Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: ggplot2
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics
48 versions
Latest release: about 1 year ago
4,921 dependent packages
2,865,232 downloads last month
Papers Mentioning ggplot2 11,441
10.3390/ijms22105354
Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated BarleyCited by: 7
Author(s): Jinhong Kan, Guang Gao, Qiang He, Qian Gao, Congcong Jiang, Sunny Ahmar, Jun Liu, Jing Zhang, Ping Yang
Software Mentions: 8
Published: over 3 years ago
10.3389/fmicb.2018.01868
Exposure to Yeast Shapes the Intestinal Bacterial Community Assembly in Zebrafish LarvaeCited by: 29
Author(s): Prabhugouda Siriyappagouder, Jorge Galindo-Villegas, Jep Lokesh, Victoriano Mulero, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0220164
Disaggregated level child morbidity in Bangladesh: An application of small area estimation methodCited by: 0
Author(s): Sumonkanti Das, Bappi Kumar, Luthful Alahi Kawsar
Software Mentions: 8
Published: over 4 years ago
10.3390/ijms21103591
Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant SoybeanCited by: 8
Author(s): Adrienne N. Moran Lauter, Lindsay Rutter, Dianne Cook, Jamie A. O’Rourke, Michelle A. Graham
Software Mentions: 8
Published: over 4 years ago
10.3390/microorganisms9061326
Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived FertilizerCited by: 5
Author(s): Thijs Van Gerrewey, Christophe El‐Nakhel, Stefania De Pascale, Jolien De Paepe, Peter Clauwaert, Frederiek‐Maarten Kerckhof, Nico Boon, Danny Geelen
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pntd.0008623
Population genomic evidence that human and animal infections in Africa come from the same populations of Dracunculus medinensisCited by: 16
Author(s): Caroline Durrant, Elizabeth A. Thiele, Nancy Holroyd, Stephen R. Doyle, Guillaume Sallé, Alan S. Tracey, Geetha Sankaranarayanan, Magda E. Lotkowska, Hayley M. Bennett, Harrison Thomas, Zahra Abdellah, Ouakou Tchindebet, Mesfin Wossen, Makoy Samuel Yibi Logora, Cheick Oumar Coulibaly, Adam Weiss, Albrecht I. Schulte‐Hostedde, Jeremy M. Foster, Christopher A. Cleveland, Michael J. Yabsley, Ernesto Ruiz‐Tiben, Matthew Berriman, Mark L. Eberhard, James A. Cotton
Software Mentions: 8
Published: almost 4 years ago
10.1186/s12859-021-04123-6
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinomaCited by: 19
Author(s): Shiming Yang, Yaping Zhou, Xiangxin Zhang, Lu Wang, Jianfeng Fu, Xiaotong Zhao, Yang Liu
Software Mentions: 8
Published: over 3 years ago
10.3389/fgene.2019.01143
Identification of a Tumor Microenvironment-Related Eight-Gene Signature for Predicting Prognosis in Lower-Grade GliomasCited by: 24
Author(s): Jun Su, Wenyong Long, Qianquan Ma, Kai Xiao, Li Yang, Qian Xiao, Gang Peng, Jian Yuan, Qing Liu
Software Mentions: 8
Published: about 5 years ago
10.3389/fgene.2019.00654
The Impact of cDNA Normalization on Long-Read Sequencing of a Complex TranscriptomeCited by: 5
Author(s): Nam V. Hoang, Agnelo Furtado, Virginie Perlo, Frederik C. Botha, Robert J. Henry
Software Mentions: 8
Published: over 5 years ago
10.7150/jca.49175
Biological functions and prognostic value of RNA Binding Proteins in clear cell Renal Cell CarcinomaCited by: 6
Author(s): Zhenpeng Zhu, Anbang He, Lanruo Lin, Chunru Xu, Tianyu Cai, Lin Jian
Software Mentions: 8
Published: almost 5 years ago
10.3389/fpls.2018.01632
Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napusCited by: 22
Author(s): Ruijuan Li, Kwangju Jeong, John Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin Maloof
Software Mentions: 8
Published: about 6 years ago
10.3389/fpls.2017.00930
The Influence of Land Use Intensity on the Plant-Associated Microbiome of Dactylis glomerata L.Cited by: 44
Author(s): Jennifer Estendorfer, Barbara Stempfhuber, Paula Haury, Gisle Vestergaard, Matthias C. Rillig, Jasmin Joshi, Peter Schröder, Michael Schloter
Software Mentions: 8
Published: over 7 years ago
