cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0225073

Next generation sequencing and RNA-seq characterization of adipose tissue in the Nile crocodile (Crocodylus niloticus) in South Africa: Possible mechanism(s) of pathogenesis and pathophysiology of pansteatitis
Cited by: 3
Author(s): O. I. Azeez, Jan G. Myburgh, Anna-Marì Bosman, Jonathan Featherston, Kgomotso P. Sibeko-Matjilla, Marinda C. Oosthuizen, Joseph Panashe Chamunorwa
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-75352-7

Machine learning to predict early TNF inhibitor users in patients with ankylosing spondylitis
Cited by: 6
Author(s): Seulkee Lee, Young‐Gyu Eun, Hyungjin Kim, Hoon‐Suk Cha, Eun‐Mi Koh, Jaejoon Lee
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-020-77179-8

Planktonic foraminifera eDNA signature deposited on the seafloor remains preserved after burial in marine sediments
Cited by: 15
Author(s): Inès Barrenechea Angeles, Franck Lejzerowicz, Tristan Cordier, Janin Scheplitz, Michal Kučera, Daniel Ariztegui, Jan Pawłowski, Raphaël Morard
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-76873-x

Deeper waters are changing less consistently than surface waters in a global analysis of 102 lakes
Cited by: 51
Author(s): Rachel M. Pilla, Craig E. Williamson, Б. В. Адамович, Rita Adrian, Orlane Anneville, Sudeep Chandra, William Colom-Montero, Shawn P. Devlin, Margaret Dix, Martin T. Dokulil, Evelyn E. Gaiser, Scott F. Girdner, K. David Hambright, David P. Hamilton, Karl E. Havens, Dag O. Hessen, Scott N. Higgins, Timo Huttula, Hannu Huuskonen, Peter D. F. Isles, Klaus Joehnk, Ian D. Jones, Wendel Keller, Lesley B. Knoll, Johanna Korhonen, Benjamin M. Kraemer, Peter R. Leavitt, Fabio Lepori, Martin Luger, Stephen C. Maberly, John M. Mélack, Stephanie J. Melles, Dörthe C. Müller-Navarra, Don Pierson, Helen V. Pislegina, Pierre Denis Plisnier, David C. Richardson, Alon Rimmer, Michela Rogora, James A. Rusak, Steven Sadro, Nico Salmaso, Jasmine E. Saros, Émilie Saulnier‐Talbot, Daniel E. Schindler, Martin Schmid, Svetlana V. Shimaraeva, Eugene A. Silow, Lewis Sitoki, Rubén Sommaruga, Dietmar Straile, Kristin E. Strock, Wim Thiery, Maxim A. Timofeyev, Piet Verburg, Rolf D. Vinebrooke, Gesa A. Weyhenmeyer, Egor Zadereev
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0229726

Environmental impact on the temporal production of chasmogamous and cleistogamous flowers in the mixed breeding system of Viola pubescens
Cited by: 12
Author(s): Anne L. Sternberger, Anirudh V. S. Ruhil, D.I. Rosenthal, Harvey E. Ballard, Sarah E. Wyatt
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0206468

Useful distracting information: ERP correlates of distractors in stimulus-response-episodes
Cited by: 1
Author(s): Lea Donata Priester, Daniel Wiswede
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-020-77835-z

Specific capture and whole-genome phylogeography of Dolphin morbillivirus
Cited by: 8
Author(s): Francesco Cerutti, Federica Giorda, Carla Grattarola, Walter Mignone, Chiara Beltramo, Nicolas Keck, Alessio Lorusso, Di Francesco G, Ludovica Di Renzo, Giovanni Di Guardo, Maria Goria, Loretta Masoero, Pier Luigi Acutis, Cristina Casalone, Simone Peletto
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-77564-3

IL-10 based immunomodulation initiated at birth extends lifespan in a familial mouse model of amyotrophic lateral sclerosis
Cited by: 4
Author(s): Michael R. Strickland, Kristen R. Ibanez, Mariya Yaroshenko, Carolina Ceballos Diaz, David R. Borchelt, Paramita Chakrabarty
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0239452

Early antiretroviral therapy for HIV-infected patients admitted to an intensive care unit (EARTH-ICU): A randomized clinical trial
Cited by: 3
Author(s): Márcio Manozzo Boniatti, José Augusto Santos Pellegrini, Leonardo da Silva Marques, Josiane França John, Luiz Gustavo Marin, Lina R. D. M. Maito, Thiago Lisboa, Lucas Petri Damiani, Diego Rodrigues Falci
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40659-020-00296-1

