cran: gplots | Projects | Ecosyste.ms: Papers

10.3390/ijms19103265

Distinct Signatures of Host Defense Suppression by Plant-Feeding Mites
Cited by: 19
Author(s): Bernardus C. J. Schimmel, Juan M. Alba, Nicky Wybouw, Joris J. Glas, Tomas Meijer, Robert C. Schuurink, Merijn R. Kant
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms20030510

Molecular Insights into the Classification of Luminal Breast Cancers: The Genomic Heterogeneity of Progesterone-Negative Tumors
Cited by: 23
Author(s): Gianluca Lopez, Jole Costanza, M. Colleoni, Laura Fontana, Stefano Ferrero, Monica Miozzo, Nicola Fusco
Software Mentions: 4
Published: almost 6 years ago

10.3390/microorganisms8060842

Transcriptome Profiling of Toxoplasma gondii-Infected Human Cerebromicrovascular Endothelial Cell Response to Treatment with Monensin
Cited by: 5
Author(s): Mohammad Syamsul Reza Harun, Mica Taylor, Xing‐Quan Zhu, Hany M. Elsheikha
Software Mentions: 4
Published: over 4 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

10.1186/s40168-018-0542-0

Pathogenic functions of host microbiota
Cited by: 64
Author(s): Silke Rath, Tatjana Rud, André Karch, Dietmar H. Pieper, Marius Vital
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms160921310

Gene Expression Variations of Red—White Skin Coloration in Common Carp (Cyprinus carpio)
Cited by: 19
Author(s): Xiaomin Li, Yijun Song, Gao Xiao, Bai-Han Zhu, Gui-Cai Xu, Mingyuan Sun, Jun Xiao, Shahid Mahboob, Khalid A. Al‐Ghanim, Xin Sun, Jiong-Tang Li
Software Mentions: 4
Published: about 9 years ago

10.1186/s40168-015-0133-2

The administration of intranasal live attenuated influenza vaccine induces changes in the nasal microbiota and nasal epithelium gene expression profiles
Cited by: 64
Author(s): Yasir Tarabichi, K. Li, Shishan Hu, Cam Nguyen, X. Wang, David Elashoff, Kazima Saira, Bryan Frank, Monika Bihan, Elodie Ghedin, Barbara A. Methé, Jane C. Deng
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-016-2694-2

RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Cited by: 21
Author(s): Maurizio Pellegrino, Adam Sciambi, Jamie Yates, Joshua D. Mast, Charles Silver, Dennis J. Eastburn
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-018-5157-0

Genome-wide identification and analysis of WD40 proteins in wheat (Triticum aestivum L.)
Cited by: 39
Author(s): Rui Hu, Jie Xiao, Tao Gu, Xiao‐Lan Yu, Yang Zhang, Junli Chang, Guangxiao Yang, Guangyuan He
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.08851

Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation
Cited by: 99
Author(s): Katia Ancelin, Laurène Syx, Maud Borensztein, Noémie Ranisavljevic, Ivaylo Vassilev, Luis Briseño-Roa, Tao Liu, Eric Metzger, Nicolas Servant, Emmanuel Barillot, Chongjian Chen, Roland Schüle, Edith Heard
Software Mentions: 4
Published: almost 9 years ago

10.7554/eLife.36998

Downregulation of ribosome biogenesis during early forebrain development
Cited by: 63
Author(s): Kevin F. Chau, Morgan L. Shannon, Ryann M. Fame, Erin Fonseca, Hillary Mullan, Matthew B. Johnson, Anoop K. Sendamarai, Mark W. Springel, Laurent Beaugerie, Maria K. Lehtinen
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms22041912

Sensitivity to Cisplatin in Head and Neck Cancer Cells Is Significantly Affected by Patient-Derived Cancer-Associated Fibroblasts
Cited by: 13
Author(s): Barbora Peltanová, Marketa Liskova, Jaromír Gumulec, Martina Raudenská, Hana Polanská, Tomáš Vaculovič, David Kalfeřt, Marek Grega, Jan Plzák, Jan Betka, Michal Masařík
Software Mentions: 4
Published: almost 4 years ago

10.1186/s40168-015-0136-z

Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries
Cited by: 43
Author(s): Joel D. Rudney, Pratik Jagtap, Cavan Reilly, Ruoqiong Chen, Todd W. Markowski, LeeAnn Higgins, James E. Johnson, Timothy J. Griffin
Software Mentions: 4
Published: almost 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