10.3390/nu13072372
Assessment of Adherence to the Healthy Food Pyramid in Pregnant and Lactating WomenCited by: 5
Author(s): Andrea Gila-Díaz, Ariadna Witte Castro, Gloria Herranz Carrillo, Pratibha Singh, William Yakah, Silvia M. Arribas, David Ramiro-Cortijo
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0257471
Deciphering the low abundance microbiota of presumed aseptic hip and knee implantsCited by: 2
Author(s): Charles Carr, Hannah Wilcox, Jeremy P. Burton, Sharanya Menon, Kait F. Al, David B. O’Gorman, Brent A. Lanting, Edward M. Vasarhelyi, Michael E. Neufeld, Matthew G. Teeter
Software Mentions: 8
Published: about 3 years ago
10.1371/journal.pone.0217804
Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeonsCited by: 12
Author(s): Kirsten Grond, Julie Perreau, Wesley T. Loo, A. James Spring, Colleen M. Cavanaugh, Sarah M. Hird
Software Mentions: 8
Published: over 5 years ago
10.1186/s12859-016-1007-8
readat: An R package for reading and working with SomaLogic ADAT filesCited by: 11
Author(s): Richard Cotton, Johannes Graumann
Software Mentions: 8
Published: over 8 years ago
10.1186/s12859-016-1051-4
gtrellis: an R/Bioconductor package for making genome-level Trellis graphicsCited by: 17
Author(s): Zuguang Gu, Roland Eils, Matthias Schlesner
Software Mentions: 8
Published: over 8 years ago
10.1172/jci.insight.138751
In utero human intestine harbors unique metabolome, including bacterial metabolitesCited by: 27
Author(s): Yujia Li, Jessica Toothaker, Shira Ben-Simon, Lital Ozeri, Ron Schweitzer, Blake McCourt, Collin C. McCourt, Lael Werner, Scott B. Snapper, Dror S. Shouval, Soliman Khatib, Omry Koren, Sameer Agnihorti, George C. Tseng, Liza Konnikova
Software Mentions: 8
Published: about 4 years ago
10.1172/jci.insight.130510
Asymmetric cell division promotes therapeutic resistance in glioblastoma stem cellsCited by: 19
Author(s): Masahiro Hitomi, Anastasia Chumakova, Daniel J. Silver, Arnon Møldrup Knudsen, William Pontius, Shaun Murphy, Neha Anand, Bjarne Winther Kristensen, Justin D. Lathia
Software Mentions: 8
Published: almost 4 years ago
10.1093/femsec/fiaa244
Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiomeCited by: 0
Author(s): Lydia-Ann J. Ghuneim, Marco A. Distaso, Tatyana Chernikova, Rafael Bargiela, Evgenii A. Lunev, Aleksei A. Korzhenkov, Stepan V. Toshchakov, David Rojo, Coral Barbas, Manuel Ferrer, Olga V. Golyshina, Peter N. Golyshin, Davey L. Jones
Software Mentions: 8
Published: almost 4 years ago
10.3758/s13428-019-01236-y
formr: A study framework allowing for automated feedback generation and complex longitudinal experience-sampling studies using RCited by: 120
Author(s): Rana Arslan, Matthias P. Walther, Cyril Tata
Software Mentions: 8
Published: over 5 years ago
10.1186/s41065-021-00201-0
Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritisCited by: 10
Author(s): Yanzhi Ge, Zuxiang Chen, Yanbin Fu, Xue Xiao, Haipeng Xu, Peijian Tong, Li Zhou
Software Mentions: 8
Published: about 3 years ago
10.1080/19490976.2021.1966263
Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen <i>Citrobacter rodentium</i>Cited by: 28
Author(s): Mareike Neumann, Alex Steimle, Erica T. Grant, Mathis Wolter, Amy Parrish, Stéphanie Willième, Dirk Brenner, Eric C. Martens, Mahesh S. Desai
Software Mentions: 8
Published: almost 4 years ago
10.1093/gigascience/giab062
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental designCited by: 16
Author(s): Lukas M. Weber, Ariel A. Hippen, Peter Hickey, Kristofer C. Berrett, Jason Gertz, Jennifer A. Doherty, Casey S. Greene, Stephanie C. Hicks
Software Mentions: 8
Published: about 3 years ago
10.18632/oncotarget.13467
Effects of <i>Abies sibirica</i> terpenes on cancer- and aging-associated pathways in human cellsCited by: 9
Author(s): Anna V. Kudryavtseva, George S. Krasnov, Anastasiya V. Lipatova, B. Ya. Alekseev, Faniya Maganova, Mikhail Shaposhnikov, Maria S. Fedorova, Anastasiya V. Snezhkina, Alexey Moskalev