Microbial communities from arid environments on a global scale. A systematic review
Cited by: 25
Author(s): Javiera Vásquez-Dean, Felipe Rodríguez Maza, Isidora Morel, Rodrigo Pulgar, Maurício González
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pntd.0004230

Tracking Cholera through Surveillance of Oral Rehydration Solution Sales at Pharmacies: Insights from Urban Bangladesh
Cited by: 14
Author(s): Andrew S. Azman, Justin Lessler, Syed Moinuddin Satter, Michael McKay, Ahad Mahmud Khan, Dilruba Ahmed, Emily S. Gurley
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-020-78314-1

Sustained organic loading disturbance favors nitrite accumulation in bioreactors with variable resistance, recovery and resilience of nitrification and nitrifiers
Cited by: 9
Author(s): Ezequiel Santillan, W. X. Phua, Florentin Constancias, Stefan Wuertz
Software Mentions: 2
Published: over 5 years ago

10.3390/nu13020533

Achievement of the Targets of the 20-Year Infancy-Onset Dietary Intervention—Association with Metabolic Profile from Childhood to Adulthood
Cited by: 7
Author(s): Miia Lehtovirta, Laurie A. Matthews, Tomi T. Laitinen, Joel Nuotio, Harri Niinikoski, Suvi Rovio, Hanna Lagström, Jorma Viikari, Tapani Rönnemaa, Antti Jula, Mika Ala‐Korpela, Olli T. Raitakari, Katja Pahkala
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0009512

Human immune response against salivary antigens of Simulium damnosum s.l.: A new epidemiological marker for exposure to blackfly bites in onchocerciasis endemic areas
Cited by: 2
Author(s): Laura Willen, Marı́a-Gloria Basáñez, Vít Dvořák, Francis B. D. Veriegh, Frank Twum Aboagye, Bright Idun, Maha E. Osman, Mike Y. Osei-Atweneboana, Orin Courtenay, Petr Volf
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-77760-1

Dynamic changes in cell size and corresponding cell fate after optic nerve injury
Cited by: 4
Author(s): Benjamin Davis, Li Guo, Nivedita Ravindran, Ehtesham Shamsher, Veerle Baekelandt, Hannah Mitchell, Anil A. Bharath, Lies De Groef, M. Francesca Cordeiro
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0005684

Immunosuppressive and angiogenic cytokine profile associated with Bartonella bacilliformis infection in post-outbreak and endemic areas of Carrion's disease in Peru
Cited by: 14
Author(s): María J. Pons, Cláudia Gomes, Ruth Aguilar, Diana Barrios, Miguel Ángel Aguilar-Luis, Joaquı́m Ruiz, Carlota Dobaño, Juana del Valle-Mendoza, Gemma Moncunill
Software Mentions: 2
Published: about 9 years ago

10.3390/nu13082700

Jujube Powder Enhances Cyclophosphamide Efficiency against Murine Colon Cancer by Enriching CD8+ T Cells While Inhibiting Eosinophilia
Cited by: 8
Author(s): Huiren Zhuang, Nan Jing, Luoyang Wang, Guoqiang Jiang, Zheng Liu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pntd.0004785

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia
Cited by: 38
Author(s): Duy Pham Thanh, Corinne N. Thompson, Maia A. Rabaa, Sona Soeng, Sun Sopheary, Varun Kumar, Catrin E. Moore, Nga Tran Vu Thieu, Lalith Wijedoru, Kathryn E. Holt, Vanessa Wong, Derek Pickard, Guy Thwaites, Nicholas P. J. Day, Gordon Dougan, Paul Turner, Christopher M. Parry, Stephen Baker
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pntd.0004346

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water
Cited by: 67
Author(s): Abhilasha Karkey, Thibaut Jombart, Alan W. Walker, Corinne N. Thompson, Andrés Torres, Sabina Dongol, Nga Tran Vu Thieu, Duy Pham Thanh, Dung Tran Thi Ngoc, Phat Voong Vinh, Andrew C. Singer, Julian Parkhill, Guy Thwaites, Buddha Basnyat, Neil M. Ferguson, Stephen Baker
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pntd.0004069

