cran: gplots | Projects | Ecosyste.ms: Papers

10.1128/mSystems.00024-17

Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence-Inducing Conditions
Cited by: 11
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
Software Mentions: 4
Published: about 7 years ago

10.1186/s13046-019-1254-4

Long noncoding RNA MYOSLID promotes invasion and metastasis by modulating the partial epithelial-mesenchymal transition program in head and neck squamous cell carcinoma
Cited by: 74
Author(s): Hong‐Gang Xiong, Hao Li, Yao Xiao, Qi‐Chao Yang, Leilei Yang, Lei Chen, Lin‐Lin Bu, Wenfeng Zhang, Jiali Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: over 5 years ago

10.1128/mBio.03348-19

An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Salmonella Infection
Cited by: 21
Author(s): Leon N. Schulte, Matthias Schweinlin, Alexander J. Westermann, Harshavardhan Janga, Sara Correia Santos, Silke Appenzeller, Heike Walles, Jörg Vogel, Marco Metzger
Software Mentions: 4
Published: over 4 years ago

10.1186/s13568-019-0747-z

Dietary supplementation with fermented Mao-tai lees beneficially affects gut microbiota structure and function in pigs
Cited by: 18
Author(s): Huan Li, Huawei Li, Peifeng Xie, Zhihua Li, Yulong Yin, François Blachier, Xiangfeng Kong
Software Mentions: 4
Published: almost 6 years ago

10.1128/mBio.02391-19

Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi
Cited by: 25
Author(s): William C. Beckerson, Ricardo C. Rodrı́guez de la Vega, Fanny E. Hartmann, Marine Duhamel, Tatiana Giraud, Michael H. Perlin
Software Mentions: 4
Published: almost 5 years ago

10.1128/mBio.02259-20

Gene Dispensability in Escherichia coli Grown in Thirty Different Carbon Environments
Cited by: 18
Author(s): Madeline Tong, Shawn French, Sara S. El Zahed, Wai Kit Ong, Peter D. Karp, Eric D. Brown
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pntd.0009062

Exploring the influence of different habitats and their volatile chemistry in modulating sand fly population structure in a leishmaniasis endemic foci, Kenya
Cited by: 2
Author(s): Iman B. Hassaballa, Baldwyn Torto, Catherine L. Sole, David P. Tchouassi
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmicb.2018.00945

Lactation Stage-Dependency of the Sow Milk Microbiota
Cited by: 47
Author(s): Wei Chen, Jiandui Mi, Ning Lv, Jin‐Ming Gao, Jun Cheng, Ruizhu Wu, Jingyun Ma, Tian Lan, Xindi Liao
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1007133

Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival
Cited by: 38
Author(s): Arie Zackay, James A. Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L. Jaffe
Software Mentions: 4
Published: almost 7 years ago

10.1093/treephys/tpaa130

Photoperiod-dependent transcriptional modifications in key metabolic pathways in Coffea arabica
Cited by: 3
Author(s): Doâa Djerrab, Benoît Bertrand, Jean‐Christophe Breitler, Sophie Léran, Eveline Déchamp, Claudine Campa, Célia Barrachina, Geneviève Conéjéro, Hervé Etienne, Ronan Sulpice
Software Mentions: 4
Published: about 4 years ago

10.1186/s12885-020-06774-9

Sepsis-associated pathways segregate cancer groups
Cited by: 5
Author(s): Himanshu Tripathi, Samanwoy Mukhopadhyay, Saroj Kant Mohapatra
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1002415

A Densely Interconnected Genome-Wide Network of MicroRNAs and Oncogenic Pathways Revealed Using Gene Expression Signatures
Cited by: 30
Author(s): Chia Huey Ooi, Hue Kian Oh, H Wang, Angie Lay Keng Tan, Jeanie Wu, Ming‐Hui Lee, Sun Young Rha, Hyun Cheol Chung, David M. Virshup, Patrick Tan
Software Mentions: 4
Published: almost 13 years ago

10.1038/s41598-021-90607-7

Defining the combined stress response in wild Arachis
Cited by: 12
Author(s): Ana Paula Zotta Mota, Ana Cristina Miranda Brasileiro, Bruna Vidigal, Thais Nicolini Oliveira, Andressa da Cunha Quintana Martins, Mario Alfredo de Passos Saraiva, Ana Cláudia Guerra Araújo, Roberto Coiti Togawa, Maria Fátima Grossi-de-Sá, P. M. Guimarães
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0047107

Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos
Cited by: 12
Author(s): Elisa A. Casanova, Michał Okoniewski, Paolo Cinelli
Software Mentions: 4
Published: about 12 years ago

