomic pilot study reveals a urine signature indicative of pediatric urinary tract infections
Cited by: 10
Author(s): Liang Dong, Joshua R. Watson, Sha Cao, Samuel Arregui, Vijay Saxena, John Ketz, Abduselam K. Awol, Daniel M. Cohen, Jeffrey M. Caterino, David S. Hains, Andrew L. Schwaderer
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0244175

Rapid detection of fast innovation under the pressure of COVID-19
Cited by: 11
Author(s): Nicola Melluso, Andrea Bonaccorsi, Filippo Chiarello, Gualtiero Fantoni
Software Mentions: 6
Published: almost 4 years ago

10.1186/s13717-020-00255-4

Current and near-term advances in Earth observation for ecological applications
Cited by: 75
Author(s): Susan L. Ustin, Elizabeth M. Middleton
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1007939

Iterative point set registration for aligning scRNA-seq data
Cited by: 3
Author(s): Amir Alavi, Ziv Bar‐Joseph
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1007800

MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
Cited by: 30
Author(s): Avtar Roopra
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0232065

Tropical fishes vanished after the operation of a nuclear power plant was suspended in the Sea of Japan
Cited by: 3
Author(s): Reiji Masuda
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1007625

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data
Cited by: 14
Author(s): Jordan A. Berg, Jonathan R Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0256457

Colombia’s bioregions as a source of useful plants
Cited by: 3
Author(s): Nadia Bystriakova, Carolina Tovar, Alexandre K. Monro, Justin Moat, Pablo Hendrigo, Julia Carretero, Germán Torres-Morales, Mauricio Diazgranados
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.ppat.1009916

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Cited by: 6
Author(s): Gonché Danesh, Victor Virlogeux, Christophe Ramière, Caroline Charre, Laurent Cotte, Samuel Alizon
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0246172

Blue-wavelength light therapy for post-traumatic brain injury sleepiness, sleep disturbance, depression, and fatigue: A systematic review and network meta-analysis
Cited by: 14
Author(s): Karan Srisurapanont, Yanisa Samakarn, Boonyasit Kamklong, Phichayakan Siratrairat, Arina Bumiputra, Montita Jaikwang, Manit Srisurapanont
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pgen.1009035

The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations
Cited by: 12
Author(s): Fredrika Åsenius, T.J. Gorrie-Stone, Ama Brew, Yasmin Panchbhaya, Elizabeth Williamson, Leonard C Schalkwyk, Vardhman K. Rakyan, Michelle L. Holland, Sarah Marzi, David Williams
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.ppat.1008408

Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response
Cited by: 16
Author(s): Dylan de Vries, Vasiliki Matzaraki, Olivier B. Bakker, Harm Brugge, Harm-Jan Westra, Mihai G. Netea, Lude Franke, Vinod Kumar, Monique G. P. van der Wijst
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0231511

Analyses of cancer incidence and other morbidities in neutron irradiated B6CF1 mice
Cited by: 5
Author(s): Alia Zander, Tatjana Paunesku, Gayle E. Woloschak
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0222898

Bayesian hierarchical models for disease mapping applied to contagious pathologies
Cited by: 7
Author(s): Sylvain Coly, Myriam Garrido, David Abrial, Anne-Françoise Yao
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1008495

Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology
Cited by: 5
Author(s): Ivan I. Borisov, Eugeniy Metelkin
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pntd.0009776

The association between tropical cyclones and dengue fever in the Pearl River Delta, China during 2013-2018: A time-stratified case-crossover study
Cited by: 7
Author(s): Chuanxi Li, Qi Zhao, Zhe Zhao, Qiyong Liu, Wei Ma
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0257726

Specificity of spiders among fear- and disgust-eliciting arthropods: Spiders are special, but phobics not so much
Cited by: 11
Author(s): Eva Landová, Markéta Janovcová, Iveta Štolhoferová, Silvie Rádlová, Petra Frýdlová, Kristýna Sedláčková, Daniel Frynta
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pcbi.1008276