Release of Small RNA-containing Exosome-like Vesicles from the Human Filarial Parasite Brugia malayi
Cited by: 134
Author(s): Mostafa Zamanian, Lisa M. Fraser, Prince N Agbedanu, Hiruni Harischandra, Andrew R. Moorhead, Tim A. Day, Lyric C. Bartholomay, Michael J. Kimber
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-020-79773-2

Environmental patterns of brown moss- and Sphagnum-associated microbial communities
Cited by: 8
Author(s): Alexander Tøsdal Tveit, Andrea Kiss, Matthias Winkel, Fabian Horn, Tomáš Hájek, Mette M. Svenning, Dirk Wagner, Susanne Liebner
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0007715

IL-17A, a possible biomarker for the evaluation of treatment response in Trypanosoma cruzi infected children: A 12-months follow-up study in Bolivia
Cited by: 6
Author(s): Clara Vásquez Velásquez, Graciela Russomando, Emilio E. Espínola, Zunilda Sánchez, Kota Mochizuki, Yelin Roca, Jimmy Revollo, Angelica Guzman, Benjamín Quiroga, Susana Rios Morgan, Roberto Vargas Ortiz, Alberto Zambrana Ortega, Eida Espinoza, Juan Eiki Nishizawa, Mohamed Gomaa Kamel, Mihoko Kikuchi, Shusaku Mizukami, Kesara Na‐Bangchang, Nguyen Tien Huy, Kenji Hirayama
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-020-79868-w

Unique behavioural modifications in the web structure of the cave orb spider Meta menardi (Araneae, Tetragnathidae)
Cited by: 5
Author(s): Daniel Simonsen, Thomas Hesselberg
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0005736

Local and global genetic diversity of protozoan parasites: Spatial distribution of Cryptosporidium and Giardia genotypes
Cited by: 39
Author(s): Juan C. García–R, Nigel P. French, Anthony Pita, Niluka Velathanthiri, Rima D. Shrestha, David T. S. Hayman
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pntd.0007513

Genetic characteristics of pathogenic Leptospira in wild small animals and livestock in Jiangxi Province, China, 2002–2015
Cited by: 21
Author(s): Cuicai Zhang, Junjun Xu, Tinglan Zhang, Haiyan Qiu, Zhenpeng Li, Enmin Zhang, Shijun Li, Yung-Fu Chang, Xiaokui Guo, Xingran Jiang, Yongzhang Zhu
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pntd.0008421

Opisthorchis felineus infection, risks, and morbidity in rural Western Siberia, Russian Federation
Cited by: 33
Author(s): О. С. Федорова, М М Федотова, Olga Zvonareva, Sofia V. Mazeina, Yulia V. Kovshirina, Tatiana S. Sokolova, Ekaterina A. Golovach, Anna E. Kovshirina, Uliana V. Konovalova, И. Л. Коломеец, Sergey Gutor, В. А. Петров, Jan Hattendorf, Л. М. Огородова, Peter Odermatt
Software Mentions: 2
Published: about 6 years ago

10.3390/nu11123025

Why Do Children in Slums Suffer from Anemia, Iron, Zinc, and Vitamin A Deficiency? Results from a Birth Cohort Study in Dhaka
Cited by: 6
Author(s): Mustafa Mahfuz, Laura E. Murray‐Kolb, S. M. Tafsir Hasan, Subhasish Das, Shah Mohammad Fahim, Ashraful Alam, Laura E. Caulfield, Tahmeed Ahmed
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-79438-0

Incorporating human mobility data improves forecasts of Dengue fever in Thailand
Cited by: 29
Author(s): Mathew V. Kiang, Mauricio Santillana, Jarvis T. Chen, Jukka‐Pekka Onnela, Nancy Krieger, Kenth Engø‐Monsen, Nattwut Ekapirat, Darin Areechokchai, Preecha Prempree, Richard J. Maude, Caroline O. Buckee
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-79831-9

Multi-pronged approach to human mesenchymal stromal cells senescence quantification with a focus on label-free methods
Cited by: 11
Author(s): Weichao Zhai, Jerome Zu Yao Tan, Tobias Russell, Sixun Chen, Dennis McGonagle, May Win Naing, Derrick Yong, Elena Jones
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0005420