10.1186/s40168-017-0362-7

Dietary changes in nutritional studies shape the structural and functional composition of the pigs’ fecal microbiome—from days to weeks
Cited by: 54
Author(s): Bruno Tilocca, Katharina Burbach, Charlotte M E Heyer, Ludwig E. Hoelzle, R. Mosenthin, Volker Stefanski, Amélia Camarinha‐Silva, Jana Seifert
Software Mentions: 4
Published: about 7 years ago

10.31557/APJCP.2020.21.6.1787

Risk Scoring System based on lncRNA Expression for Predicting Survival in Hepatocellular Carcinoma with Cirrhosis
Cited by: 13
Author(s): Jiaxiang Ye, Haixia Li, Jiazhang Wei, Yue Luo, Hongmei Li, Jinyan Zhang, Xi Luo
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-017-3884-2

Identification of long non-coding RNA in the horse transcriptome
Cited by: 16
Author(s): Elaine P. Scott, Tamer Mansour, Rebecca R. Bellone, C. Titus Brown, Michael J. Mienaltowski, M. C. T. Penedo, Pablo J. Ross, Stephanie J. Valberg, James D. Murray, Carrie J. Finno
Software Mentions: 4
Published: over 7 years ago

10.3389/fgene.2021.700489

Comparative Transcriptome Analysis of Milk Somatic Cells During Lactation Between Two Intensively Reared Dairy Sheep Breeds
Cited by: 4
Author(s): Sofia Michailidou, Athanasios Ι. Gelasakis, Georgios Banos, G. Arsenos, Anagnostis Argiriou
Software Mentions: 4
Published: over 3 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

10.3389/fgene.2020.594569

Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks
Cited by: 6
Author(s): Isaiah Catalino M. Pabuayon, Ai Kitazumi, Glenn B. Gregorio, Rakesh Kumar Singh, Benildo G. de los Reyes
Software Mentions: 4
Published: about 4 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

10.1038/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

10.1038/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/fcimb.2020.00433

The Microbiome Composition of a Man's Penis Predicts Incident Bacterial Vaginosis in His Female Sex Partner With High Accuracy
Cited by: 34
Author(s): Supriya D. Mehta, Dan Zhao, Stefan J. Green, Walter Agingu, Fredrick Otieno, Runa Bhaumik, Dulal K. Bhaumik, Robert C. Bailey
Software Mentions: 4
Published: over 4 years ago

10.1099/mgen.0.000319

Landscape of gene expression variation of natural isolates of Cryptococcus neoformans in response to biologically relevant stresses
Cited by: 22
Author(s): Yu Chen, Chen Yuan, Christopher A. Desjardins, Jennifer L. Tenor, Dena L. Toffaletti, Charles Giamberardino, Anastasia P. Litvintseva, John R. Perfect, Christina A. Cuomo
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2019.01036

Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase
Cited by: 5
Author(s): Sandra Grossi Gava, Naiara Clemente Tavares, Franco H. Falcone, Guilherme Oliveira, Marina Moraes Mourão
Software Mentions: 4
Published: about 5 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.0212359

Rosellinia necatrix infection induces differential gene expression between tolerant and susceptible avocado rootstocks
Cited by: 16
Author(s): Adela Zumaquero, Elsa Martínez-Ferri, Antonio J. Matas, Bianca Reeksting, Nicholas Abraham Olivier, Fernando Pliego‐Alfaro, Araceli Barceló, Noëlani van den Berg, Clara Pliego
Software Mentions: 4
Published: almost 6 years ago

10.1111/acel.12293

Genetic variants modify the effect of age on<scp>APOE</scp>methylation in the<scp>G</scp>enetics of<scp>L</scp>ipid<scp>L</scp>owering<scp>D</scp>rugs and<scp>D</scp>iet<scp>N</scp>etwork study
Cited by: 34
Author(s): Yiyi Ma, Caren E. Smith, Chao‐Qiang Lai, Marguerite R. Irvin, Laurence D. Parnell, Yu Chi Lee, Lucia D. Pham, Stella Aslibekyan, Steven A. Claas, Michael Y. Tsai, Ingrid B. Borecki, Edmond K. Kabagambe, Silvia Berciano, José M. Ordovás, Devin Absher, Donna K. Arnett
Software Mentions: 4
Published: almost 10 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

