cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.3390/s20113031

Performance of a Low-Cost Sensor Community Air Monitoring Network in Imperial County, CA
Cited by: 8
Author(s): Paul English, Heather K. Amato, Esther Bejarano, Graeme Carvlin, Humberto Lugo, Michael Jerrett, Galatea King, Daniel Madrigal, Dan Meltzer, Amanda Northcross, Luis José Imedio Olmedo, Edmund Seto, Christian Torres, A. S. Wilkie, Michelle Wong
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.5293

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit
Cited by: 37
Author(s): Jessica G. Wallace, Isabelle Laforest‐Lapointe, Steven W. Kembel
Software Mentions: 4
Published: about 8 years ago

10.3389/fpls.2020.00993

Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?
Cited by: 14
Author(s): Zhiguang Qiu, Juntao Wang, Manuel Delgado‐Baquerizo, Pankaj Trivedi, Eleonora Egidi, Yi-Min Chen, Haiyang Zhang, Brajesh K. Singh
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2020.567249

Molecular Mechanism Underlying Derepressed Male Production in Hexaploid Persimmon
Cited by: 7
Author(s): Kanae Masuda, Naoko Fujita, Ho Wen Yang, Koichiro Ushijima, Yasutaka Kubo, Ryutaro Tao, Takashi Akagi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-49952-x

The polymorphic variant rs1800734 influences methylation acquisition and allele-specific TFAP4 binding in the MLH1 promoter leading to differential mRNA expression
Cited by: 6
Author(s): Russell J. Thomas, Davide Trapani, Lily Goodyer-Sait, Markéta Tomková, Ceres Fernández–Rozadilla, Nora Sahnane, Connor Woolley, Hayley L. Belnoue-Davis, Laura Chegwidden, Skirmantas Kriaucionis, Tim Maughan, Simon J. Leedham, Claire Palles, Daniela Furlan, Ian Tomlinson, Annabelle Lewis
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-48963-y

Daylight affects human thermal perception
Cited by: 64
Author(s): Giorgia Chinazzo, Jan Wienold, Marilyne Andersen
Software Mentions: 4
Published: almost 7 years ago

10.1186/s40168-018-0610-5

The bacterial community significantly promotes cast iron corrosion in reclaimed wastewater distribution systems
Cited by: 30
Author(s): Guijuan Zhang, Bing Li, Jie Liu, Mingqiang Luan, Yao Long, Xiaotao Jiang, Ke Yu, Yuntao Guan
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0185087

A novel molecular toolkit for rapid detection of the pathogen and primary vector of thousand cankers disease
Cited by: 20
Author(s): Emel Ören, William E. Klingeman, Romina Gazis, John K. Moulton, Paris Lambdin, Mark V. Coggeshall, Jiří Hulcr, Steven J. Seybold, Ðenita Hadziabdic
Software Mentions: 4
Published: over 8 years ago

10.3390/insects12060493

Warm Temperatures Reduce Flower Attractiveness and Bumblebee Foraging
Cited by: 17
Author(s): Charlotte Descamps, Anne Jambrek, Muriel Quinet, Anne‐Laure Jacquemart
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.00267

Metatranscriptomic Insights Into the Response of River Biofilm Communities to Ionic and Nano-Zinc Oxide Exposures
Cited by: 8
Author(s): Jordyn Bergsveinson, James W. Roy, Christine Maynard, Sylvie Sanschagrin, Claire N. Freeman, G. D. W. Swerhone, James J. Dynes, Julien Tremblay, Charles W. Greer, Darren R. Korber, John R. Lawrence
Software Mentions: 4
Published: over 6 years ago

10.3390/biology10080811

Polyploidy Improves Photosynthesis Regulation within the Ranunculus auricomus Complex (Ranunculaceae)
Cited by: 7
Author(s): Fuad Bahrul Ulum, Franz Hadaček, Elvira Hörandl
Software Mentions: 4
Published: about 5 years ago

10.1186/1472-6947-11-31

PKreport: report generation for checking population pharmacokinetic model assumptions
Cited by: 6
Author(s): Xiaoyong Sun, Jun Li
Software Mentions: 4
Published: over 15 years ago