Single locus genotyping to track Leishmania donovani in the Indian subcontinent: Application in Nepal
Cited by: 16
Author(s): Keshav Rai, Narayan Bhattarai, Manu Vanaerschot, Hideo Imamura, Gebreyohans Gebru, Basudha Khanal, Suman Rijal, Marleen Boelaert, Chiranjib Pal, Prahlad Karki, Jean‐Claude Dujardin
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pntd.0005347

Dispersal of male and female Culex quinquefasciatus and Aedes albopictus mosquitoes using stable isotope enrichment
Cited by: 61
Author(s): Matthew C. I. Medeiros, Emily Cale Boothe, E. Brendan Roark, Gabriel L. Hamer
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pntd.0007570

Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites
Cited by: 13
Author(s): John N. Filosa, Corbett T. Berry, Gordon Ruthel, Stephen M. Beverley, Wesley C. Warren, Chad Tomlinson, Peter J. Myler, Elizabeth A. Dudkin, Megan L. Povelones, Michael Povelones
Software Mentions: 2
Published: about 7 years ago

10.3390/nu11112822

Temporal Trends in Maternal Food Intake Frequencies and Associations with Gestational Diabetes: The Cambridge Baby Growth Study
Cited by: 8
Author(s): Clive J Petry, Ken K. Ong, Ieuan A. Hughes, Carlo L. Acerini, David Dunger
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1006993

Fibroblast growth factor signaling is required for early somatic gonad development in zebrafish
Cited by: 53
Author(s): Dena M. Leerberg, Kōkichi Sano, Bruce W. Draper
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-021-81257-w

Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle
Cited by: 10
Author(s): David P. Jacobson, Tanvi P. Honap, Andrew T. Ozga, Nicolas Méda, Thérèse Kagoné, Hélène Carabin, Paul Spicer, Raúl Y. Tito, Alexandra J. Obregón-Tito, Luis Marín Reyes, Luzmila Troncoso-Corzo, Emilio Guija-Poma, Krithivasan Sankaranarayanan, Cecil M. Lewis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1002525

Mixed Effects Modeling of Proliferation Rates in Cell-Based Models: Consequence for Pharmacogenomics and Cancer
Cited by: 29
Author(s): Hae Kyung Im, Eric R. Gamazon, Amy L. Stark, R. Stephanie Huang, Nancy J. Cox, M. Eileen Dolan
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pgen.1008125

The evolution of hybrid fitness during speciation
Cited by: 53
Author(s): Andrius J. Dagilis, Mark Kirkpatrick, Daniel I. Bolnick
Software Mentions: 2
Published: over 7 years ago

10.1242/bio.058676

Dorso-ventral heterogeneity in tracheal basal stem cells
Cited by: 2
Author(s): Tomomi Tadokoro, Keisuke Tanaka, Shun Osakabe, Mimoko Kato, Hisato Kobayashi, Brigid L.M. Hogan, Hideki Taniguchi
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-82287-0

Multiplexed CRISPR-Cas9 system in a single adeno-associated virus to simultaneously knock out redundant clock genes
Cited by: 5
Author(s): Boil Kim, Jihoon Kim, Minjeong Chun, Inah Park, Damhyeon Kwak, Mijung Choi, Kyungjin Kim, Han Kyoung Choe
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1009082

Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations
Cited by: 14
Author(s): Yann Bourgeois, Robert P. Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.01189-20

Tumble Suppression Is a Conserved Feature of Swarming Motility
Cited by: 11
Author(s): Jonathan D. Partridge, Nguyen T. Q. Nhu, Y. Dufour, Rasika M. Harshey
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1004438

Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex
Cited by: 80
Author(s): Christine Grossen, Lukas F. Keller, Iris Biebach, Daniel Croll
Software Mentions: 2
Published: about 12 years ago

10.1128/mBio.00814-20

Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes
Cited by: 4
Author(s): Laura Bricio-Moreno, Chrispin Chaguza, Reham Yahya, Rebecca K. Shears, Jennifer Cornick, Karsten Hokamp, Marie Yang, Daniel R. Neill, Neil French, Jay C. D. Hinton, Dean Everett, Aras Kadioglu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1005096

Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus
Cited by: 65
Author(s): Abigail Lind, Jennifer H. Wisecaver, Timothy D. Smith, Xuehuan Feng, Ana M. Calvo, Antonis Rokas
Software Mentions: 2
Published: over 11 years ago