10.1186/s12987-021-00269-w

Characterization of the blood–brain barrier in genetically diverse laboratory mouse strains
Cited by: 16
Author(s): Johanna Schaffenrath, Sheng‐Fu Huang, Tania Wyss, Mauro Delorenzi, Annika Keller
Software Mentions: 4
Published: over 3 years ago

10.3389/fnagi.2017.00383

Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment
Cited by: 38
Author(s): Lara Ianov, Matt De Both, Monica K. Chawla, Asha Rani, Andrew Kennedy, Ignazio S. Piras, Jeremy J. Day, Ashley L. Siniard, Ashok Kumar, J. David Sweatt, Carol A. Barnes, Matthew J. Huentelman, Thomas C. Foster
Software Mentions: 4
Published: almost 7 years ago

10.12688/f1000research.2-71.v2

Using Akaike's information theoretic criterion in mixed-effects modeling of pharmacokinetic data: a simulation study
Cited by: 17
Author(s): Erik Olofsen, Albert Dahan
Software Mentions: 4
Published: over 10 years ago

10.3390/metabo9100210

Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy
Cited by: 41
Author(s): Hemalatha Babu, Maike Sperk, Anoop T. Ambikan, Gladys Rachel, Vinod Kumar Viswanathan, Srikanth Tripathy, Piotr Nowak, Luke Elizabeth Hanna, Ujjwal Neogi
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0155536

Combined Effects of Soil Biotic and Abiotic Factors, Influenced by Sewage Sludge Incorporation, on the Incidence of Corn Stalk Rot
Cited by: 10
Author(s): R. Ghini, Nara Lúcia Perondi Fortes, Juan A Navas‐Cortés, Carlos Alberto Silva, W. Bettiol
Software Mentions: 4
Published: over 8 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

10.1038/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

10.1186/s12862-016-0592-5

Age-related association of venom gene expression and diet of predatory gastropods
Cited by: 16
Author(s): Dan Chang, Thomas F. Duda
Software Mentions: 4
Published: almost 9 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

10.1186/1471-2164-15-155

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses
Cited by: 36
Author(s): Xin Luo, Minho Chae, Raga Krishnakumar, Charles G. Danko, W. Lee Kraus
Software Mentions: 4
Published: over 10 years ago

10.1186/s12936-021-03918-5

Transcriptome-based analysis of blood samples reveals elevation of DNA damage response, neutrophil degranulation, cancer and neurodegenerative pathways in Plasmodium falciparum patients
Cited by: 1
Author(s): Akua A. Karikari, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: about 3 years ago

10.1080/15592294.2016.1182272

Bisphenol A causes reproductive toxicity, decreases dnmt1 transcription, and reduces global DNA methylation in breeding zebrafish (Danio rerio)
Cited by: 138
Author(s): Lauren V. Laing, Joana Viana, Emma Dempster, Maciej Trznadel, L. A. Trunkfield, Tamsyn M. Uren Webster, Ronny van Aerle, Gregory C. Paull, Robert J. Wilson, Jonathan Mill, Eduarda M. Santos
Software Mentions: 4
Published: over 8 years ago

10.1186/s12864-021-07902-w

Increased abundance of secreted hydrolytic enzymes and secondary metabolite gene clusters define the genomes of latent plant pathogens in the Botryosphaeriaceae
Cited by: 16
Author(s): Jan Hendrik Nagel, Michael J. Wingfield, Bernard Slippers
Software Mentions: 4
Published: over 3 years ago

10.1186/1471-213X-13-13

miRNA regulated pathways in late stage murine lung development
Cited by: 47
Author(s): Sana Mujahid, Tanya Logvinenko, MaryAnn V. Volpe, Heber C. Nielsen
Software Mentions: 4
Published: over 11 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/s41598-019-56051-4

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

10.1038/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/s41598-018-32448-5

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

10.1038/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

10.1002/ece3.4944

Conservation of genetic diversity hotspots of the high‐valued relic yellowhorn ( Xanthoceras sorbifolium ) considering climate change predictions
Cited by: 1
Author(s): Renbin Zhu, Qing Wang, Wei Guan, Yanjia Mao, Bin Tian, Jimin Cheng, Yousry A. El‐Kassaby
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-27376-3