Uncertainty-driven regulation of learning and exploration in adolescents: A computational account
Cited by: 19
Author(s): Marieke Jepma, Jessica V. Schaaf, Ingmar Visser, Hilde M. Huizenga
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0240010

Framing COVID-19: How we conceptualize and discuss the pandemic on Twitter
Cited by: 135
Author(s): Philipp Wicke, Marianna Bolognesi
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1008277

EventEpi—A natural language processing framework for event-based surveillance
Cited by: 11
Author(s): Auss Abbood, Alexander Ullrich, Rüdiger Busche, Stéphane Ghozzi
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0241848

Genome-wide identification of major genes and genomic prediction using high-density and text-mined gene-based SNP panels in Hanwoo (Korean cattle)
Cited by: 3
Author(s): Hyo Jun Lee, Young Jin Chung, Sungbong Jang, Dongil Seo, Hak Kyo Lee, Duhak Yoon, Dajeong Lim, Seung Hwan Lee
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0255667

Towards a better characterisation of deep-diving whales’ distributions by using prey distribution model outputs?
Cited by: 7
Author(s): Auriane Virgili, Laura Hedon, Matthieu Authier, Beatriz Calmettes, Diane Claridge, Timothy V. N. Cole, Peter J. Corkeron, Ghislain Dorémus, Charlotte Dunn, Timothy E. Dunn, Sophie Laran, Patrick Lehodey, Mark Lewis, Maité Louzao, Laura Mannocci, José Martínez‐Cedeira, Pascal Monestiez, Debra L. Palka, Emeline Pettex, Jason J. Roberts, Leire Ruiz, Camilo Saavedra, M.B. Santos, Olivier Van Canneyt, José Antonio Vázquez Bonales, Vincent Ridoux
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0249231

Risk factors for in-hospital mortality in laboratory-confirmed COVID-19 patients in the Netherlands: A competing risk survival analysis
Cited by: 16
Author(s): Gerine Nijman, Maike H M Wientjes, Jordache Ramjith, Nico Janssen, Jacobien J. Hoogerwerf, Evertine J. Abbink, Marc Blaauw, Ton Dofferhoff, Marjan van Apeldoorn, Karin Veerman, Quirijn de Mast, Jaap ten Oever, Wouter Hoefsloot, Monique H. Reijers, Reinout van Crevel, Josephine S. van de Maat
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1009263

A multi-objective genetic algorithm to find active modules in multiplex biological networks
Cited by: 7
Author(s): Elva María Novoa-del-Toro, Efrén Mezura-Montes, Matthieu Vignes, Morgane Térézol, Frédérique Magdinier, Laurent Tichit, Anaı̈s Baudot
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pntd.0009633

Identification of potential biomarkers in dengue via integrated bioinformatic analysis
Cited by: 5
Author(s): Lisha Xie, Xin Yin, Jie Bi, Hongyu Luo, Xun‐Jie Cao, Yu-Wen Ma, Ye-Ling Liu, Jianwen Su, Geng-Ling Lin, Xu‐Guang Guo
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1008414

Modelling thalamocortical circuitry shows that visually induced LTP changes laminar connectivity in human visual cortex
Cited by: 4
Author(s): Rachael L. Sumner, Meg J. Spriggs, Alexander D Shaw
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1007553

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes
Cited by: 18
Author(s): David Moi, Laurent Kilchoer, Pablo S. Aguilar, Christophe Dessimoz
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0240802

OrganoidTracker: Efficient cell tracking using machine learning and manual error correction
Cited by: 32
Author(s): Rutger Nico Ulbe Kok, Laetitia Hebert, Guizela Huelsz-Prince, Yvonne J. Goos, Xuan Zheng, Katarzyna Bożek, Greg J. Stephens, Sander J. Tans, Jeroen S. van Zon
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pntd.0008617

Human exposure to zoonotic malaria vectors in village, farm and forest habitats in Sabah, Malaysian Borneo
Cited by: 16
Author(s): Rebecca Brown, Tock Hing Chua, Kimberly Fornace, Chris Drakeley, Indra Vythilingam, Heather M. Ferguson
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pmed.1003789