10.1038/s41598-021-93097-9

Identification of natural product modulators of Merkel cell carcinoma cell growth and survival
Cited by: 2
Author(s): Emily A. Smith, Natasha T. Hill, Tara Gelb, Khalid A. Garman, Ekaterina I. Goncharova, Heidi R. Bokesch, Chang‐Kwon Kim, Karen L. Wendt, Robert H. Cichewicz, Kirk R. Gustafson, Isaac Brownell, Curtis J. Henrich
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-96576-1

Dissection of the genetic basis of genotype-by-environment interactions for grain yield and main agronomic traits in Iranian bread wheat landraces and cultivars
Cited by: 9
Author(s): Hadi Alipour, Hossein Abdi, Yousef Rahimi, Mohammad Reza Bihamta
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-021-87805-8

Integrin αvβ5 heterodimer is a specific marker of human pancreatic beta cells
Cited by: 4
Author(s): Jacqueline V. Schiesser, Thomas Loudovaris, Helen E. Thomas, Andrew G. Elefanty
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pgen.1004924

The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse
Cited by: 29
Author(s): Clement Y. Chow, Xiaozhu Wang, David D. Riccardi, Mariana F. Wolfner, Andrew G. Clark
Software Mentions: 4
Published: almost 10 years ago

10.1038/s41598-021-88743-1

Identification of candidate PAX2-regulated genes implicated in human kidney development
Cited by: 6
Author(s): Yuta Yamamura, Kengo Furuichi, Yuji Murakawa, Shigeki Hirabayashi, Masahito Yoshihara, Keisuke Sako, Shinji Kitajima, Tadashi Toyama, Yasunori Iwata, Norihiko Sakai, Kazuyoshi Hosomichi, Philip M. Murphy, Atsushi Tajima, Keisuke Okita, Kenji Osafune, Shuichi Kaneko, Takashi Wada
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-83886-7

Using protein turnover to expand the applications of transcriptomics
Cited by: 2
Author(s): Marissa A. Smail, James Reigle, Robert E. McCullumsmith
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1005211

Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model
Cited by: 12
Author(s): Ashley P Ng, Yifang Hu, Donald Metcalf, Craig D. Hyland, Helen Ierino, Belinda Phipson, Di Wu, Tracey M. Baldwin, Maria Kauppi, Hiu Kiu, Ladina Di Rago, Douglas J. Hilton, Gordon K. Smyth, Warren S. Alexander
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-021-84308-4

Elucidating the genetics of grain yield and stress-resilience in bread wheat using a large-scale genome-wide association mapping study with 55,568 lines
Cited by: 11
Author(s): Philomin Juliana, Ravi P. Singh, Jesse Poland, Sandesh Shrestha, Julio Huerta‐Espino, Velu Govindan, Suchismita Mondal, Leonardo Crespo‐Herrera, Uttam Kumar, Arun Kumar Joshi, Thomas Payne, Pradeep Kumar Bhati, Vipin Tomar, Franjel Consolacion, Jaime Amador Campos Serna
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-90250-2

Proteomic analysis-based discovery of a novel biomarker that differentiates intestinal Behçet’s disease from Crohn’s disease
Cited by: 4
Author(s): Jihye Park, Da-Eun Jeong, Youn Wook Chung, Seunghan Han, Da Hye Kim, Jongwook Yu, Jae Hee Cheon, Ji Hwan Ryu
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-97306-3

Differentially expressed genes in the femur cartilage transcriptome clarify the understanding of femoral head separation in chickens
Cited by: 3
Author(s): Ludmila Mudri Hul, A. M. G. Ibelli, Igor Ricardo Savoldi, Débora Ester Petry Marcelino, Lana Teixeira Fernandes, J. O. Peixoto, Maurício Egídio Cantão, R. H. Higa, P. F. Giachetto, Luiz Lehmann Coutinho, Mônica Corrêa Ledur
Software Mentions: 4
Published: about 3 years ago

10.3389/fmicb.2019.00635

Denitrifying Bacteria Active in Woodchip Bioreactors at Low-Temperature Conditions
Cited by: 31
Author(s): Jeonghwan Jang, Emily L. Anderson, Rodney T. Venterea, Michael J. Sadowsky, Carl J. Rosen, Gary W. Feyereisen, Satoshi Ishii
Software Mentions: 4
Published: over 5 years ago

10.1155/2020/3968279

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma
Cited by: 1
Author(s): Ana Carolina de Moraes Mello, Martiela Vaz de Freitas, Laura Coutinho, Tiago Falcón, Úrsula da Silveira Matte
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-79436-2

Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima
Cited by: 12
Author(s): David J. Quispe-Parra, Joshua G. Medina-Feliciano, Sebastián Cruz-González, Humberto Ortíz-Zuazaga, José E. García‐Arrarás
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-020-71888-w

Local management and landscape structure determine the assemblage patterns of spiders in vegetable fields
Cited by: 11
Author(s): Hafiz Sohaib Ahmed Saqib, Junhui Chen, Wei Chen, Gábor Pozsgai, Komivi Senyo Akutse, Muhammad Furqan Ashraf, Minsheng You, Geoff M. Gurr
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2019.02474

Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment
Cited by: 7
Author(s): Yufan Wu, Peng Xing, Shuang‐Jiang Liu, Qinglong L. Wu
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2014.00352

Phenotypic profiling of ABC transporter coding genes in Myxococcus xanthus
Cited by: 5
Author(s): Jinyuan Yan, Michael D. Bradley, Jannice Friedman, Roy D. Welch
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pcbi.1002753

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data
Cited by: 44
Author(s): Art F. Y. Poon, Luke C. Swenson, Evelien M. Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B. van 't Wout, P. Richard Harrigan
Software Mentions: 4
Published: about 12 years ago

10.1038/s41598-021-98423-9

Non-invasive diagnostic tool for Parkinson’s disease by sebum RNA profile with machine learning
Cited by: 11
Author(s): Yuya Uehara, Shinichi Ueno, Haruka Amano-Takeshige, Shuji Suzuki, Yoko Imamichi, Mitsuhisa Fujimaki, Noriyasu Ota, Takatoshi Murase, Tsukasa Inoue, Sachio Saiki, Nobutaka Hattori
Software Mentions: 4
Published: about 3 years ago

10.6026/97320630016567

Bacterial community dynamics with rhizosphere of Calotropis procera and Senna alexandrina desert plants in Saudi Arabia
Cited by: 4
Author(s): Diana A. Al-Quwaie
Software Mentions: 4
Published: about 4 years ago

10.6026/97320630013202

Serum and Plasma Metabolomic Biomarkers for Lung Cancer
Cited by: 42
Author(s): Nishith Kumar, Md. Shahjaman, Md. Nurul Haque Mollah, Shahidul Islam, Hongxia Ma
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2019.00473

Variability in the Composition of Pacific Oyster Microbiomes Across Oyster Families Exhibiting Different Levels of Susceptibility to OsHV-1 μvar Disease
Cited by: 44
Author(s): William L. King, Nachshon Siboni, Nathan L. R. Williams, Tim Kahlke, Khue Viet Nguyen, Cheryl Jenkins, Michael Dove, Wayne A. O’Connor, Justin R. Seymour, Maurizio Labbate
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-019-6043-0

Exploration of tissue-specific gene expression patterns underlying timing of breeding in contrasting temperature environments in a song bird
Cited by: 12
Author(s): Veronika N. Laine, Irene Verhagen, A. Christa Mateman, Agata Pijl, Tony Williams, Phillip Gienapp, Kees van Oers, Marcel E. Visser
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pbio.3000358

Global proteomic analyses define an environmentally contingent Hsp90 interactome and reveal chaperone-dependent regulation of stress granule proteins and the R2TP complex in a fungal pathogen
Cited by: 30
Author(s): Teresa R. O’Meara, Matthew J. O’Meara, Elizabeth J. Polvi, Mohammad Reza Pourhaghighi, Sean D. Liston, Zhen‐Yuan Lin, Amanda O. Veri, Andrew Emili, Anne‐Claude Gingras, Leah E. Cowen
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2021.657471

Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family Asfarviridae
Cited by: 15
Author(s): Sangita Karki, Mohammad Moniruzzaman, Frank O. Aylward
Software Mentions: 4
Published: over 3 years ago

10.3389/fmicb.2017.00340

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study
Cited by: 33
Author(s): Sébastien Boutin, Daniel Hagenfeld, Heiko Zimmermann, Nihad El Sayed, Tanja Höpker, Halina Greiser, Heiko Becher, Ti‐Sun Kim, Alexander H. Dalpke
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-68222-9

The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development
Cited by: 6
Author(s): Estefanía Garibay‐Valdez, Luis Rafael Martínez‐Córdova, Marco Antonio López‐Torres, F.J. Almendáriz-Tapia, Marcel Martínez‐Porchas, Kadiya Calderón
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2020.586614

Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural Fermentations
Cited by: 18
Author(s): Marine Penland, Stéphanie-Marie Deutsch, Hélène Falentin, Audrey Pawtowski, Elisabeth Poirier, Giorgia Visenti, Christophe Le Meur, Marie-Bernadette Maillard, Anne Thierry, Jérôme Mounier, Monika Coton
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2164-15-133

Virus-independent and common transcriptome responses of leafhopper vectors feeding on maize infected with semi-persistently and persistent propagatively transmitted viruses
Cited by: 33
Author(s): Bryan J. Cassone, Saranga Wijeratne, Andrew P. Michel, Lucy R. Stewart, Yuting Chen, Pearlly S. Yan, Margaret G. Redinbaugh
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2021.682989

Microbiome and Metabolomics Reveal the Effects of Different Feeding Systems on the Growth and Ruminal Development of Yaks
Cited by: 26
Author(s): Chun Hua Huang, Fei Ge, Xixi Yao, Xian Guo, Pengjia Bao, Xiaoming Ma, Xiaoyun Wu, Min Kyung Chu, Ping Yan, Chunnian Liang
Software Mentions: 4
Published: over 3 years ago

10.1186/s12917-018-1691-x

An intensive milk replacer feeding program benefits immune response and intestinal microbiota of lambs during weaning
Cited by: 17
Author(s): Qian Zhang, Chong Li, Xiaolin Niu, Zhian Zhang, Fadi Li, Fēi Li
Software Mentions: 4
Published: almost 6 years ago

10.1186/1752-0509-7-S5-S1

Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
Cited by: 68
Author(s): Akshata R. Udyavar, Megan D. Hoeksema, Jonathan E. Clark, Yong Zou, Zuojian Tang, Zhiguo Li, Ming Li, Heidi Chen, Alexander Statnikov, Yu Shyr, Daniel C. Liebler, John K. Field, Rosana Eisenberg, Lourdes Estrada, Pierre P. Massion, Vito Quaranta
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2018.01339

Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean
Cited by: 29
Author(s): Gustavo Henrique Recchia, Enéas Ricardo Konzen, Fernanda Cassieri, Danielle Gregório Gomes Caldas, Siu Mui Tsai
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2017.02099

Cyanobacteria and Alphaproteobacteria May Facilitate Cooperative Interactions in Niche Communities
Cited by: 32
Author(s): Marc W. Van Goethem, Thulani P. Makhalanyane, Don A. Cowan, Ángel Valverde
Software Mentions: 4
Published: about 7 years ago

10.3390/plants10040793

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum
Cited by: 4
Author(s): Mariano Soliman, Maricel Podio, G. Marconi, Marco Di Marsico, Juan Pablo Amelio Ortiz, Emidio Albertini, Luciana Delgado
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-020-59549-4

Similar genomic patterns of clinical infective endocarditis and oral isolates of Streptococcus sanguinis and Streptococcus gordonii
Cited by: 7
Author(s): Katrine Højholt Iversen, Louise Rasmussen, Kosai Al-Nakeeb, José Juan Almagro Armenteros, Christian Salgård Jensen, Rimtas Dargis, Oksana Lukjancenko, Ulrik Stenz Justesen, Claus Moser, Flemming Schønning Rosenvinge, Xiaohui Chen Nielsen, Jens Jørgen Christensen, Simon Rasmussen
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0252026

Differential association between inflammatory cytokines and multiorgan dysfunction in COVID-19 patients with obesity
Cited by: 8
Author(s): Marie-Agnès Dragon-Durey, Xiaoyi Chen, Amos Kirilovsky, Nadine Benhamouda, Carine El Sissy, Jules Russick, Etienne Charpentier, Yannick Binois, Florence Marliot, Maxime Meylan, Clémence Granier, Hélène Péré, Antonin Saldmann, Bastien Rance, Anne Sophie Jannot, Stéphanie Baron, M. Chebbi, Antoine Fayol, Nathalie Josseaume, Claire Rives‐Lange, Pierre‐Louis Tharaux, Bernard Cholley, Jean‐Luc Diehl, Jean‐Benoît Arlet, Michel Azizi, Alexandre Karras, Sébastien Czernichow, David Smadja, Jean‐Sébastien Hulot, Isabelle Cremer, Éric Tartour, Élie Mousseaux, Franck Pagès
Software Mentions: 4
Published: over 3 years ago

10.1186/s12893-020-01033-x

Prognostic factors in patients who underwent surgery for common peroneal nerve injury: a nest case–control study
Cited by: 2
Author(s): Zhenhui Liu, Maimaiaili Yushan, Yanshi Liu, Aihemaitijiang Yusufu
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-019-56051-4