Transcriptional analysis of adipose tissue during development reveals depot-specific responsiveness to maternal dietary supplementation
Cited by: 16
Author(s): Hernan P. Fainberg, Mark Birtwistle, Reham I. Alagal, Ahmad Alhaddad, Mark Pope, Graeme R. Davies, Rachel Woods, Marcos Castellanos, Sean May, Catharine A. Ortori, David A. Barrett, V.E.A. Perry, Frank Wiens, Bernd Stahl, Eline van der Beek, Harold S. Sacks, Helen Budge, Michael Symonds
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-020-6483-6

Virus expression detection reveals RNA-sequencing contamination in TCGA
Cited by: 21
Author(s): Sara R. Selitsky, David Marron, Daniel P. Hollern, Lisle E. Mose, Katherine A. Hoadley, Corbin D. Jones, Joel S. Parker, Dirk P. Dittmer, Charles M. Perou
Software Mentions: 4
Published: almost 5 years ago

10.1002/ece3.1824

Earlier breeding, lower success: does the spatial scale of climatic conditions matter in a migratory passerine bird?
Cited by: 10
Author(s): Annegret Grimm, B. Weiß, Lars Kulik, Jean‐Baptiste Mihoub, Roger Mundry, Ulrich Köppen, Tomas Brueckmann, Ruth Thomsen, Anja Widdig
Software Mentions: 4
Published: about 9 years ago

10.1289/ehp.1002546

Global Gene Expression Profiling of a Population Exposed to a Range of Benzene Levels
Cited by: 94
Author(s): Cliona M. McHale, Luoping Zhang, Qing Lan, Roel Vermeulen, Guilan Li, Alan Hubbard, Kristin E. Porter, Reuben Thomas, Christopher J. Portier, Min Shen, Stephen M. Rappaport, Shu Yin, Martyn T. Smith, Nathaniel Rothman
Software Mentions: 4
Published: over 13 years ago

10.1002/emmm.201201974

Alteration of the micro <scp>RNA</scp> network during the progression of Alzheimer's disease
Cited by: 393
Author(s): Pierre Lau, Koen Bossers, Rekin’s Janky, Evgenia Salta, Carlo Sala Frigerio, Shahar Barbash, Roy Rothman, Annerieke Sierksma, Amantha Thathiah, David Greenberg, Aikaterini S. Papadopoulou, Tilmann Achsel, Torik Ayoubi, Hermona Soreq, Joost Verhaagen, Dick F. Swaab, Stein Aerts, Bart De Strooper
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0179901

Microarray analyses of otospheres derived from the cochlea in the inner ear identify putative transcription factors that regulate the characteristics of otospheres
Cited by: 2
Author(s): Takehiro Iki, Michihiro Tanaka, Shin‐ichiro Kitajiri, Tomoko Kita, Yoshihisa Kawasaki, Akifumi Mizukoshi, Wataru Fujibuchi, Takayuki Nakagawa, Tatsutoshi Nakahata, Juichi Ito, Koichi Omori, Megumu K. Saito
Software Mentions: 4
Published: over 7 years ago

10.1093/bib/bbw008

A benchmark of gene expression tissue-specificity metrics
Cited by: 231
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 4
Published: almost 9 years ago

10.15252/emmm.202013131

Synaptic disruption and CREB‐regulated transcription are restored by K + channel blockers in ALS
Cited by: 19
Author(s): Alberto Catanese, Sandeep Rajkumar, Daniel Sommer, Dennis Freisem, Alexander Wirth, Amr Aly, David Massa-López, Andrea Olivieri, Federica Torelli, Valentin Ioannidis, Joanna Lipecka, Ida Chiara Guerrera, Daniel Zytnicki, Albert C. Ludolph, Edor Kabashi, Medhanie Mulaw, Francesco Roselli, Tobias M. Böckers
Software Mentions: 4
Published: over 3 years ago

10.15252/embj.2019103667

Arabidopsis shoot stem cells display dynamic transcription and <scp>DNA</scp> methylation patterns
Cited by: 40
Author(s): Ruben Gutzat, Klaus Rembart, Thomas Nußbaumer, Falko Hofmann, Rahul Pisupati, Gabriele Bradamante, Nina Daubel, Angelika Gaidora, Nicole Lettner, Mattia Donà, Magnus Nordborg, Michael D. Nodine, Ortrun Mittelsten Scheid
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0250514

Insights into the microbial diversity and structure in a full-scale municipal wastewater treatment plant with particular regard to Archaea
Cited by: 8
Author(s): Grażyna Płaza, Łukasz Jałowiecki, Dominika Głowacka, Jakub Hubeny, Monika Harnisz, Ewa Korzeniewska
Software Mentions: 4
Published: over 3 years ago