All-cause and cause-specific mortality during and following incarceration in Brazil: A retrospective cohort study
Cited by: 2
Author(s): Yiran E. Liu, Everton Ferreira Lemos, Crhistinne Cavalheiro Maymone Gonçalves, Roberto Dias de Oliveira, Andréa da Silva Santos, Agne Oliveira do Prado Morais, Mariana Garcia Croda, Maria de Lourdes Delgado Alves, Júlio Croda, Katharine S. Walter, Jason R Andrews
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0240538

Populations of arable weed species show intra-specific variability in germination base temperature but not in early growth rate
Cited by: 5
Author(s): Jana Bürger, Andrey V. Malyshev, Nathalie Colbach
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pone.0230509

Influence of light availability and soil productivity on insect herbivory on bilberry (Vaccinium myrtillus L.) leaves following mammalian herbivory
Cited by: 1
Author(s): Marcel Schrijvers-Gonlag, Christina Skarpe, Harry P. Andreassen
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0226666

Habitat quality, configuration and context effects on roe deer fecundity across a forested landscape mosaic
Cited by: 7
Author(s): Valentina Zini, Kristin Wäber, Paul M. Dolman
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1007973

XDream: Finding preferred stimuli for visual neurons using generative networks and gradient-free optimization
Cited by: 9
Author(s): Will Xiao, Gabriel Kreiman
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pcbi.1008315

Leveraging functional annotation to identify genes associated with complex diseases
Cited by: 13
Author(s): Wei Liu, Mo Li, Wenfeng Zhang, Geyu Zhou, Weijie Xing, Jiawei Wang, Qiongshi Lu, Hongyu Zhao
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pcbi.1009197

Multidimensional analysis of immune responses identified biomarkers of recent Mycobacterium tuberculosis infection
Cited by: 1
Author(s): Tessa Lloyd, Pia Steigler, Cheleka A M Mpande, Virginie Rozot, Boitumelo Mosito, Constance Schreuder, Timothy D. Reid, Mark Hatherill, Thomas J. Scriba, Francesca Little, Elisa Nemes
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0254607

Disseminated disease due to non-tuberculous mycobacteria in HIV positive patients: A retrospective case control study
Cited by: 3
Author(s): Nils Wetzstein, Ari Geil, Gerrit Kann, Annette Lehn, Gundolf Schüttfort, Johanna Kessel, Tobias M. Bingold, Claus P. Küpper-Tetzel, Annette Haberl, Christiana Graf, Maria J. G. T. Vehreschild, Christoph Stephan, Michael Hogardt, Thomas A. Wichelhaus, Timo Wolf
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007869

PenDA, a rank-based method for personalized differential analysis: Application to lung cancer
Cited by: 8
Author(s): Magali Richard, Clémentine Decamps, Florent Chuffart, Élisabeth Brambilla, Sophie Rousseaux, Saadi Khochbin, Daniel Jost
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0233211

Molecular diversity and genetic structure of Saccharum complex accessions
Cited by: 15
Author(s): Carolina Medeiros, Thiago Willian Almeida Balsalobre, Monalisa Sampaio Carneiro
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pmed.1002984

Incidence of maternal peripartum infection: A systematic review and meta-analysis
Cited by: 64
Author(s): Susannah Woodd, Ana Montoya, María Barreix, Li Pi, Clara Calvert, Andrea M. Rehman, Doris Chou, Oona M. R. Campbell
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pcbi.1008569

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data
Cited by: 16
Author(s): Andreas Tjärnberg, Omar Mahmood, Christopher Jackson, Giuseppe-Antonio Saldi, Kyunghyun Cho, Lionel Christiaen, Richard Bonneau
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1008044

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
Cited by: 15
Author(s): Craig A. Glastonbury, Sara L. Pulit, Julius Honecker, Jenny C Censin, Samantha Laber, Hanieh Yaghootkar, Nilüfer Rahmioğlu, Emilie Pastel, Katarina Kos, Andrew M. Pitt, Michelle Hudson, Christoffer Nellåker, Nicola L. Beer, Hans Hauner, Christian M. Becker, Krina T. Zondervan, Timothy M. Frayling, Melina Claussnitzer, Cecilia M. Lindgren
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0256793