Reduced central and peripheral inflammatory responses and increased mitochondrial activity contribute to diet-induced obesity resistance in WSB/EiJ mice
Cited by: 8
Author(s): Jérémy Terrien, Isabelle Seugnet, Bolaji Seffou, María Jesús Presentación Herrero, James Bowers, Lamis Chamas, Stéphanie Decherf, Evelyne Duvernois-Berthet, Chakib Djédiat, Bertrand Ducos, Barbara Demeneix, Marie-Stéphanie Clerget-Froidevaux
Software Mentions: 4
Published: almost 5 years ago

10.3389/fimmu.2021.701273

Immune Signature Linked to COVID-19 Severity: A SARS-Score for Personalized Medicine
Cited by: 5
Author(s): Jules Russick, Pierre-Emmanuel Foy, Nathalie Josseaume, Maxime Meylan, Nadine Benhamouda, Amos Kirilovsky, Carine El Sissy, Éric Tartour, David Smadja, Alexandre Karras, Jean‐Sébastien Hulot, Marine Livrozet, Antoine Fayol, Jean‐Benoît Arlet, Jean‐Luc Diehl, Marie-Agnès Dragon-Durey, Franck Pagès, Isabelle Cremer
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-019-51423-2

Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/adenine methylation changes
Cited by: 12
Author(s): G. Marconi, Stefano Capomaccio, Cinzia Comino, Alberto Acquadro, Ezio Portis, Andrea Porceddu, Emidio Albertini
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.00380

Diet and Genotype of an Aquatic Invertebrate Affect the Composition of Free-Living Microbial Communities
Cited by: 32
Author(s): Emilie Macke, Martijn Callens, François Massol, Isabel Vanoverberghe, Luc De Meester, Ellen Decaestecker
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-019-44991-w

Identification of a Radiosensitivity Molecular Signature Induced by Enzalutamide in Hormone-sensitive and Hormone-resistant Prostate Cancer Cells
Cited by: 15
Author(s): Maryam Ghashghaei, Tamim Niazi, Adriana Aguilar‐Mahecha, Kathleen Klein, Celia M.T. Greenwood, Mark Basik, Thierry Muanza
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-53023-6

Generation of a Comprehensive Transcriptome Atlas and Transcriptome Dynamics in Medicinal Cannabis
Cited by: 42
Author(s): Shivraj Braich, Rebecca C. Baillie, Larry S. Jewell, Germán Spangenberg, Noel O. I. Cogan
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-019-39733-x

HER2 and p95HER2 differentially regulate miRNA expression in MCF-7 breast cancer cells and downregulate MYB proteins through miR-221/222 and miR-503
Cited by: 15
Author(s): Andrej Gorbatenko, Rolf Søkilde, Ester E. Sørensen, Inga Newie, Helena Persson, Beatriz Morancho, Joaquı́n Arribas, Thomas Litman, Carlos Rovira, Stine Falsig Pedersen
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-40992-x

A comparison between the abdominal and femoral adipose tissue proteome of overweight and obese women
Cited by: 18
Author(s): Max Vogel, Ping Wang, Freek G. Bouwman, Nicole Hoebers, Ellen E. Blaak, Johan Renes, E.C.M. Mariman, Gijs H. Goossens
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-021-03058-7

Reduced free asparagine in wheat grain resulting from a natural deletion of TaASN-B2: investigating and exploiting diversity in the asparagine synthetase gene family to improve wheat quality
Cited by: 10
Author(s): Joseph Oddy, Rocío Alarcón‐Reverte, Mark Wilkinson, Karl Ravet, Sarah Raffan, Andrea Minter, Andrew Mead, J. Stephen Elmore, Isabel Moreira de Almeida, Nicholas C. Cryer, Nigel G. Halford, Stephen Pearce
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2015.00531

In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire
Cited by: 70
Author(s): Jacob D. Galson, Johannes Trück, Anna Fowler, Márton Münz, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter, Dominic F. Kelly
Software Mentions: 4
Published: about 9 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 3 years ago

10.3389/fimmu.2017.01351

Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16
Cited by: 11
Author(s): Xi Yang, Niamh M. Troy, Denise Anderson, Olga M. Pena, Jason P. Lynch, Simon Phipps, Anthony Bosco, John W. Upham
Software Mentions: 4
Published: about 7 years ago

10.1186/s12870-020-02392-6

Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses
Cited by: 37
Author(s): Colin Kruse, Alexander Meyers, Proma Basu, Sarahann Hutchinson, Darron R. Luesse, Sarah E. Wyatt
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2407-14-739