10.1128/mBio.03338-20

Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System
Cited by: 24
Author(s): Ville Hoikkala, Janne J. Ravantti, Cesar Díez‐Villaseñor, Marja Tiirola, Rachel A. Conrad, Mark J. McBride, Sylvain Moineau, Lotta‐Riina Sundberg
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1007874

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting
Cited by: 26
Author(s): Orsolya Symmons, Marcello Chang, Ian A. Mellis, Jennifer M. Kalish, Jihwan Park, Katalin Suszták, Marisa S. Bartolomei, Arjun Raj
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1009017

ZNF423 patient variants, truncations, and in-frame deletions in mice define an allele-dependent range of midline brain abnormalities
Cited by: 7
Author(s): Ojas Deshpande, Raquel Z. Lara, Oliver Zhang, Dorothy Concepcion, Bruce A. Hamilton
Software Mentions: 2
Published: almost 6 years ago

10.1128/mBio.00927-21

Experimental-Evolution-Driven Identification of Arabidopsis Rhizosphere Competence Genes in Pseudomonas protegens
Cited by: 13
Author(s): Erqin Li, Hao Zhang, Henan Jiang, Corné M. J. Pieterse, Alexandre Jousset, Peter A. H. M. Bakker, Ronnie de Jonge
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.4848

The global burden of HIV-1 drug resistance in the past 20 years
Cited by: 24
Author(s): Maurizio Zazzi, Hui Hu, Mattia Prosperi
Software Mentions: 2
Published: about 8 years ago

10.1128/mBio.00873-21

Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria
Cited by: 4
Author(s): Spiridon E. Papoulis, Steven W. Wilhelm, David Talmy, Erik R. Zinser
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.9653

Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw
Cited by: 7
Author(s): Qiang Ma, Jiwei Li, Muhammad Aamer, Huang Guo-qin
Software Mentions: 2
Published: about 6 years ago

10.1093/bioinformatics/bty614

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations
Cited by: 5
Author(s): Alex N. Salazar, Thomas Abeel
Software Mentions: 2
Published: almost 8 years ago

10.1093/bioinformatics/btw325

GenVisR: Genomic Visualizations in R
Cited by: 220
Author(s): Zachary L. Skidmore, Alex H. Wagner, Robert Lesurf, Katie M. Campbell, Jason Kunisaki, Obi L. Griffith
Software Mentions: 2
Published: about 10 years ago

10.7717/peerj.2529

Bacterial community diversity of the deep-sea octocoralParamuricea placomus
Cited by: 49
Author(s): Christina A. Kellogg, Steve W. Ross, Sandra Brooke
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.11813

Aberrant expression of PROS1 correlates with human papillary thyroid cancer progression
Cited by: 4
Author(s): Jing Wang, Minxiang Lei, Zhijie Xu
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.10729

Increased precipitation enhances soil respiration in a semi-arid grassland on the Loess Plateau, China
Cited by: 7
Author(s): Yutao Wang, Yi Xie, Gillian L. Rapson, Hao Ma, Le Jing, Yi Zhang, Juan Zhang, Jianping Li
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.7740

Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion
Cited by: 4
Author(s): Anpei Zhou, Peihua Gan, Dan Zong, Fu‐Zhen Xuan, Yuanyuan Zhong, Siqi Li, Jian Yu, Chengzhong He
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.12075

Prediction of the mechanism of miRNAs in laryngeal squamous cell carcinoma based on the miRNA-mRNA regulatory network
Cited by: 1
Author(s): Jun Ma, Xiaodong Hu, Baoqiang Dai, Qiang Wang, Hongqin Wang
Software Mentions: 2
Published: almost 5 years ago

10.7717/peerj.5710

Co-occurrence patterns of litter decomposing communities in mangroves indicate a robust community resistant to disturbances
Cited by: 9
Author(s): Rodrigo Gouvêa Taketani, Marta Alves Moitinho, Tim H. Mauchline, I. S. de Melo
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.2777

Towards quantitative viromics for both double-stranded and single-stranded DNA viruses
Cited by: 138
Author(s): Simon Roux, Natalie Solonenko, Dang Vinh, Bonnie T. Poulos, Sarah M. Schwenck, Dawn B. Goldsmith, Maureen L. Coleman, Mya Breitbart, Matthew B. Sullivan
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.3089