Designing and validating a Markov model for hospital-based addiction consult service impact on 12-month drug and non-drug related mortality
Cited by: 5
Author(s): Caroline King, Honora Englander, P Todd Korthuis, Joshua A. Barocas, K. John McConnell, Cynthia D. Morris, Ryan Cook
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pmed.1003750

The prevalence of mental disorders among homeless people in high-income countries: An updated systematic review and meta-regression analysis
Cited by: 80
Author(s): Stefan Gutwinski, Stefanie Schreiter, Karl Deutscher, Seena Fazel
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-018-31866-9

Child Weight Gain Trajectories Linked To Oral Microbiota Composition
Cited by: 38
Author(s): Sarah Jane Craig, Daniel Blankenberg, Alice Parodi, Ian M. Paul, Leann L. Birch, Jennifer S. Savage, Michele Marini, Jennifer L. Stokes, Anton Nekrutenko, Matthew Reimherr, Francesca Chiaromonte, Kateryna D. Makova
Software Mentions: 6
Published: about 6 years ago

10.1371/journal.pcbi.1008302

Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals
Cited by: 28
Author(s): Etienne Combrisson, Timothy Nest, Andrea Brovelli, Robin A. A. Ince, Juan L.P. Soto, Aymeric Guillot, Karim Jerbi
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pgen.1009691

Induction of a chromatin boundary in vivo upon insertion of a TAD border
Cited by: 11
Author(s): Andréa Willemin, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, Eddie Rodríguez-Carballo
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pcbi.1007549

BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis
Cited by: 41
Author(s): Manoj Kumar, Cameron T. Ellis, Qingming Lu, Hejia Zhang, Mihai Capotă, Theodore L. Willke, Peter J. Ramadge, Nicholas B. Turk‐Browne, Kenneth A. Norman
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0243807

Optimised generation of iPSC-derived macrophages and dendritic cells that are functionally and transcriptionally similar to their primary counterparts
Cited by: 17
Author(s): Susan J. Monkley, Jayendra Kumar Krishnaswamy, Melker Göransson, Maryam Clausen, Johan Meuller, Kristofer Thörn, Ryan Hicks, Stephen Delaney, Louise Stjernborg
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0232648

Climatic drivers of Verticillium dahliae occurrence in Mediterranean olive-growing areas of southern Spain
Cited by: 1
Author(s): Juan M. Requena‐Mullor, José Manuel Garcı́a-Garrido, Pilar Garcı́a Garcı́a, Estefanı́a Rodrı́guez
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0256929

Modelling the effects of the repellent scent marks of pollinators on their foraging efficiency and the plant-pollinator community
Cited by: 0
Author(s): Elise Verrier, Emmanuelle Baudry, Carmen Bessa‐Gomes
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0252069

A machine learning prediction model for waiting time to kidney transplant
Cited by: 7
Author(s): Juliana Feiman Sapiertein Silva, Gustavo Fernandes Ferreira, Marcelo Perosa, Hong Si Nga, Luís Gustavo Modelli de Andrade
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0229001

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome
Cited by: 45
Author(s): Samuel J. Bowers, Fernando Vargas, Antonio González, Shannon He, Peng Jiang, Pieter C. Dorrestein, Rob Knight, Kenneth P. Wright, Christopher A. Lowry, Monika Fleshner, Martha Hotz Vitaterna, Fred W. Turek
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pntd.0009500

Lay attitudes and misconceptions and their implications for the control of brucellosis in an agro-pastoral community in Kilombero district, Tanzania
Cited by: 6
Author(s): Caroline M. Mburu, Salome A. Bukachi, Kathrin H. Tokpa, Gilbert Fokou, Khamati Shilabukha, Mangi J. Ezekiel, Bassirou Bonfoh, Rudovick Kazwala, Katharina Kreppel
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1008804