MicroRNA expression as risk biomarker of breast cancer metastasis: a pilot retrospective case-cohort study
Cited by: 42
Author(s): Augusto L F Marino, Adriane Feijó Evangelista, René Aloísio da Costa Vieira, Taciane Macedo, Lígia Maria Kerr, Lucas Faria Abrahão-Machado, Adhemar Longatto‐Filho, Henrique C. S. Silveira, Márcia Maria Chiquitelli Marques
Software Mentions: 4
Published: about 10 years ago

10.1186/1471-2164-15-1179

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis
Cited by: 34
Author(s): Kate J. Howell, Lucy A. Weinert, Roy R. Chaudhuri, Shi-Lu Luan, Sarah Peters, Jukka Corander, David Harris, Øystein Angen, Virginia Aragón, Albert Bensaid, Susanna Williamson, Julian Parkhill, Paul R. Langford, Andrew N. Rycroft, Brendan W. Wren, Matthew T. G. Holden, Alexander W. Tucker, Duncan J. Maskell
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-018-35974-4

Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity
Cited by: 29
Author(s): Trine B. Rounge, Sinan Uğur Umu, Andreas Keller, Eckart Meese, Giske Ursin, Steinar Tretli, Robert Lyle, Hilde Langseth
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-57546-1

Genomic Survey of Salt Acclimation-Related Genes in the Halophilic Cyanobacterium Euhalothece sp. Z-M001
Cited by: 14
Author(s): Hee Wook Yang, Ji-Young Song, Sung Mi Cho, Hak Cheol Kwon, Cheol‐Ho Pan, Youn‐Il Park
Software Mentions: 4
Published: almost 5 years ago

10.1002/pmic.201500264

Micro‐proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level
Cited by: 28
Author(s): Dalila Bensaddek, Vikram Narayan, Armel Nicolas, Alejandro Brenes Murillo, Anton Gartner, Cynthia Kenyon
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-018-5255-z

Phenotypic plasticity and the evolution of azole resistance in Aspergillus fumigatus; an expression profile of clinical isolates upon exposure to itraconazole
Cited by: 23
Author(s): Margriet W.J. Hokken, Jan Zoll, Jordy P. M. Coolen, Bas J. Zwaan, Paul E. Verweij, Willem J. G. Melchers
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12958-021-00818-w

Single-cell transcriptome and cell-specific network analysis reveal the reparative effect of neurotrophin-4 in preantral follicles grown in vitro
Cited by: 4
Author(s): Yingchun Guo, Peigen Chen, Tingting Li, Jia Lu, Yi Zhou, Jiana Huang, Xiaoyan Liang, Chuanchuan Zhou, Cong Fang
Software Mentions: 4
Published: about 3 years ago

10.7717/peerj.4970

Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam
Cited by: 22
Author(s): Ton That Huu Dat, Georg Steinert, Nguyễn Thị Kim Cúc, Hauke Smidt, Detmer Sipkema
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1009208

A multi-omics approach to Epstein-Barr virus immortalization of B-cells reveals EBNA1 chromatin pioneering activities targeting nucleotide metabolism
Cited by: 20
Author(s): Jason Lamontagne, Samantha S. Soldan, Chenhe Su, Andreas Wiedmer, Kyoung Jae Won, Fang Lü, Aaron R. Goldman, Jayamanna Wickramasinghe, Hsin‐Yao Tang, David W. Speicher, Louise C. Showe, Andrew V. Kossenkov, Paul M. Lieberman
Software Mentions: 4
Published: almost 4 years ago

10.1073/pnas.2003407117

Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae
Cited by: 76
Author(s): Sophia David, Victoria Cohen, Sandra Reuter, Anna E. Sheppard, Tommaso Giani, Julian Parkhill, Gian María Rossolini, Edward J. Feil, Hajo Grundmann, David M. Aanensen
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.ppat.1002949

Identification of FAM111A as an SV40 Host Range Restriction and Adenovirus Helper Factor
Cited by: 54
Author(s): Debrah A. Fine, Orit Rozenblatt-Rosen, Megha Padi, Anna Korkhin, Robert James, Guillaume Adelmant, Rosa Yoon, Lifei Guo, Christian Berrios, Ying Zhang, Michael A. Calderwood, Soundarapandian Velmurgan, Jingwei Cheng, Jarrod A. Marto, David E. Hill, Michael E. Cusick, Marc Vidal, Laurence Florens, Michael P. Washburn, Larisa Litovchick, James A. DeCaprio
Software Mentions: 4
Published: about 12 years ago