From big data to diagnosis and prognosis: gene expression signatures in liver hepatocellular carcinoma
Cited by: 30
Author(s): Hong Yang, Xin Zhang, Xiujun Cai, Dong‐Yue Wen, Zhihua Ye, Liang Liang, Lu Zhang, Hanlin Wang, Gang Chen, Zhaoyong Feng
Software Mentions: 2
Published: over 9 years ago

10.1128/mSphere.00248-19

High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments
Cited by: 12
Author(s): Hani Nakhoul, Zhen Lin, Xia Wang, Claire Roberts, Yan Dong, Erik K. Flemington
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSphere.00761-19

Dominance of Gas-Eating, Biofilm-Forming Methylobacterium Species in the Evaporator Cores of Automobile Air-Conditioning Systems
Cited by: 2
Author(s): Chulwoo Park, Hye Su Jung, Tae Sun Park, Che Ok Jeon, Woojun Park
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.9088

Effect of predation risk and ectoparasitic louse flies on physiological stress condition of the red-tailed tropicbird (Phaethon rubricauda) from Rapa Nui and Salas & Gómez islands
Cited by: 1
Author(s): Nicolás Luna, Andrea I. Varela, Guillermo Luna‐Jorquera, Katherina Brokordt
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.10926

Identification of fibroblast activation-related genes in two acute kidney injury models
Cited by: 4
Author(s): Weiming Deng, Xuxia Wei, Zhanwen Dong, Jinhua Zhang, Zhengyu Huang, Ning Na
Software Mentions: 2
Published: over 5 years ago

10.1093/bioinformatics/bty832

A systematic method for surveying data visualizations and a resulting genomic epidemiology visualization typology: GEViT
Cited by: 11
Author(s): Anamaria Crisan, Jennifer L. Gardy, Tamara Munzner
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSphere.00151-20

Pseudohyphal Growth of the Emerging Pathogen Candida auris Is Triggered by Genotoxic Stress through the S Phase Checkpoint
Cited by: 42
Author(s): Gustavo Bravo Ruiz, Zoe K. Ross, Neil A. R. Gow, Alexander Lorenz
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.7265

Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
Cited by: 43
Author(s): Gareth Trubl, Simon Roux, Natalie Solonenko, Yueh Fen Li, Benjamin Bolduc, Josué A. Rodríguez-Ramos, Emiley A. Eloe‐Fadrosh, V. I. Rich, Matthew B. Sullivan
Software Mentions: 2
Published: about 7 years ago

10.1128/mSphere.00048-20

Observational Cohort Study of Oral Mycobiome and Interkingdom Interactions over the Course of Induction Therapy for Leukemia
Cited by: 17
Author(s): Sarah N. Robinson, Christine B. Peterson, Pranoti Sahasrabhojane, Nadim J. Ajami, Samuel A. Shelburne, Dimitrios P. Kontoyiannis, Jessica Galloway-Peña
Software Mentions: 2
Published: over 6 years ago

10.1186/s42234-020-00057-1

The role of nicotinic receptors in SARS-CoV-2 receptor ACE2 expression in intestinal epithelia
Cited by: 5
Author(s): Anne S. ten Hove, David J. Brinkman, Andrew Y. Li Yim, Caroline Verseijden, Theo B.M. Hakvoort, Iris Admiraal, Olaf Welting, Patricia H. P. van Hamersveld, Valérie Sinniger, Bruno Bonaz, Misha D. P. Luyer, Wouter J. de Jonge
Software Mentions: 2
Published: almost 6 years ago

10.3897/BDJ.6.e27722

An interactive key to Central European species of the Pteromalus albipennis species group and other species of the genus (Hymenoptera: Chalcidoidea: Pteromalidae), with the description of a new species
Cited by: 8
Author(s): Fabian Klimmek, Hannes Baur
Software Mentions: 2
Published: almost 8 years ago

10.7717/peerj.10183

A 14 immune-related gene signature predicts clinical outcomes of kidney renal clear cell carcinoma
Cited by: 8
Author(s): Yong Zou, Chuan Hu
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.5741

Effects of wine-capStrophariacultivation on soil nutrients and bacterial communities in forestlands of northern China
Cited by: 17
Author(s): Sai Gong, Chen Chen, Jingxian Zhu, Guang-Yao Qi, Shuxia Jiang
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSphere.01014-20