Software Mentions: 8
Published: about 8 years ago
10.18632/oncotarget.14443
Investigating the utility of human melanoma cell lines as tumour modelsCited by: 48
Author(s): Krista Vincent, Lynne-Marie Postovit
Software Mentions: 8
Published: almost 8 years ago
10.18632/oncotarget.6793
Annexin A1 sustains tumor metabolism and cellular proliferation upon stable loss of HIF1ACited by: 12
Author(s): Nadine Rohwer, Fabian Bindel, Christina Grimm, Suling J. Lin, Jessica Wappler, Bertram Klinger, Nils Blüthgen, Ilona Du Bois, Bernd Schmeck, Hans Lehrach, Marjo de Graauw, Emanuel Gonçalvès, Julio Sáez-Rodríguez, Patrick Tan, Heike Grabsch, Alessandro Prigione, Stefan Kempa, Thorsten Cramer
Software Mentions: 8
Published: almost 9 years ago
10.1371/journal.pone.0231526
Disentangling the influence of ecological and historical factors on seed germination and seedling types in a Neotropical dry forestCited by: 5
Author(s): Jorge Cortés‐Flores, Guadalupe Cornejo‐Tenorio, María Esther Sánchez‐Coronado, Alma Orozco‐Segovia, Guillermo Ibarra‐Manríquez
Software Mentions: 8
Published: over 4 years ago
10.1523/ENEURO.0339-19.2020
Function, Innervation, and Neurotransmitter Signaling in Mice Lacking Type-II Taste CellsCited by: 16
Author(s): Eric D. Larson, Aurélie Vandenbeuch, Catherine B. Anderson, Sue C. Kinnamon
Software Mentions: 8
Published: almost 5 years ago
10.1186/s12859-020-3389-x
ushr: Understanding suppression of HIV in RCited by: 3
Author(s): Sinead E. Morris, Luise Dziobek-Garrett, Andrew J. Yates
Software Mentions: 8
Published: almost 5 years ago
10.1155/2021/7488188
m6A-Related lncRNA to Develop Prognostic Signature and Predict the Immune Landscape in Bladder CancerCited by: 28
Author(s): Zuwei Li, Yuwu Li, Weizhang Zhong, Peiyuan Huang
Software Mentions: 8
Published: over 3 years ago
10.3389/fgene.2020.568223
Taxonomic Novelty and Distinctive Genomic Features of Hot Spring CyanobacteriaCited by: 32
Author(s): Jaime Alcorta, Tomás Alarcón-Schumacher, Óscar Rivero Salgado, Beatriz Dı́ez
Software Mentions: 8
Published: about 4 years ago
10.12688/f1000research.18002.1
Epidemic curves made easy using the R package incidenceCited by: 38
Author(s): Zhian N. Kamvar, Jun Cai, Juliet R. C. Pulliam, Jakob Schumacher, Thibaut Jombart
Software Mentions: 8
Published: almost 6 years ago
10.12688/f1000research.2-192.v2
Cyrface: An interface from Cytoscape to R that provides a user interface to R packagesCited by: 3
Author(s): Emanuel Gonçalvès, Franz Mirlach, Julio Sáez-Rodríguez
Software Mentions: 8
Published: over 10 years ago
10.12688/f1000research.13541.1
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systemsCited by: 20
Author(s): Benjamin Delory, Li Mao, Christopher N. Topp, Guillaume Lobet
Software Mentions: 8
Published: almost 7 years ago
10.1128/mSphere.00916-19
Dual and Triple Epithelial Coculture Model Systems with Donor-Derived Microbiota and THP-1 Macrophages To Mimic Host-Microbe Interactions in the Human Sinonasal CavitiesCited by: 15
Author(s): Charlotte De Rudder, Marta Calatayud, Sarah Lebeer, Tom Van de Wiele
Software Mentions: 8
Published: almost 5 years ago
10.1523/ENEURO.0426-17.2018
Circadian and Brain State Modulation of Network Hyperexcitability in Alzheimer’s DiseaseCited by: 31
Author(s): Rosalind Brown, Alice Lam, Alfredo Gonzalez-Sulser, Andrew Ying, Mary Jones, Robert Chang-Chih Chou, Makis Tzioras, Crispin Y. Jordan, Izabela Jedrasiak‐Cape, Anne-Laure Hemonnot-Girard, Maurice Abou Jaoude, Andrew J. Cole, Sydney S. Cash, Takashi Saito, Takaomi C. Saido, Richard R. Ribchester, K. Hashemi, Iris Oren
Software Mentions: 8
Published: over 6 years ago
10.1155/2021/8892479
PDZ Binding Kinase/T-LAK Cell-Derived Protein Kinase Plays an Oncogenic Role and Promotes Immune Escape in Human TumorsCited by: 4
Author(s): Tingting Feng, Yan Zhang, Sunbin Ling, Chenyang Xu, Yingqi Lyu, Tingting Lu, Xinyuan Liu, Ying Liu, Yiming Wan, Zhong Huang, Dan Su