10.1186/s13058-016-0718-0

Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus
Cited by: 30
Author(s): Chenjie Zeng, Xingyi Guo, Jirong Long, Karoline Kuchenbaecker, Arnaud Droit, Kyriaki Michailidou, Maya Ghoussaini, Siddhartha Kar, Adam N. Freeman, John L. Hopper, Roger L. Milne, Manjeet K. Bolla, Qin Wang, Joe Dennis, Simona Agata, Shahana Ahmed, Kristiina Aittomäki, Irene L. Andrulis, Hoda Anton‐Culver, Natalia Antonenkova, Aðalgeir Arason, Volker Arndt, Banu K. Arun, Brita Arver, François Bertucci, Daniel Barrowdale, Caroline Baynes, Alicia Beeghly–Fadiel, Javier Benı́tez, Marina Bermisheva, Carl Blomqvist, William J. Blot, Natalia Bogdanova, Stig E. Bojesen, Bernardo Bonanni, Anne Lise Børresen-Dale, Judith S. Brand, Hiltrud Brauch, Paul Brennan, Hermann Brenner, Annegien Broeks, Thomas Brüning, Barbara Burwinkel, Saundra S. Buys, Qiuyin Cai, Trinidad Caldés, Ian Campbell, Jane Carpenter, Jenny Chang‐Claude, Ji Yeob Choi, Kathleen Claes, Christine L. Clarke, Angela Cox, Simon S. Cross, Kamila Czene, Mary B. Daly, Miguel de la Hoya, Kim De Leeneer, Peter Devilee, Orland Díez, Susan M. Domchek, Michele M. Doody, Cecilia M. Dorfling, Thilo Dörk, Isabel dos‐Santos‐Silva, Martine Dumont, Miriam Dwek, Bernd Dworniczak, Kathleen M. Egan, Ursula Eilber, Zakaria Einbeigi, Bent Ejlertsen, Steve Ellis, Debra Frost, Fiona Lalloo, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Michael Friedlander, Eitan Friedman, Gaetana Gambino, Yu Tang Gao, Judy E. Garber, Montserrat García‐Closas, Andrea Gehrig, Francesca Damiola, Fabienne Lesueur, Sylvie Mazoyer, Dominique Stoppa‐Lyonnet, Graham G. Giles, Andrew K. Godwin, David E. Goldgar, Anna González‐Neira, Mark H. Greene, Pascal Guénel, Lothar Haeberle, Christopher A. Haiman, Emily Hallberg, Ute Hamann, Thomas V.O. Hansen, Steven N. Hart, Jaana M. Hartikainen, Mikael Hartman, Norhashimah Hassan, Sue Healey, Frans B.L. Hogervorst, Senno Verhoef, Carolyn B. Hendricks, Peter Hillemanns, Antoinette Hollestelle, Peter J. Hulick, David J. Hunter, Evgeny N. Imyanitov, Claudine Isaacs, Hidemi Ito, Anna Jakubowska, Ramūnas Janavičius, Katarzyna Jaworska–Bieniek, Uffe Birk Jensen, Esther M. John, Charles Joly Beauparlant, Michael E. Jones, Maria Kabisch, Daehee Kang, Beth Y. Karlan, Saila Kauppila, Michael J. Kerin, Sofia Khan, Э. К. Хуснутдинова, Julia A. Knight, Irene Konstantopoulou, Peter Kraft, Ava Kwong, Yael Laitman, Diether Lambrechts, Conxi Lázaro, Loı̈c Le Marchand, Chuen Neng Lee, Min Hyuk Lee, Jenny Lester, Jingmei Li, Annelie Liljegren, Annika Lindblom, Artitaya Lophatananon, Jan Lubiński, L. Phuong, Arto Mannermaa, Siranoush Manoukian, Sara Margolin, Frederik Marmé, Keitaro Matsuo, Lesley McGuffog, Alfons Meindl, Florence Ménégaux, Marco Montagna, Kenneth Muir, Anna Marie Mulligan, Katherine L. Nathanson, Susan L. Neuhausen, Heli Nevanlinna, Polly A. Newcomb, Silje Nord, Robert L. Nussbaum, Kenneth Offit, Edith Olàh, Olufunmilayo I. Olopade, Curtis Olswold, Ana Osorio, Laura Papi, Tjoung Won Park-Simon, Ylva Paulsson-Karlsson, Stéphanie Peeters, Bernard Peissel, Paolo Peterlongo, Julian Peto, Georg Pfeiler, Catherine M. Phelan, Nadège Presneau, Paolo Radice, Nazneen Rahman, Susan J. Ramus, Muhammad Usman Rashid, Gad Rennert, Kerstin Rhiem, Anja Rudolph, Ritu Salani, Suleeporn Sangrajrang, Elinor J. Sawyer, Marjanka K. Schmidt, Rita K. Schmutzler, Minouk J. Schoemaker, Peter Schürmann, Caroline Seynaeve, Chen Shen, Martha J. Shrubsole, Xiao Ou Shu, Alice J. Sigurdson, Christian F. Singer, Susan L. Slager, Penny Soucy, Melissa C. Southey, Doris Steinemann, Anthony Swerdlow, Csilla I. Szabo, Sandrine Tchatchou, Manuel R. Teixeira, Soo Hwang Teo, Mary Beth Terry, Daniel C. Tessier, Àlex Teulé, Mads Thomassen, Laima Tihomirova, Marc Tischkowitz, Amanda E. Toland, Nadine Tung, Clare Turnbull, Ans M.W. van den Ouweland, Elizabeth J. van Rensburg, David ven den Berg, Joseph Vijai, Shan Wang-Gohrke, Jeffrey N. Weitzel, Alice S. Whittemore, Robert Winqvist, Tien Yin Wong, Anna H. Wu, Drakoulis Yannoukakos, Jyh Cherng Yu, Paul D.P. Pharoah, Per Hall, Georgia Chenevix-Trench, Alison M. Dunning, Jacques Simard, Fergus J. Couch, Antonis C. Antoniou, Douglas F. Easton, Zheng Wang
Software Mentions: 4
Published: about 10 years ago