TsrA Regulates Virulence and Intestinal Colonization in Vibrio cholerae
Cited by: 1
Author(s): Cory D. DuPai, Ashley L. Cunningham, Aaron R. Conrado, Claus O. Wilke, Bryan William Davies
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.10460

Multi-year pair-bonding in Murray cod (Maccullochella peelii)
Cited by: 2
Author(s): Alan J Couch, Fiona Dyer, Mark Lintermans
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.5649

Molecular analysis of oral microflora in patients with primary Sjögren’s syndrome by using high-throughput sequencing
Cited by: 24
Author(s): Zhifang Zhou, Guanghui Ling, Ning Ding, Zhe Xun, Ce Zhu, Hong Hua, Xiaochi Chen
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSphere.01160-20

Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils
Cited by: 11
Author(s): Carolyn R. Cornell, Ya Ping Zhang, Joy D. Van Nostrand, Pradeep Wagle, Xiangming Xiao, Jizhong Zhou
Software Mentions: 2
Published: about 5 years ago

10.1128/mSphere.00588-21

A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the bla NDM-1 Gene in Proteus mirabilis
Cited by: 19
Author(s): Jintao He, Long Sun, Linghong Zhang, Sebastian Leptihn, Yunsong Yu, Xiaoting Hua
Software Mentions: 2
Published: almost 5 years ago

10.3390/nu13041141

Adherence to a Supplemented Mediterranean Diet Drives Changes in the Gut Microbiota of HIV-1-Infected Individuals
Cited by: 11
Author(s): Roque Pastor-Ibáñez, Juan Blanco-Heredia, Florencia Etcheverry, Sonsoles Sánchez-Palomino, Francisco Díez-Fuertes, Rosa Casas, María A Navarrete-Muñoz, Sara Castro‐Barquero, Claudia Lucero, Irene Fernández, Lorna Leal, José María Sánchez Benito, Marc Noguera-Julián, Roger Paredes, Norma Rallón, Ramón Estruch, David Torrents, Felipe García
Software Mentions: 2
Published: over 5 years ago

10.1128/mSystems.00052-16

Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir
Cited by: 186
Author(s): Aaron M. Walsh, Fiona Crispie, Kieran N. Kilcawley, Órla O’Sullivan, Maurice G. O’Sullivan, Marcus J. Claesson, Paul D. Cotter
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.8160

Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog
Cited by: 9
Author(s): Miquéias Ferrão, Jiří Moravec, Leandro João Carneiro de Lima Moraes, Vinícius T. de Carvalho, Marcelo Gordo, Albertina P. Lima
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00061-17

Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features
Cited by: 74
Author(s): Sander Wuyts, Stijn Wittouck, Ilke De Boeck, Camille Nina Allonsius, Edoardo Pasolli, Nicola Segata, Sarah Lebeer
Software Mentions: 2
Published: almost 9 years ago

10.1128/mSystems.00096-17

Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont
Cited by: 46
Author(s): Juan Lopera, Ian Miller, Kerry L. McPhail, Jason C. Kwan
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.8923

Dynamic changes in intestinal microbiota in young forest musk deer during weaning
Cited by: 6
Author(s): Yimeng Li, Minghui Shi, Tianxiang Zhang, Xin Hu, Baofeng Zhang, Sheng‐Quan Xu, Jianhong Ding, Defu Hu, Shuqiang Liu
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.494

RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
Cited by: 125
Author(s): Henning Seedorf, Sandra Kittelmann, Gemma Henderson, Peter H. Janssen
Software Mentions: 2
Published: about 12 years ago

10.7717/peerj.2910

The wild tomato speciesSolanum chilenseshows variation in pathogen resistance between geographically distinct populations
Cited by: 21
Author(s): Remco Stam, Daniela Scheikl, Aurélien Tellier
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.8176

Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing
Cited by: 6
Author(s): Xuan Chen, Shouguo Fang, Lili Wei, Qiuyan Zhong
Software Mentions: 2
Published: over 6 years ago

10.3897/BDJ.5.e20577

Understory dominance and the new climax: Impacts of Japanese knotweed (Fallopia japonica) invasion on native plant diversity and recruitment in a riparian woodland
Cited by: 9
Author(s): Matthew Wilson, Anna Freundlich, Christopher T. Martine
Software Mentions: 2
Published: almost 9 years ago