Software Mentions: 8
Published: about 3 years ago
10.1093/gigascience/giz004
The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approachesCited by: 103
Author(s): Darshan B. Dhakan, Abhijit Maji, Ashok Sharma, Rituja Saxena, Joby Pulikkan, Tony Grace, Andrés Gómez, Joy Scaria, Katherine R. Amato, Vineet K. Sharma
Software Mentions: 8
Published: almost 6 years ago
10.1186/s12974-020-01931-0
Effects of long-term and brain-wide colonization of peripheral bone marrow-derived myeloid cells in the CNSCited by: 28
Author(s): Lindsay A. Hohsfield, Allison R. Najafi, Yasamine Ghorbanian, Neelakshi Soni, Edna E. Hingco, Sung Jin Kim, Ayer Darling Jue, Vivek Swarup, Mathew A. Inlay, Kim N. Green
Software Mentions: 8
Published: about 4 years ago
10.1186/s12859-021-04130-7
Correlation AnalyzeR: functional predictions from gene co-expression correlationsCited by: 35
Author(s): Henry E. Miller, Alexander J.R. Bishop
Software Mentions: 8
Published: over 3 years ago
10.1093/gigascience/giz092
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillanceCited by: 112
Author(s): Alexander M. Piper, Jana Batovska, Noel O. I. Cogan, John Weiss, John Paul Cunningham, Brendan Rodoni, Mark J. Blacket
Software Mentions: 8
Published: over 5 years ago
10.1186/s12864-020-06971-7
Comparative genomic analysis of Flavobacteriaceae: insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesisCited by: 44
Author(s): Asimenia Gavriilidou, Johanna Gutleben, Dennis Versluis, Francesca Forgiarini, Mark W. J. van Passel, Colin J. Ingham, Hauke Smidt, Detmer Sipkema
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pone.0253847
TeamTree analysis: A new approach to evaluate scientific productionCited by: 2
Author(s): Frank W. Pfrieger
Software Mentions: 8
Published: over 3 years ago
10.1186/s42523-021-00111-6
Characterization of the gut microbiome in wild rocky mountainsnails (Oreohelix strigosa)Cited by: 2
Author(s): Bridget Chalifour, Jingchun Li
Software Mentions: 8
Published: over 3 years ago
10.1186/s12889-021-10979-3
Associations of meeting 24-h movement guidelines with stress and self-rated health among adults: is meeting more guidelines associated with greater benefits?Cited by: 16
Author(s): Kaja Kastelic, Željko Pedišić, Dean Lipovac, Nika Kastelic, Sitong Chen, Nejc Šarabon
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.ppat.1009933
Trypanosoma brucei triggers a broad immune response in the adipose tissueCited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: about 3 years ago
10.1186/s12889-018-5235-x
The fundamental association between mental health and life satisfaction: results from successive waves of a Canadian national surveyCited by: 121
Author(s): Patrick Lombardo, Wayne Jones, Liangliang Wang, Xin Shen, Elliot M. Goldner
Software Mentions: 8
Published: over 6 years ago
10.1002/evl3.110
Comparative genomics of 10 new<i>Caenorhabditis</i>speciesCited by: 105
Author(s): Lewis Stevens, Marie‐Anne Félix, Toni Beltran, Christian Braendle, Carlos Caurcel, Sarah Fausett, David Fitch, Lise Frézal, Charlie Gosse, Taniya Kaur, Karin Kiontke, Matthew D. Newton, Luke M. Noble, Aurélien Richaud, Matthew V. Rockman, Walter Sudhaus, Mark Blaxter
Software Mentions: 8
Published: over 5 years ago
10.1016/j.gpb.2019.09.007
Antidiabetic Effects of Gegen Qinlian Decoction via the Gut Microbiota Are Attributable to Its Key Ingredient BerberineCited by: 59
Author(s): Xizhan Xu, Zezheng Gao, Fuchao Yang, Yingying Yang, Liang Chen, Han Chieh Lin, Na Zhao, Jiayue Xu, Xinmiao Wang, Yue Ma, Lian Shu, Xueyou Hu, Na Lyu, Yuanlong Pan, Baoli Zhu, Linhua Zhao, Xiaolin Tong, Jun Wang
Software Mentions: 8
Published: almost 4 years ago
10.3390/v11060492
Culex torrentium: A Potent Vector for the Transmission of West Nile Virus in Central EuropeCited by: 33
Author(s): Stéphanie Jansen, Anna Heitmann, Renke Lühken, Mayke Leggewie, Michelle Helms, Marlis Badusche, Giada Rossini, Jonas Schmidt‐Chanasit, Egbert Tannich