10.3389/fimmu.2020.00395

In Human Autoimmunity, a Substantial Component of the B Cell Repertoire Consists of Polyclonal, Barely Mutated IgG+ve B Cells
Cited by: 13
Author(s): Gillian Cowan, Katherine Miles, Lorenzo Capitani, Sophie Giguere, Hanna Johnsson, Carl S. Goodyear, Iain B. McInnes, Steffen Breusch, David Gray, Mohini Gray
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-020-00757-2

Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma
Cited by: 40
Author(s): Arash Poursheikhani, Mohammad Reza Abbaszadegan, Negin Nokhandani, Mohammad Amin Kerachian
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-40737-w

A study of the relationship between the level of anxiety declared by MRI patients in the STAI questionnaire and their respiratory rate acquired by a fibre-optic sensor system
Cited by: 26
Author(s): Łukasz Dziuda, Piotr Zieliński, Paulina Baran, Mariusz Krej, Lech Kopka
Software Mentions: 4
Published: over 7 years ago

10.1186/s42523-021-00120-5

Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta)
Cited by: 7
Author(s): Klara Filek, Adriana Trotta, Romana Gračan, Antonio Di Bello, Marialaura Corrente, Sunčica Bosak
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12920-021-00954-7

Identification of genes and pathways involved in malignant pleural mesothelioma using bioinformatics methods
Cited by: 3
Author(s): Xingsheng Liu, Kun Qian, Gaojun Lu, Peng Chen, Yi Zhang
Software Mentions: 4
Published: over 5 years ago

10.3389/fpls.2020.500479

Contrasting Dependencies of Photosynthetic Capacity on Leaf Nitrogen in Early- and Late-Successional Tropical Montane Tree Species
Cited by: 8
Author(s): Camille Ziegler, Mirindi Eric Dusenge, Brigitte Nyirambangutse, Etienne Zibera, Göran Wallin, Johan Uddling
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-40495-9

Differential gene expression induced by Verteporfin in endometrial cancer cells
Cited by: 8
Author(s): Lisa Bang, Venkata Ramesh Dasari, Dokyoon Kim, Radhika Gogoi
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-11-45

NeatMap - non-clustering heat map alternatives in R
Cited by: 77
Author(s): Satwik Rajaram, Yoshitsugu Oono
Software Mentions: 4
Published: over 16 years ago

10.1186/bcr3684

Transforming growth factor beta receptor type III is a tumor promoter in mesenchymal-stem like triple negative breast cancer
Cited by: 45
Author(s): Bojana Jovanović, J. Scott Beeler, Michael W. Pickup, Anna Chytil, Agnieszka E. Gorska, William J. Ashby, Brian D. Lehmann, Andries Zijlstra, Jennifer A. Pietenpol, Harold L. Moses
Software Mentions: 4
Published: about 12 years ago

10.3390/insects11090645

Diet Breadth Affects Bacterial Identity but Not Diversity in the Pollen Provisions of Closely Related Polylectic and Oligolectic Bees
Cited by: 10
Author(s): Jason A. Rothman, Diana Cox-Foster, Corey J. Andrikopoulos, Quinn S. McFrederick
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12920-020-0682-5

A pan-cancer study of class-3 semaphorins as therapeutic targets in cancer
Cited by: 37
Author(s): Xiaoli Zhang, Brett Klamer, Jin Li, Soledad Fernández, Lang Li
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2021.689051

Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea
Cited by: 11
Author(s): Lara Schmittmann, Sören Franzenburg, Lucía Pita
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00982

Functional and Structural Responses of Arctic and Alpine Soil Prokaryotic and Fungal Communities Under Freeze-Thaw Cycles of Different Frequencies
Cited by: 27
Author(s): Carla Perez-Mon, Beat Frey, Aline Frossard
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.25382

Aberration hubs in protein interaction networks highlight actionable targets in cancer
Cited by: 4
Author(s): Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi, Yasser Riazalhosseini
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.4088

PlantCV v2: Image analysis software for high-throughput plant phenotyping
Cited by: 191
Author(s): Malia Gehan, Arash Abbasi, Jeffrey C. Berry, Steven T. Callen, Leonardo Chavez, Andrew N. Doust, Max Feldman, Kerrigan B. Gilbert, John G. Hodge, J. Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael D. Miller, Éric Platon, Monica Tessman, Tony Sax
Software Mentions: 4
Published: over 8 years ago

10.7717/peerj.10140

Spatial modeling could not differentiate early SARS-CoV-2 cases from the distribution of humans on the basis of climate in the United States
Cited by: 6
Author(s): Robert S. Harbert, Seth W. Cunningham, Michael Tessler
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13395-020-00227-4

Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity
Cited by: 31
Author(s): Takako I. Jones, Guo-Liang Chew, Pamela Barraza‐Flores, Spencer Schreier, Monique Ramirez, Ryan D. Wuebbles, Dean J. Burkin, Robert K. Bradley
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.4512

Playing by the rules? Phenotypic adaptation to temperate environments in an American marsupial
Cited by: 16
Author(s): Sergio Nigenda‐Morales, Ryan J. Harrigan, Robert K. Wayne
Software Mentions: 4
Published: over 8 years ago

10.3389/fmicb.2019.00479

Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species
Cited by: 72
Author(s): Marko Verce, Luc De Vuyst, Stefan Weckx
Software Mentions: 4
Published: over 7 years ago

10.1038/s41419-021-04144-2

LncRNA PCBP1-AS1-mediated AR/AR-V7 deubiquitination enhances prostate cancer enzalutamide resistance
Cited by: 19
Author(s): Boya Zhang, Mingpeng Zhang, Chunyi Shen, Guancong Liu, Fan Zhang, Jingyu Hou, Weitao Yao
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13058-019-1170-8

Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers
Cited by: 17
Author(s): Christian Fougner, Helga Bergholtz, Raoul V. Kuiper, Jens Henrik Norum, Thérese Sørlie
Software Mentions: 4
Published: about 7 years ago

10.1186/s13287-019-1218-9

Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics
Cited by: 25
Author(s): Ramil Hakim, Ruxandra Covacu, Vasilios Zachariadis, Arvid Frostell, Sreenivasa Raghavan Sankavaram, Lou Brundin, Mikael Svensson
Software Mentions: 4
Published: over 7 years ago

10.3390/insects11070441

Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol
Cited by: 11
Author(s): Thomas W. R. Harrop, Marissa F. Le Lec, Ruy Jáuregui, Shannon E. Taylor, Sarah N Inwood, Tracey Van Stijn, Hannah M. Henry, John Skelly, Siva Ganesh, Rachael Ashby, Jeanne M. E. Jacobs, S. L. Goldson, Peter K. Dearden
Software Mentions: 4
Published: about 6 years ago

10.1038/s42003-021-01834-7

High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity
Cited by: 51
Author(s): Vlad Dincă, Leonardo Dapporto, Panu Somervuo, Raluca Vodă, Sylvain Cuvelier, Martin Gascoigne‐Pees, Peter Huemer, Marko Mutanen, Paul D. N. Hebert, Roger Vila
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10572

Genomic diversity of Escherichia coli from healthy children in rural Gambia
Cited by: 7
Author(s): Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Usman N. Ikumapayi, Golam Sarwar, Catherine Okoi, Peggy-Estelle Tientcheu, Marianne Defernez, Justin O’Grady, Martín Antonio, Mark J. Pallen
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2020.01092

Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics
Cited by: 8
Author(s): Balázs Brankovics, A.D. van Diepeningen, G. Sybren de Hoog, Theo A. J. van der Lee, C. Waalwijk
Software Mentions: 4
Published: about 6 years ago

10.3389/fcell.2021.714718

Opposite Roles of Tumor Cell Proliferation and Immune Cell Infiltration in Postoperative Liver Metastasis of PDAC
Cited by: 0
Author(s): Guangfu Wang, Shangnan Dai, Hao Gao, Yong Gao, Lingdi Yin, Kai Zhang, Xumin Huang, Zipeng Lu, Yi Miao
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0229873

Development of a methodology to make individual estimates of the precision of liquid chromatography-tandem mass spectrometry drug assay results for use in population pharmacokinetic modeling and the optimization of dosage regimens
Cited by: 7
Author(s): Gellért Balázs Karvaly, Michael Neely, K Kovács, István Vincze, Barna Vásárhelyi, Roger W. Jelliffe
Software Mentions: 4
Published: over 6 years ago

10.1038/s42003-021-02189-9

Claudin-2 promotes colorectal cancer liver metastasis and is a biomarker of the replacement type growth pattern
Cited by: 24
Author(s): Sébastien Tabariès, Matthew G. Annis, Anthoula Lazaris, Stephanie Petrillo, Jennifer Huxham, A. Achour, Vincent Palmieri, Jaclyn M. Chabot, Radia Marie Johnson, Steven Van Laere, Cornelis Verhoef, Yasmina Hachem, Sara Yumeen, Nicholas Meti, Atilla Ömeroğlu, Gulbeyaz Altinel, Zu‐Hua Gao, Alan Yu, Dirk J. Grünhagen, Peter B. Vermeulen, Peter Metrakos, Peter M. Siegel
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.00766-20

Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation
Cited by: 9
Author(s): José Luis López, Mauricio Javier Lozano, María Laura Fabre, Antonio Lagares
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.11948

Quantifying bite force in coexisting tayassuids and feral suids: a comparison between morphometric functional proxies and in vivo measurements
Cited by: 1
Author(s): Fernando Lencastre Sicuro, Luiz Flamarion B. Oliveira, Carla Deonísia Hendges, Carlos Fonseca
Software Mentions: 4
Published: about 5 years ago