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
Cited by: 24
Author(s): Maya Hiltpold, Guanglin Niu, Naveen Kumar Kadri, Danang Crysnanto, Zih-Hua Fang, Mirjam Spengeler, F. Schmitz‐Hsu, Christian Fuerst, Hermann Schwarzenbacher, Franz R. Seefried, Frauke Seehusen, Ulrich Witschi, Angelika Schnieke, R. Fries, Heinrich Bollwein, Krzysztof Flisikowski, Hubert Pausch
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1009801

Tramtrack acts during late pupal development to direct ant caste identity
Cited by: 6
Author(s): Karl M. Glastad, Linyang Ju, Shelley L. Berger
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pgen.1008531

ELF5 modulates the estrogen receptor cistrome in breast cancer
Cited by: 16
Author(s): Catherine Piggin, Daniel Roden, Andrew M. K. Law, Mark P. Molloy, Christoph Krisp, Alexander Swarbrick, Matthew J. Naylor, Maria Kalyuga, Warren Kaplan, Samantha Oakes, David Gallego‐Ortega, Susan J. Clark, Jason S. Carroll, Nenad Bartoniček, Christopher J. Ormandy
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pntd.0009537

Spatio-temporal modelling of the first Chikungunya epidemic in an intra-urban setting: The role of socioeconomic status, environment and temperature
Cited by: 10
Author(s): Laís Picinini Freitas, Alexandra M. Schmidt, William Cossich, Oswaldo Gonçalves Cruz, Marília Sá Carvalho
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1009591

RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility
Cited by: 17
Author(s): Peiwei Chen, Yicheng Luo, Alexei A. Aravin
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pntd.0008962

Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination
Cited by: 14
Author(s): Lucas E. Buyon, Ana María Santamaría, Angela M. Early, Mario Quijada, Itza Barahona, José Lasso, Mario Ávila, Sarah K. Volkman, Matthias Marti, Daniel E. Neafsey, Nicanor Obaldía
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0243746

Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs
Cited by: 7
Author(s): Ryuta Shioi, Fumika Karaki, Hirosuke Yoshioka, Tomomi Noguchi‐Yachide, Minoru Ishikawa, Kosuke Dodo, Yuichi Hashimoto, Mikiko Sodeoka, Kenji Ohgane
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0221543

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas
Cited by: 18
Author(s): Paltu Kumar Dhal, Gérmán A. Kopprio, Astrid Gärdes
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0254178

Addressing cluster-constant covariates in mixed effects models via likelihood-based boosting techniques
Cited by: 3
Author(s): Colin Griesbach, Andreas Groll, Elisabeth Bergherr
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1009398

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies
Cited by: 37
Author(s): Arjun Bhattacharya, Yun Li, Michael I. Love
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0227639

Characterization of black patina from the Tiber River embankments using Next-Generation Sequencing
Cited by: 15
Author(s): Federica Antonelli, Alfonso Esposito, Ludovica Calvo, Valerio Licursi, Philippe Tisseyre, Sandra Ricci, Manuela Romagnoli, Silvano Piazza, Francesca Guerrieri
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pone.0254366

A clinical prediction model to identify children at risk for revisits with serious illness to the emergency department: A prospective multicentre observational study
Cited by: 5
Author(s): Ruud Nijman, Dorine H. Borensztajn, Joany M Zachariasse, Carine Hajema, Paulo Freitas, Susanne Greber‐Platzer, Frank J Smit, Claudio F. Alves, Johan van der Lei, Ewout W. Steyerberg, Ian Maconochie, Henriëtte A. Moll
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0236186

Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat
Cited by: 16
Author(s): Liangjie Lv, Wenying Zhang, Lijing Sun, Aiju Zhao, Yingjun Zhang, Limei Wang, Yuping Liu, Ziqian Li, Xiyong Chen
Software Mentions: 6
Published: about 4 years ago

10.1371/journal.pgen.1008864

­­­­­­Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods
Cited by: 52
Author(s): Samuel H. Lewis, Laura Ross, Stevie A. Bain, Eleni Pahita, Stephen A. Smith, Richard Cordaux, Eric A. Miska, Boris Lenhard, Francis M. Jiggins, Peter Sarkies
Software Mentions: 6
Published: over 4 years ago