Software Mentions: 8
Published: over 5 years ago
10.1186/s13073-020-00799-2
Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activitiesCited by: 20
Author(s): Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg, Olli Lohi, Merja Heinäniemi
Software Mentions: 8
Published: about 4 years ago
10.7554/eLife.65228
Egr2 induction in spiny projection neurons of the ventrolateral striatum contributes to cocaine place preference in miceCited by: 8
Author(s): Diptendu Mukherjee, Ben J. Gonzales, Reut Ashwal-Fluss, Hagit Turm, Maya Groysman, Ami Citri
Software Mentions: 8
Published: over 3 years ago
10.7554/eLife.69937
CLAMP and Zelda function together to promote Drosophila zygotic genome activationCited by: 33
Author(s): Jianan Duan, Leila E. Rieder, Megan M Colonnetta, Annie Huang, Mary Mckenney, Scott Watters, Girish Deshpande, William T. Jordan, Nicolas L. Fawzi, Erica Larschan
Software Mentions: 8
Published: over 3 years ago
10.1371/journal.pone.0231875
Soil fungal communities differ between shaded and sun-intensive coffee plantations in El SalvadorCited by: 10
Author(s): M. V. Rao, Robert A. Rice, Robert C. Fleischer, Carly R. Muletz‐Wolz
Software Mentions: 8
Published: over 4 years ago
10.1111/eva.12761
Pervasive admixture between eucalypt species has consequences for conservation and assisted migrationCited by: 15
Author(s): Brenton von Takach, Cameron Jack, Justin O. Borevitz, David B. Lindenmayer, Sam C. Banks
Software Mentions: 8
Published: almost 6 years ago
10.7554/eLife.60122
Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onsetCited by: 68
Author(s): Benny Borremans, Amandine Gamble, Katherine C. Prager, Sarah K Helman, Abby M. McClain, Caitlin Cox, Van Savage, James O. Lloyd‐Smith
Software Mentions: 8
Published: about 4 years ago
10.1186/s13073-019-0615-0
Single-cell analysis reveals congruence between kidney organoids and human fetal kidneyCited by: 144
Author(s): Alexander N. Combes, Luke Zappia, Pei X. Er, Alicia Oshlack, Melissa H. Little
Software Mentions: 8
Published: almost 6 years ago
10.7554/eLife.59442
Collagen-rich omentum is a premetastatic niche for integrin α2-mediated peritoneal metastasisCited by: 33
Author(s): Yen‐Lin Huang, Ching-Yeu Liang, Danilo Ritz, Ruimário Inácio Coelho, Dedy Septiadi, Manuela Estermann, Cécile Cumin, Natalie Rimmer, Andreas Schötzau, Mónica Núñez López, André Fedier, Martina Konantz, Tatjana Vlajnic, Diego Calabrese, Claudia Lengerke, Leonor David, Barbara Rothen‐Rutishauser, Francis Jacob, Viola Heinzelmann‐Schwarz
Software Mentions: 8
Published: about 4 years ago
10.1038/s41380-020-0844-z
Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoidsCited by: 66
Author(s): Tomoyo Sawada, Thomas E. Chater, Yohei Sasagawa, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J.M. Benjamin, Apuã C.M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Takeshi Kato
Software Mentions: 8
Published: over 4 years ago
10.18632/aging.202515
Cell differentiation trajectory predicts patient potential immunotherapy response and prognosis in gastric cancerCited by: 18
Author(s): Renshen Xiang, Yuping Rong, Yuhang Ge, Wei Song, Jun Ren, Tao Fu
Software Mentions: 8
Published: almost 4 years ago
10.1186/s13059-020-02195-w
Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiomeCited by: 107
Author(s): Alon Shaiber, Amy Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch, A. Murat Eren
Software Mentions: 8
Published: almost 4 years ago
10.1186/s13059-020-01998-1
Wheat chromatin architecture is organized in genome territories and transcription factoriesCited by: 89
Author(s): Lorenzo Concia, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Azahara Martin-Ramirez, Ying Huang, Magali Perez, Séverine Domenichini, Natalia Y. Rodriguez Granados, Soon-Kap Kim, Thomas Blein, Susan Duncan, Clement Pichot, Deborah Manza‐Mianza, Caroline Juéry, Etienne Paux, Graham Moore, Heribert Hirt, Catherine Bergounioux, Martín Crespi, Magdy M. Mahfouz, Abdelhafid Bendahmane, Chang Liu, Anthony Hall, Cécile Raynaud, David Latrasse, Moussa Benhamed