10.1038/s42003-021-01828-5

Hyperthermophilic methanogenic archaea act as high-pressure CH4 cell factories
Cited by: 26
Author(s): Lisa‐Maria Mauerhofer, Sara Zwirtmayr, Patricia Pappenreiter, Sébastien Bernacchi, Arne H. Seifert, Barbara Reischl, Tilman Schmider, Ruth-Sophie Taubner, Christian Paulik, Simon K.-M. R. Rittmann
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.643731

Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives
Cited by: 11
Author(s): Rowena Hill, Theo Llewellyn, Elizabeth Downes, Joseph Oddy, Catriona MacIntosh, Simon Kallow, Bart Panis, John B. Dickie, Ester Gaya
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.02254-20

CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
Cited by: 27
Author(s): Wen Li, Parmit K. Singh, Gregory A. Sowd, Gregory J. Bedwell, Sungwoo Jang, Vasudevan Achuthan, Amarachi V. Oleru, Doris Wong, Hind J. Fadel, Kyeongeun Lee, Vineet N. KewalRamani, Eric M. Poeschla, Alon Herschhorn, Alan Engelman
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.6377

Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis
Cited by: 50
Author(s): Bettina Glasl, Caitlin E. Smith, David G. Bourne, Nicole S. Webster
Software Mentions: 4
Published: over 7 years ago

10.3390/cancers12113447

Convergence of Plasma Metabolomics and Proteomics Analysis to Discover Signatures of High-Grade Serous Ovarian Cancer
Cited by: 23
Author(s): Hee‐Sung Ahn, Jeonghun Yeom, Jeesuk Yu, Young-Il Kwon, Jae Hoon Kim, Kyunggon Kim
Software Mentions: 4
Published: almost 6 years ago

10.1111/1751-7915.13393

Black soldier fly larvae (Hermetia illucens) strengthen the metabolic function of food waste biodegradation by gut microbiome
Cited by: 107
Author(s): Cheng-Liang Jiang, Wei-Zheng Jin, Xin-Hua Tao, Qian Zhang, Jun Zhu, Shiyun Feng, Xinhua Xu, Hongyi Li, Zehua Wang, Zhijian Zhang
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.11956

Small-scale variation in a pristine montane cloud forest: evidence on high soil fungal diversity and biogeochemical heterogeneity
Cited by: 1
Author(s): Patricia Vélez, Yunuen Tapia-Torres, Felipe Garcı́a-Oliva, Jaime Gasca-Pineda
Software Mentions: 4
Published: about 5 years ago

10.1111/1751-7915.13353

Microbial communities in swine lungs and their association with lung lesions
Cited by: 24
Author(s): Tao Huang, Mingpeng Zhang, Xinkai Tong, Jiaqi Chen, Guorong Yan, Shouguo Fang, Yuanmei Guo, Bin Yang, Shijun Xiao, Congying Chen, Lusheng Huang, Huashui Ai
Software Mentions: 4
Published: over 7 years ago

10.1128/mBio.02318-20

Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat
Cited by: 11
Author(s): Michael E. Hibbing, Karen W. Dodson, Vasilios Kalas, Swaine L. Chen, Scott J. Hultgren
Software Mentions: 4
Published: almost 6 years ago

10.1590/1414-431X2021e11372

Profiles of immune infiltration in abdominal aortic aneurysm and their associated marker genes: a gene expression-based study
Cited by: 5
Author(s): Tan Li, Tianlong Wang, Xin Zhao
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmed.2021.737007

Severe SARS-CoV-2 Breakthrough Reinfection With Delta Variant After Recovery From Breakthrough Infection by Alpha Variant in a Fully Vaccinated Health Worker
Cited by: 64
Author(s): Jayanthi Shastri, Swapneil Parikh, Veena Aggarwal, Sachee Agrawal, Nirjhar Chatterjee, Rajit Shah, Priti Devi, Priyanka Mehta, Rajesh Pandey
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj.8133

The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity
Cited by: 19
Author(s): Lauren V. Carruthers, Moses Arinaitwe, Moses Adriko, Christina L. Faust, Edridah M. Tukahebwa, Lindsay J. Hall, Lisa Ranford-Cartwright, Poppy H. L. Lamberton
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-51211-y

Long-term efficacy of imatinib mesylate in patients with advanced Tenosynovial Giant Cell Tumor
Cited by: 38
Author(s): Floortje G M Verspoor, Monique J L Mastboom, Gerjon Hannink, Robert G. Maki, Andrew J. Wagner, Emmanuelle Bompas, Jayesh Desai, Antoîne Italiano, Beatrice Seddon, Winette T.A. van der Graaf, Jean‐Yves Blay, Mehdi Brahmi, Lauriane Eberst, Silvia Stacchiotti, Olivier Mir, Michiel A.J. van de Sande, Hans Gelderblom, P. A. Cassier
Software Mentions: 4
Published: almost 7 years ago