10.3897/BDJ.9.e67677

Morphometric variation in wolves and golden jackal in India (Mammalia, Carnivora)
Cited by: 5
Author(s): Yellapu Srinivas, Yadvendradev V. Jhala
Software Mentions: 2
Published: almost 5 years ago

10.1128/mSystems.00046-18

Combinatorial Approaches to Viral Attenuation
Cited by: 4
Author(s): Matthew L. Paff, Benjamin R. Jack, Bartram L Smith, James J. Bull, Claus O. Wilke
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12957-021-02174-w

Identification and validation of three core genes in p53 signaling pathway in hepatitis B virus-related hepatocellular carcinoma
Cited by: 11
Author(s): Mingxue Yu, Wenli Xu, Yusheng Jie, Jiahui Pang, Siqi Huang, Jing Cao, Jiao Gong, Xinhua Li, Yutian Chong
Software Mentions: 2
Published: over 5 years ago

10.1007/s00268-017-4235-9

Recovery of Voice After Reconstruction of the Recurrent Laryngeal Nerve and Adjuvant Nimodipine
Cited by: 22
Author(s): Per Mattsson, Arvid Frostell, Gunnar Björck, Jonas Persson, Ramil Hakim, Jan Zedenius, Mikael Svensson
Software Mentions: 2
Published: over 8 years ago

10.1186/s40413-018-0212-5

Comparison of microbiota and allergen profile in house dust from homes of allergic and non-allergic subjects- results from the GUSTO study
Cited by: 16
Author(s): Evelyn Xiu Ling Loo, Lamony Jian Ming Chew, A Zulkifli, Le Duc Huy Ta, I-Chun Kuo, Angela Goh, Oon Hoe Teoh, Hugo Van Bever, Peter D. Gluckman, Fabian Yap, Kok Hian Tan, Yap Seng Chong, Bee Wah Lee, Lynette Pei‐Chi Shek
Software Mentions: 2
Published: over 8 years ago

10.12688/wellcomeopenres.15304.3

Representing antibiotic relationships using measurements of efficacy against clinical isolates
Cited by: 1
Author(s): Liam P. Shaw
Software Mentions: 2
Published: almost 6 years ago

10.12688/wellcomeopenres.15452.1

Untargeted metabolomics to understand the basis of phenotypic differences in amphotericin B-resistant Leishmania parasites
Cited by: 10
Author(s): Andrew W. Pountain, Michael P. Barrett
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSystems.00261-19

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults
Cited by: 193
Author(s): Jacobo de la Cuesta-Zuluaga, Scott T. Kelley, Yingfeng Chen, Juan S. Escobar, Noel T. Mueller, Ruth E. Ley, Daniel McDonald, Shi Huang, Austin D. Swafford, Rob Knight, Varykina G. Thackray
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.wroa.2020.100051

Practical implementation of true on-site water recycling systems for hand washing and toilet flushing
Cited by: 10
Author(s): Eva Reynaert, Esther E. Greenwood, Bonginkosi Ndwandwe, Michel E. Riechmann, Rebecca Sindall, Kai M. Udert, Eberhard Morgenroth
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00320-19

Uncovering the Diversity and Activity of Methylotrophic Methanogens in Freshwater Wetland Soils
Cited by: 26
Author(s): Adrienne B. Narrowe, Mikayla A. Borton, David Hoyt, Garrett J. Smith, Rebecca A. Daly, Jordan C. Angle, Elizabeth K. Eder, Allison R. Wong, Richard A. Wolfe, Alexandra Pappas, Gil Bohrer, Christopher S. Miller, Kelly Wrighton
Software Mentions: 2
Published: over 6 years ago

10.3897/BDJ.8.e52233

New insights from museum specimens: a case of Viviparidae (Caenogastropoda: Mollusca) in Iwakawa’s collection preserved in the National Museum of Nature and Science, Tokyo
Cited by: 1
Author(s): Takahito Saito, Osamu Kagawa
Software Mentions: 2
Published: over 5 years ago

10.3390/v13081443

A Mortality-Based Description of EHDV and BTV Prevalence in Farmed White-Tailed Deer (Odocoileus virginianus) in Florida, USA
Cited by: 8
Author(s): Sydney L. Cottingham, Zoe S. White, Samantha M. Wisely, Juan M. Campos-Krauer
Software Mentions: 2
Published: about 5 years ago

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