Software Mentions: 8
Published: over 4 years ago
10.1128/AEM.02601-17
Assessing Performance of Spore Samplers in Monitoring Aeromycobiota and Fungal Plant Pathogen Diversity in CanadaCited by: 23
Author(s): Wen Chen, Sarah Hambleton, Keith A. Seifert, Odile Carisse, Moussa S. Diarra, R. D. Peters, Christine Lowe, Julie T. Chapados, C. André Lévesque
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0247476
Small area estimation and childhood obesity surveillance using electronic health recordsCited by: 5
Author(s): Ying‐Qi Zhao, Derek Norton, Larry Hanrahan
Software Mentions: 8
Published: almost 4 years ago
10.1038/s42003-020-01156-0
Artificial eyespots on cattle reduce predation by large carnivoresCited by: 12
Author(s): Cameron Radford, J. Weldon McNutt, Tracey L. Rogers, Ben Maslen, Neil R. Jordan
Software Mentions: 8
Published: over 4 years ago
10.1186/s13059-021-02260-y
LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regionsCited by: 31
Author(s): Maša Roller, Ericca L. Stamper, Diego Villar, Osagie Izuogu, Fergal J. Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: almost 4 years ago
10.5696/2156-9614-10.27.200912
Levels of PM10 and PM2.5 and Respiratory Health Impacts on School-Going Children in KenyaCited by: 8
Author(s): Faridah Hussein Were, Godfrey A. Wafula, Cromwel B Lukorito, Timothy Kamanu
Software Mentions: 8
Published: about 4 years ago
10.1186/s12870-019-2182-3
A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preferenceCited by: 9
Author(s): Enrique Ostria‐Gallardo, Giovanni Larama, Graciela Berríos, Ana Fallard, Ana Gutiérrez-Moraga, Ingo Ensminger, León A. Bravo
Software Mentions: 8
Published: almost 5 years ago
10.1186/s13059-018-1567-1
Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disordersCited by: 119
Author(s): Heath O’Brien, Eilís Hannon, Matthew Hill, Carolina Toste, Matthew J. Robertson, Joanne Morgan, Gemma M. McLaughlin, Cathryn M. Lewis, Leonard C Schalkwyk, Lynsey S. Hall, Antonio F. Pardiñas, Michael John Owen, Michael O’Donovan, Jonathan Mill, Nicholas John Bray
Software Mentions: 8
Published: about 6 years ago
10.7150/ijms.47073
A Novel Nomogram Predicting Distant Metastasis in T1 and T2 Gallbladder Cancer: A SEER-based StudyCited by: 10
Author(s): Yulong Cai, Yixin Lin, Lingjun Jiang, Hui Ye, Fuyu Li, Nan‐Sheng Cheng
Software Mentions: 8
Published: almost 5 years ago
10.1186/s13059-018-1435-z
RNA m6A methylation participates in regulation of postnatal development of the mouse cerebellumCited by: 152
Author(s): Chunhui Ma, Mengqi Chang, Hongyi Lv, Zhiwei Zhang, Weilong Zhang, Xue He, Gaolang Wu, Shuaiyang Zhao, Yao Zhang, Di Wang, Xufei Teng, Chunying Liu, Qing Li, Arne Klungland, Yamei Niu, Shuhui Song, Wei‐Min Tong
Software Mentions: 8
Published: over 6 years ago
10.1186/s13058-019-1123-2
Separation of breast cancer and organ microenvironment transcriptomes in metastasesCited by: 33
Author(s): Mohammad A. Alzubi, Tia H. Turner, Amy L. Olex, Sahib S. Sohal, Nicholas P. Tobin, Susana Garcia Recio, Jonas Bergh, Thomas Hatschek, Joel S. Parker, Carol A. Sartorius, Charles M. Perou, Mikhail G. Dozmorov, J. Chuck Harrell
Software Mentions: 8
Published: over 5 years ago
10.1186/s12864-021-07918-2
CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysisCited by: 10
Author(s): Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson A. Silva
Software Mentions: 8
Published: over 3 years ago
10.1186/s12864-020-6703-0
Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical predictionCited by: 26
Author(s): Xubo Qian, Yong‐Xin Liu, Xiaohong Ye, Wen Jie Zheng, Shaoxia Lv, Miaojun Mo, Jinjing Lin, Wen-Qin Wang, Weihan Wang, Xianning Zhang, Meiping Lu
Software Mentions: 8
Published: over 4 years ago
10.7717/peerj.7816