10.1128/mBio.01229-21

Diverse Humoral Immune Responses in Younger and Older Adult COVID-19 Patients
Cited by: 18
Author(s): Jennifer Sasson, Joseph J. Campo, Rebecca Carpenter, Mary K. Young, Arlo Randall, Krista Trappl-Kimmons, Amit Oberai, Christopher Hung, Joshua Edgar, Andy Teng, Jozelyn Pablo, Xiaowu Liang, Angela Yee, William A. Petri, David Camerini
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2019.01361

Biochar Amendment Stimulates Utilization of Plant-Derived Carbon by Soil Bacteria in an Intercropping System
Cited by: 33
Author(s): Hongkai Liao, Yaying Li, Huaiying Yao
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.3394

SIX4 promotes metastasis via activation of the PI3K-AKT pathway in colorectal cancer
Cited by: 26
Author(s): Guodong Li, Fang Hu, Xuelai Luo, Jian Hu, Yongzeng Feng
Software Mentions: 4
Published: about 9 years ago

10.1186/s12879-020-05600-8

Describing nearly two decades of Chagas disease in Germany and the lessons learned: a retrospective study on screening, detection, diagnosis, and treatment of Trypanosoma cruzi infection from 2000 – 2018
Cited by: 10
Author(s): Jessica Michelle Guggenbühl Noller, Günter Fröschl, Philip Eisermann, Johannes Jochum, Stefanie Theuring, Ingrid Reiter‐Owona, Alfred Lennart Bissinger, Michael Höelscher, Abhishek Bakuli, Franz-Josef Falkner von Sonnenburg, Camilla Rothe, Gisela Bretzel, Pedro Albajar-Viñas, Lise Grout, Michael Pritsch
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.10231

Comparing sediment DNA extraction methods for assessing organic enrichment associated with marine aquaculture
Cited by: 22
Author(s): John K. Pearman, Nigel Keeley, Susanna A. Wood, Olivier Laroche, Anastasija Zaiko, Georgia Thomson‐Laing, Laura Biessy, Javier Atalah, Xavier Pochon
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.39231

Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera
Cited by: 24
Author(s): Michal Tupec, Aleš Buček, Václav Janous̆ek, Heiko Vogel, Darina Prchalová, Jiří Kindl, Tereza Pavlíčková, Petra Wenzelová, Ullrich Jahn, Irena Valterová, Iva Pichová
Software Mentions: 4
Published: over 7 years ago

10.3389/fcell.2021.688855

Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells
Cited by: 7
Author(s): Dilek Cansu Gürer, İpek Erdoğan, Ulvi Ahmadov, Merve Başol, Osama Sweef, Gulcin Cakan-Akdogan, Bünyamin Akgül
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.01937-21

Mucosal Bacteria Modulate Candida albicans Virulence in Oropharyngeal Candidiasis
Cited by: 16
Author(s): Martinna Bertolini, Roberto Vázquez-Muñoz, Linda Archambault, Siddharth Shah, João Gabriel Silva Souza, Raphael Cavalcante Costa, Angela Thompson, Yanjiao Zhou, Takanori Sobue, Anna Dongari-Bagtzoglou
Software Mentions: 4
Published: almost 5 years ago

10.1111/irv.12574

Primary care influenza-like illness surveillance in Ho Chi Minh City, Vietnam 2013-2015
Cited by: 8
Author(s): Stacy Todd, Nguyễn Thị Cẩm Hường, Nguyen Thi Le Thanh, Nguyen Ha Thao Vy, Nguyễn Thành Hưng, Tran Thi Nhu Thao, Huynh Thi Phuong, H. Rogier van Doorn, Vu Thi Ty Hang, Nguyễn Văn Vĩnh Châu, Jonathan M. Read, David G. Lalloo, Maciej F. Boni
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-020-69218-1

Validity of dynamical analysis to characterize heart rate and oxygen consumption during effort tests
Cited by: 5
Author(s): Denis Mongin, C. Chabert, Adriana Uribe Caparros, Aurélie Collado, Éric Hermand, Olivier Hue, José Ramón Alvero Cruz, Delphine S. Courvoisier
Software Mentions: 4
Published: about 6 years ago

10.1128/mSphere.00226-16

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City
Cited by: 22
Author(s): Holly M. Bik, Julia M. Maritz, Albert Luong, Hakdong Shin, Maria Gloria Domínguez-Bello, Jane M. Carlton
Software Mentions: 4
Published: over 9 years ago

10.18632/aging.203323

An immune-related lncRNA signature for the prognosis of pancreatic adenocarcinoma
Cited by: 10
Author(s): Bing Qi, Han Liu, Qi Zhou, Ji Li, Xueying Shi, Yu‐Shan Wei, Yinmin Gu, Akio Mizushima, Shilin Xia
Software Mentions: 4
Published: about 5 years ago

10.1186/s12865-014-0040-5

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
Cited by: 53
Author(s): Victor Greiff, Ulrike Menzel, Ulrike Haessler, Skylar C. Cook, Simon Friedensohn, Tarik A. Khan, Mark Pogson, Ina Hellmann, Sai T. Reddy
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12859-021-04120-9