10.1371/journal.ppat.1006348

HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation
Cited by: 32
Author(s): Yoshiaki Nakano, Naoko Misawa, Guillermo Juarez-Fernandez, Miyu Moriwaki, Shinji Nakaoka, Takaaki Funo, Eri Yamada, Andrew Soper, Rokusuke Yoshikawa, Diako Ebrahimi, Yuuya Tachiki, Shingo Iwami, Reuben S. Harris, Yoshio Koyanagi, Kei Sato
Software Mentions: 4
Published: over 7 years ago

10.1016/j.dib.2016.05.007

Whole transcriptome data analysis of zebrafish mutants affecting muscle development
Cited by: 7
Author(s): Olivier Armant, Victor Gourain, Christelle Etard, Uwe Strähle
Software Mentions: 4
Published: about 8 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: over 3 years ago

10.1038/s41598-018-32448-5

The relationship between transgenerational acquired resistance and global DNA methylation in Arabidopsis
Cited by: 51
Author(s): Joost H. M. Stassen, Ana López, Ritushree Jain, David Pascual-Pardo, Estrella Luna, Lisa M. Smith, Jurriaan Ton
Software Mentions: 4
Published: about 6 years ago

10.1186/s40104-020-00459-w

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens
Cited by: 33
Author(s): Joel J. Maki, Elizabeth Bobeck, Matthew J. Sylte, Torey Looft
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0252452

Comprehensive analysis of lncRNA biomarkers in kidney renal clear cell carcinoma by lncRNA-mediated ceRNA network
Cited by: 4
Author(s): Ke Gong, Ting Xie, Yiliao Luo, Hui Guo, Jinlan Chen, Zhiping Tan, Yifeng Yang, Li Xie
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0066829

Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest
Cited by: 47
Author(s): Yu Wu, Tesfaye Wubet, Stefan Trogisch, Sabine Both, Thomas Scholten, Helge Bruelheide, François Buscot
Software Mentions: 4
Published: over 11 years ago

10.12688/wellcomeopenres.16320.2

Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data
Cited by: 2
Author(s): Carolyne Ndila, Vysaul Nyirongo, Alexander Macharia, Anna E. Jeffreys, Kate Rowlands, Christina Hubbart, George B.J. Busby, Gavin Band, Rosalind M. Harding, Kirk A. Rockett, Thomas N. Williams
Software Mentions: 4
Published: about 3 years ago

10.1186/s12870-019-2055-9

Metabolite profiling during graft union formation reveals the reprogramming of primary metabolism and the induction of stilbene synthesis at the graft interface in grapevine
Cited by: 25
Author(s): Duyên Prodhomme, Josep Valls, Cyril Hévin, Céline Franc, Ghislaine Hilbert, Gilles de Revel, Tristan Richard, Nathalie Ollat, Sarah Jane Cookson
Software Mentions: 4
Published: almost 5 years ago

10.1128/mBio.01280-18

Evolution of the U.S. Biological Select Agent Rathayibacter toxicus
Cited by: 8
Author(s): Edward W. Davis, Javier F. Tabima, Alexandra J. Weisberg, Lucas Dantas Lopes, Michele S. Wiseman, Michael S. Wiseman, Tal Pupko, Michael S. Belcher, A. Sechler, Matt A. Tancos, Brenda K. Schroeder, Timothy Murray, Douglas G. Luster, William L. Schneider, Elizabeth E. Rogers, Fernando Dini Andreote, Niklaus J. Grünwald, M. L. Putnam, Jeff H. Chang
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2017.02499

Comparative Metagenomics Reveals the Distinctive Adaptive Features of the Spongia officinalis Endosymbiotic Consortium
Cited by: 36
Author(s): Elham Karimi, Maria João Ramos, Jorge M. S. Gonçalves, Joana R. Xavier, Margarida Reis, Rodrigo Costa
Software Mentions: 4
Published: almost 7 years ago

10.3390/cancers12030632

Model-Based Integration Analysis Revealed Presence of Novel Prognostic miRNA Targets and Important Cancer Driver Genes in Triple-Negative Breast Cancers
Cited by: 6
Author(s): Masood Zaka, Chris W. Sutton, Yonghong Peng, Savas Konur
Software Mentions: 4
Published: over 4 years ago

10.1186/s13148-019-0804-0

Frameshift mutations at the C-terminus of HIST1H1E result in a specific DNA hypomethylation signature
Cited by: 36
Author(s): Andrea Ciolfi, Erfan Aref‐Eshghi, Simone Pizzi, Lucia Pedace, Evelina Miele, Jennifer Kerkhof, Elisabetta Flex, Simone Martinelli, Francesca Clementina Radio, Claudia Ruivenkamp, Gijs W.E. Santen, Emilia K. Bijlsma, Daniela Q.C.M. Barge-Schaapveld, Katrin Õunap, Victoria Mok Siu, R. Frank Kooy, Bruno Dallapiccola, Bekim Sadiković, Marco Tartaglia
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2229-14-169

RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
Cited by: 190
Author(s): Lei Wang, Chenlong Cao, Qibin Ma, Qiaoying Zeng, Haifeng Wang, Zhihao Cheng, Genfeng Zhu, Ji Qi, Hong Mā, Hai Nian, Yingxiang Wang
Software Mentions: 4
Published: almost 11 years ago

10.1002/cti2.1190

BDCA1 + cDC2s, BDCA2 + pDCs and BDCA3 + cDC1s reveal distinct pathophysiologic features and impact on clinical outcomes in melanoma patients
Cited by: 11
Author(s): Eleonora Sosa Cuevas, Laurissa Ouaguia, Stéphane Mouret, J. Charles, Florence de Fraipont, Olivier Manches, Jenny Valladeau‐Guilemond, Nathalie Bendriss‐Vermare, Laurence Chaperot, Caroline Aspord
Software Mentions: 4
Published: almost 5 years ago

10.3390/v13010009

Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus–Host Interaction Signatures
Cited by: 14
Author(s): Paula Luize Camargos Fonseca, Flávia V Ferreira, Felipe Silva, Liliane Santana Oliveira, João Trindade Marques, Aristóteles Goés-Neto, Eric Roberto Guimarães Rocha Aguiar, Arthur Gruber
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-34127-x

Bacterial and fungal gut communities of Agrilus mali at different developmental stages and fed different diets
Cited by: 26
Author(s): Zhengqing Zhang, Shuo Jiao, Xiaohui Li, LI Meng-lou
Software Mentions: 4
Published: about 6 years ago

10.1186/s12985-014-0236-6

Differential regulation of cytotoxicity pathway discriminating between HIV, HCV mono- and co-infection identified by transcriptome profiling of PBMCs
Cited by: 4
Author(s): Jing Qin Wu, Monica Miranda Saksena, Vincent Soriano, Eugenia Vispo, Nitin K. Saksena
Software Mentions: 3
Published: almost 10 years ago

10.1186/s13020-021-00436-z

Bioconversion variation of ginsenoside CK mediated by human gut microbiota from healthy volunteers and colorectal cancer patients
Cited by: 6
Author(s): Yinping Guo, Li Shao, Li Wang, Man‐Yun Chen, Wei Zhang, Weihua Huang
Software Mentions: 3
Published: over 3 years ago

10.3390/cells10030647

ACPA Status Correlates with Differential Immune Profile in Patients with Rheumatoid Arthritis
Cited by: 17
Author(s): Achilleas Floudas, Mary Canavan, Trudy McGarry, Ronan Mullan, Sunil Nagpal, Douglas J. Veale, Ursula Fearon
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-9-37

Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
Cited by: 38
Author(s): Rekin’s Janky, Jacques van Helden
Software Mentions: 3
Published: almost 17 years ago

10.1186/s40673-016-0042-6

Patterns of motor signs in spinocerebellar ataxia type 3 at the start of follow-up in a reference unit
Cited by: 6
Author(s): Irene Pulido-Valdeolivas, David Gómez‐Andrés, Irene Sanz-Gallego, Estrella Rausell, Javier Arpa
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2180-8-109

Dictyostelium transcriptional responses to Pseudomonas aeruginosa: common and specific effects from PAO1 and PA14 strains
Cited by: 40
Author(s): Sergio Carilla-Latorre, Javier Calvo‐Garrido, Gareth Bloomfield, Jason Skelton, Robert R. Kay, Alasdair Ivens, José Luis Martínez, Ricardo Escalante
Software Mentions: 3
Published: over 16 years ago

10.1002/iid3.246

Flow Plex —A tool for unbiased comprehensive flow cytometry data analysis
Cited by: 0
Author(s): Johannes Nowatzky, Ezra Resnick, Julia Manasson, Cristy Stagnar, Arshed Al-Obeidi, Olivier Manches
Software Mentions: 3
Published: over 5 years ago

10.3390/cells9051149

Large-Scale Profiling of Signaling Pathways Reveals a Distinct Demarcation between Normal and Extended Liver Resection
Cited by: 3
Author(s): Pieter Borger, Anton Buzdin, Maksim Sorokin, Ekaterina Kachaylo, Bostjan Humar, Rolf Graf, Pierre-Alien Clavien
Software Mentions: 3
Published: over 4 years ago

Projects: cran: gplots

Papers Mentioning gplots 2,122