CELSR3 mRNA expression is increased in hepatocellular carcinoma and indicates poor prognosisCited by: 11
Author(s): Xuefeng Gu, Hongbo Li, Ling Sha, Man Yuan, Chao Shi, Wei Zhao
Software Mentions: 8
Published: about 5 years ago
10.7150/ijms.51064
Tumor Mutation Burden, Immune Cell Infiltration, and Construction of Immune-Related Genes Prognostic Model in Head and Neck CancerCited by: 32
Author(s): Aimin Jiang, Mengdi Ren, Na Liu, Huan Gao, Jingjing Wang, Xiaoqiang Zheng, Xiao Fu, Xuan Liu, Zhiping Ruan, Tao Tian, Yu Yao
Software Mentions: 8
Published: almost 4 years ago
10.1038/s41598-018-24733-0
Insular threat associations within taxa worldwideCited by: 39
Author(s): Camille Leclerc, Franck Courchamp, Céline Bellard
Software Mentions: 8
Published: over 6 years ago
10.1371/journal.pone.0199841
Spatially explicit action research for coastal fisheries managementCited by: 7
Author(s): Tara N. Lawrence, R. S. Bhalla
Software Mentions: 8
Published: over 6 years ago
10.1093/aobpla/plaa019
Genetic variation in early fitness traits across European populations of silver birch (Betula pendula)Cited by: 7
Author(s): Aida Solé-Medina, Katrin Heer, Lars Opgenoorth, Phillip Kaldewey, Darius Danusevičius, Eduardo Notivol, Juan J. Robledo‐Arnuncio, José Alberto Ramírez‐Valiente
Software Mentions: 8
Published: over 4 years ago
10.1186/s12864-020-6534-z
Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoniCited by: 17
Author(s): Lijun Lu, Eric S. Loker, Si-Ming Zhang, Sarah Kay Buddenborg, Lijing Bu
Software Mentions: 8
Published: over 4 years ago
10.3390/antiox10060864
Blood Plasma Quality Control by Plasma Glutathione StatusCited by: 2
Author(s): Tamara Tomin, Natalie Bordag, Elmar Zügner, A Al-Baghdadi, Maximilian Schinagl, Ruth Birner‐Gruenberger, Matthias Schittmayer
Software Mentions: 8
Published: over 3 years ago
10.1186/s13059-019-1641-3
dStruct: identifying differentially reactive regions from RNA structurome profiling dataCited by: 20
Author(s): Krishna Choudhary, Yi-Chun Lai, Elizabeth Tran, Sharon Aviran
Software Mentions: 8
Published: almost 6 years ago
10.1371/journal.pone.0143666
Pathogenesis of Primary Foot-and-Mouth Disease Virus Infection in the Nasopharynx of Vaccinated and Non-Vaccinated CattleCited by: 44
Author(s): Carolina Stenfeldt, Michael Eschbaumer, Juan M. Pacheco, Steven I. Rekant, Luis L. Rodrı́guez, Jonathan Arzt
Software Mentions: 8
Published: about 9 years ago
10.1093/ije/dyz208
Association between ambient and household air pollution with carotid intima-media thickness in peri-urban South India: CHAI-ProjectCited by: 16
Author(s): Otávio T. Ranzani, Carles Milà, Margaux Sanchez, Santhi Bhogadi, Bharati Kulkarni, Kalpana Balakrishnan, Sankar Sambandam, Jordi Sunyer, Julian Marshall, Sanjay Kinra, Cathryn Tonne
Software Mentions: 8
Published: about 5 years ago
10.7554/eLife.58331
An essential role for MEF2C in the cortical response to loss of sleep in miceCited by: 19
Author(s): Theresa E. Bjorness, Ashwinikumar Kulkarni, Volodymyr Rybalchenko, Ayako Suzuki, Catherine Bridges, Adam J. Harrington, Christopher W. Cowan, Joseph S. Takahashi, Genevieve Konopka, Robert Greene
Software Mentions: 8
Published: over 4 years ago
10.1002/dad2.12066
Semantic loss marks early Alzheimer's disease‐related neurodegeneration in older adults without dementiaCited by: 20
Author(s): Jet M.J. Vonk, Vincent Bouteloup, Jean‐François Mangin, Bruno Dubois, Frederic Blanc, Audrey Gabelle, Mathieu Ceccaldi, Cédric Annweiler, Pierre Krolak‐Salmon, Cathérine Belin, Thérèse Rivasseau‐Jonveaux, Adrien Julian, François Sellal, Éloi Magnin, Marie Chupin, Marie‐Odile Habert, Geneviève Chêne, Carole Dufouil
Software Mentions: 8
Published: almost 5 years ago
10.1098/rspb.2017.0905
The evolution of dual meat and milk cattle husbandry in Linearbandkeramik societiesCited by: 43
Author(s): Rosalind Gillis, Lenka Kovačíková, Stéphanie Bréhard, Émilie Guthmann, Ivana Vostrovská, Hana Nohálová, Rose‐Marie Arbogast, László Domboróczki, Joachim Pechtl, Alexander Anders, Arkadiusz Marciniak, Anne Tresset, Jean‐Denis Vigne