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
Cited by: 15
Author(s): Sagnik Banerjee, Priyanka Bhandary, Margaret R. Woodhouse, Taner Z. Sen, Roger P. Wise, Carson M. Andorf
Software Mentions: 4
Published: over 5 years ago

10.1186/s12865-020-00344-1

Identification of differentially expressed circulating exosomal lncRNAs in IgA nephropathy patients
Cited by: 17
Author(s): Na Guo, Qin Zhou, Xiang Huang, Jia-Kuo Yu, Qianqian Han, Baoting Nong, Yuanyan Xiong, Peifeng Liang, Jiajia Li, Min Feng, Jun Lv, Qiongqiong Yang
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.67173

Associations of topic-specific peer review outcomes and institute and center award rates with funding disparities at the National Institutes of Health
Cited by: 16
Author(s): Michael S. Lauer, Jamie Mihoko Doyle, Joy Wang, Deepshikha Roychowdhury
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.8938

Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates
Cited by: 11
Author(s): Wyatt L. Patry, MacKenzie M Bubel, Cypress Hansen, Thomas Knowles
Software Mentions: 4
Published: over 6 years ago

10.18632/aging.103859

Weighted gene coexpression network analysis identifies the key role associated with acute coronary syndrome
Cited by: 4
Author(s): Yong Wang, Miao Liu, Tao Lin, Jianhong Chen, Chuan-Meng Zhu, Ye Li, Bin Qi, Fei Liao, Rongshan Li
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.5738

The relationship between social rank and spatial learning in pheasants, Phasianus colchicus: cause or consequence?
Cited by: 15
Author(s): Ellis J. G. Langley, Jayden O. van Horik, Mark Whiteside, Christine E. Beardsworth, Joah R. Madden
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0251121

Melanocytes determine angiogenesis gene expression across human tissues
Cited by: 3
Author(s): Shirly Freilikhman, Marianna Halasi, Alal Eran, Irit Adini
Software Mentions: 4
Published: over 5 years ago

10.1002/ece3.2794

Synergistic effects of floral phytochemicals against a bumble bee parasite
Cited by: 46
Author(s): Evan C. Palmer‐Young, Ben M. Sadd, Rebecca E. Irwin, Lynn S. Adler
Software Mentions: 4
Published: over 9 years ago

10.3389/fcell.2021.709241

Characterization of Immune-Related Long Non-coding RNAs to Construct a Novel Signature and Predict the Prognosis and Immune Landscape of Soft Tissue Sarcoma
Cited by: 1
Author(s): Zhengjun Lin, Ke Pang, Hongli Liu, Xianghong Zhang, Jia Wan, Tao Zheng, Tang Liu, Weijun Peng
Software Mentions: 4
Published: almost 5 years ago

10.3390/ijms22084267

smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites
Cited by: 4
Author(s): Kristian Persson Hodén, Xinyi Hu, Gabriel García Martínez, Christina Dixelius
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21093187

Season Affects Yield and Metabolic Profiles of Rice (Oryza sativa) under High Night Temperature Stress in the Field
Cited by: 18
Author(s): Stephanie Schaarschmidt, Lovely Mae F Lawas, Ulrike Glaubitz, Xia Li, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Dirk K. Hincha, Ellen Zuther
Software Mentions: 4
Published: over 6 years ago

10.3389/fcell.2020.562662

Identifying Mechanisms of Normal Cognitive Aging Using a Novel Mouse Genetic Reference Panel
Cited by: 6
Author(s): Amy R. Dunn, Niran Hadad, Sarah M. Neuner, Jigang Zhang, Vivek Philip, Logan Dumitrescu, Timothy J. Hohman, Jeremy H. Herskowitz, Kathryn A O’Connell, Catherine C. Kaczorowski
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.9883

Mayfly emergence production and body length response to hydrology in a tropical lowland stream
Cited by: 4
Author(s): Pablo E. Gutiérrez‐Fonseca, Alonso Ramírez
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.102782

A nomogram combining long non-coding RNA expression profiles and clinical factors predicts survival in patients with bladder cancer
Cited by: 30
Author(s): Yifan Wang, Du Li, Xuemei Yang, Juan Li, Peilong Li, Yinghui Zhao, Weili Duan, Yingjie Chen, Yunshan Wang, Hongzhi Mao, Chuanxin Wang
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.5583

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico
Cited by: 22
Author(s): Ma. Fernanda Sánchez-Soto Jiménez, Daniel Cerqueda‐García, Jorge L. Montero-Muñoz, M. Leopoldina Aguirre-Macedo, José Q. García-Maldonado
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSphereDirect.00283-18

Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture
Cited by: 46
Author(s): Alexander L. Greninger, Pavitra Roychoudhury, Hong Xie, Amanda M. Casto, Anne Cent, Gregory Pepper, David M. Koelle, Meei‐Li Huang, Anna Wald, Christine Johnston, Keith R. Jerome
Software Mentions: 4
Published: about 8 years ago