Software Mentions: 8
Published: over 7 years ago
10.1371/journal.pntd.0007305
A community-based knowledge, attitude, and practice survey on rabies among cattle owners in selected areas of BhutanCited by: 26
Author(s): Sangay Rinchen, Tenzin Tenzin, David C. Hall, Frank van der Meer, Basant Sharma, Kinzang Dukpa, Susan C. Cork
Software Mentions: 8
Published: over 5 years ago
10.3390/diagnostics11061079
Identification of Diagnostic Biomarkers and Their Correlation with Immune Infiltration in Age-Related Macular DegenerationCited by: 3
Author(s): Yuyang Zeng, Xiujuan Yin, Changzheng Chen, Yiqiao Xing
Software Mentions: 8
Published: over 3 years ago
10.1128/mSystems.00122-17
Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic DevelopmentCited by: 27
Author(s): Keaton Stagaman, Tara J Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan
Software Mentions: 8
Published: almost 7 years ago
10.1371/journal.pone.0211196
Myopia is associated with education: Results from NHANES 1999-2008Cited by: 31
Author(s): Stefan Nickels, Susanne Hopf, Norbert Pfeiffer, Alexander K. Schuster
Software Mentions: 8
Published: almost 6 years ago
10.7717/peerj.2436
RBioplot: an easy-to-use R pipeline for automated statistical analysis and data visualization in molecular biology and biochemistryCited by: 65
Author(s): Jing Zhang, Kenneth B. Storey
Software Mentions: 8
Published: about 8 years ago
10.3389/fphys.2021.660906
Genome-Wide DNA Methylation Changes Associated With High-Altitude Acclimatization During an Everest Base Camp TrekCited by: 6
Author(s): Ainash Childebayeva, Taylor Harman, Julien Weinstein, Trevor A. Day, Tom D. Brutsaert, Abigail W. Bigham
Software Mentions: 8
Published: over 3 years ago
10.3390/microorganisms8091265
Modulation of Gut Microbiota in Korean Navy Trainees following a Healthy Lifestyle ChangeCited by: 10
Author(s): Young Hun Jung, Setu Bazie Tagele, HyunWoo Son, Jerald Conrad Ibal, Dorsaf Kerfahi, Hyunju Yun, Bora Lee, Clara Yongjoo Park, Eun Soo Kim, Sang-Jun Kim, Jae‐Ho Shin
Software Mentions: 8
Published: over 4 years ago
10.3389/fmicb.2018.00570
SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP ExperimentsCited by: 37
Author(s): Nicholas D. Youngblut, Samuel E. Barnett, Daniel H. Buckley
Software Mentions: 8
Published: over 6 years ago
10.3389/fmicb.2021.627437
A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial SystemsCited by: 4
Author(s): Gilda Varliero, Alexandre M. Anesio, Gary Barker
Software Mentions: 8
Published: about 3 years ago
10.18632/aging.102513
Daily decrease of post-operative alpha-fetoprotein by 9% discriminates prognosis of HCC: A multicenter retrospective studyCited by: 6
Author(s): Pei‐Yun Zhou, Chao‐Ping Yang, Zheng Tang, Yong Yi, Wei‐Ren Liu, Min Tian, Huang Ji, Wei Gan, Xi‐Fei Jiang, Liu Gao, Han Wang, Chenyang Tao, Yuan Fang, Wei‐Feng Qu, Cheng Zhou, Ruijuan Guan, Bao-Ye Sun, Yu‐Fu Zhou, Shushu Song, Zhen‐Bin Ding, Yuan‐Fei Peng, Zhi Dai, Jian Zhou, Jia Fan, Guozhong Gong, Ying‐Hong Shi, Shuang–Jian Qiu
Software Mentions: 8
Published: almost 5 years ago
10.1186/s40168-017-0235-0
Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogensCited by: 30
Author(s): Jessica Chopyk, Suhana Chattopadhyay, Prachi Kulkarni, Emma Claye, Kelsey R. Babik, Molly C. Reid, Eoghan M. Smyth, Lauren E. Hittle, Joseph N. Paulson, Raul Cruz‐Cano, Mihai Pop, Stephanie Buehler, Pamela I. Clark, Amy R. Sapkota, Emmanuel F. Mongodin
Software Mentions: 8
Published: almost 8 years ago
10.1186/s12863-020-00936-1
Separating two tightly linked species-defining phenotypes in Bactrocera with hybrid recombinant analysisCited by: 7
Author(s): Heng Lin Yeap, Siu Fai Lee, Freya Robinson, Roslyn Mourant, J. A. Sved, Michael Frommer, Alexie Papanicolaou, Owain Edwards, John G. Oakeshott
Software Mentions: 8
Published: almost 4 years ago