10.1002/ece3.6989

Effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on associated soil bacterial communities: A field‐based experiment
Cited by: 9
Author(s): Hayley Craig, John Paul Kennedy, Donna J. Devlin, Richard D. Bardgett, Jennifer K. Rowntree
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-020-07260-z

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum
Cited by: 18
Author(s): Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen, Wuwei Ye
Software Mentions: 4
Published: over 5 years ago

10.1186/s12934-021-01658-4

Transcriptomics reveal different metabolic strategies for acid resistance and gamma-aminobutyric acid (GABA) production in select Levilactobacillus brevis strains
Cited by: 7
Author(s): Sagarika Banerjee, M. H. Poore, Svetlana Gerdes, Derek Nedveck, Lene Lauridsen, Heidi Thomsen Kristensen, Henrik Max Jensen, Phillip M. Byrd, Arthur C. Ouwehand, Elaine Patterson, Wesley Morovic
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40168-020-00986-8

Acquisition of oral microbiota is driven by environment, not host genetics
Cited by: 31
Author(s): Chiranjit Mukherjee, Christina O. Moyer, Heidi M. Steinkamp, Shahr B. Hashmi, Clifford J. Beall, Xiaohan Guo, Ai Ni, Eugene J. Leys, Ann L. Griffen
Software Mentions: 4
Published: over 5 years ago

10.7717/peerj.3766

The Plasmodium berghei RC strain is highly diverged and harbors putatively novel drug resistance variants
Cited by: 0
Author(s): Warangkhana Songsungthong, Supasak Kulawonganunchai, Alisa Wilantho, Sissades Tongsima, Pongpisid Koonyosying, Chairat Uthaipibull, Sumalee Kamchonwongpaisan, Philip Shaw
Software Mentions: 4
Published: almost 9 years ago

10.7717/peerj.11074

Identification of a novel autophagy signature for predicting survival in patients with lung adenocarcinoma
Cited by: 6
Author(s): Jian Duan, Youming Lei, Guoli Lv, Yinqiang Liu, Zhao Wei, Qingmei Yang, Xin Su, Zhijian Song, Leilei Lu, Yunfei Shi
Software Mentions: 4
Published: over 5 years ago

10.3389/fneur.2020.00605

Subtle Cerebellar Features in Relatives of Essential Tremor Cases
Cited by: 1
Author(s): Evan A. Hale, Ruby Hickman, Hollie Dowd, Deepti Varathan, Gina Liu, Elan D. Louis
Software Mentions: 4
Published: about 6 years ago

10.3389/fmed.2020.00161

Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana
Cited by: 14
Author(s): Prince Asare, Isaac Darko Otchere, Edmund Bedeley, Daniela Brites, Chloé Loiseau, Nyonuku Akosua Baddoo, Adwoa Asante-Poku, Stephen Osei-Wusu, Diana Ahu Prah, Sònia Borrell, Miriam Reinhard, Audrey Forson, Kwadwo A. Koram, Sébastien Gagneux, Dorothy Yeboah-Manu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-51118-8

Extensive vegetation browning and drying in forests of India’s Tiger Reserves
Cited by: 7
Author(s): Pradeep Koulgi, Nicholas Clinton, Krithi K. Karanth
Software Mentions: 4
Published: almost 7 years ago

10.3389/fpls.2020.00912

More Filtering on SNP Calling Does Not Remove Evidence of Inter-Nucleus Recombination in Dikaryotic Arbuscular Mycorrhizal Fungi
Cited by: 6
Author(s): Eric C. Chen, Stephanie Mathieu, Anne Hoffrichter, Jeanne Ropars, Steven Dreißig, Joerg Fuchs, Andreas Brachmann, Nicolas Corradi
Software Mentions: 4
Published: about 6 years ago

10.3390/antibiotics9110735

Pathogenic Escherichia coli Possess Elevated Growth Rates under Exposure to Sub-Inhibitory Concentrations of Azithromycin
Cited by: 4
Author(s): Tran Tuan-Anh, Ha Thanh Tuyen, Nguyen Ngoc Minh Chau, Nguyen Duc Toan, Tran Hanh Triet, Le Minh Triet, Nguyen Hoang Thu Trang, Nguyen Thi Nguyen To, Josefin Bartholdson Scott, Duy Pham Thanh, Hannah E. Clapham, Stephen Baker
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.11421

nCov2019: an R package for studying the COVID-19 coronavirus pandemic
Cited by: 9
Author(s): Tianzhi Wu, Erqiang Hu, Xijin Ge, Yu Guo
Software Mentions: 4
Published: about 5 years ago

10.1038/s41438-019-0214-7

Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)
Cited by: 4
Author(s): Henry O. Awika, Thiago G. Marconi, Renesh Bedre, Kranthi K. Mandadi, Carlos A. Avila
Software Mentions: 4
Published: over 6 years ago

Projects: cran: ggplot2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning ggplot2 11,441