10.15252/embj.2019104202

Systematic analysis of the <scp>IL</scp> ‐17 receptor signalosome reveals a robust regulatory feedback loop
Cited by: 14
Author(s): Helena Draberova, Sarka Janusova, Daniela Knizkova, Tereza Šemberová, Michaela Přibíková, Andrea Ujevic, Karel Harant, Sofija Knápková, Matouš Hrdinka, Viola Fanfani, Giovanni Stracquadanio, Ales Drobek, Klara Ruppova, Ondřej Štěpánek, Peter Dráber
Software Mentions: 4
Published: over 4 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/s41598-017-02761-6

Transcription Factor Networks derived from Breast Cancer Stem Cells control the immune response in the Basal subtype
Cited by: 27
Author(s): Willian A. da Silveira, Patrícia Vianna Bonini Palma, Renata Danielle Sicchieri, Rolando A R Villacis, Larissa Raquel Mouro Mandarano, Tatiane Oliveira, Heriton Mr Antonio, Jurandyr Moreira de Andrade, Valdair Francisco Muglia, Sílvia Regina Rogatto, Charles Theillet, Stanislas du Manoir, Daniel Guimarães Tiezzi
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-14-320

Sequencing platform and library preparation choices impact viral metagenomes
Cited by: 88
Author(s): Sergei A. Solonenko, J. Cesar Ignacio‐Espinoza, Adriana Alberti, Corinne Cruaud, Steven J. Hallam, Kostas Konstantinidis, Gene W. Tyson, Patrick Wincker, Matthew B. Sullivan
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0166944

Transcriptomic Analysis Shows Decreased Cortical Expression of NR4A1, NR4A2 and RXRB in Schizophrenia and Provides Evidence for Nuclear Receptor Dysregulation
Cited by: 23
Author(s): Susan M. Corley, Shan-Yuan Tsai, Marc R. Wilkins, Cynthia Shannon Weickert
Software Mentions: 4
Published: almost 8 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/s41598-017-01032-8

Transcriptomic analysis reveals a previously unknown role for CD8+ T-cells in rVSV-EBOV mediated protection
Cited by: 28
Author(s): Andrea Menicucci, Suhas Sureshchandra, Andrea Marzi, Heinz Feldmann, Ilhem Messaoudi
Software Mentions: 4
Published: over 7 years ago

10.1128/AEM.02658-18

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile
Cited by: 5
Author(s): Urse Scheel Krüger, Arnaud Dechesne, Friedhelm Bak, Nora Badawi, Ole Nybroe, Jens Aamand
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0001274

Gene Expression Patterns in Larval Schistosoma mansoni Associated with Infection of the Mammalian Host
Cited by: 88
Author(s): Sophia J. Parker-Manuel, Alasdair Ivens, G. Dillon, R. A. Wilson
Software Mentions: 4
Published: about 13 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

10.1038/srep20759

Comparative transcriptome analysis of peripheral blood mononuclear cells in hepatitis B-related acute-on-chronic liver failure
Cited by: 10
Author(s): Qian Zhou, Wenchao Ding, Liangliang Jiang, Jiaojiao Xin, Tianzhou Wu, Dongyan Shi, Jing Jiang, Cao H, Lanjuan Li, Jun Li
Software Mentions: 4
Published: almost 9 years ago

10.1038/srep11671

Genome-scale long noncoding RNA expression pattern in squamous cell lung cancer
Cited by: 27
Author(s): Ji‐Ye Yin, Chenyue Qian, Xiangping Li, Yu Zhang, Huijuan He, Jingjing Wang, Juan Chen, Jiajia Cui, Rongrong Liu, Hui Zhou, Xiao Lin, Xiaojing Xu, Yi Zheng, Yilan Fu, Zi-Yu Chen, Xiang Chen, Wei Zhang, Cheng-Cheng Ye, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 4
Published: over 9 years ago

10.1038/srep24048

RXR controlled regulatory networks identified in mouse brain counteract deleterious effects of Aβ oligomers
Cited by: 27
Author(s): Kyong Nyon Nam, Anaïs Mounier, Nicholas F. Fitz, Cody M. Wolfe, Jonathan Schug, Iliya Lefterov, Radosveta Koldamova
Software Mentions: 4
Published: over 8 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

10.1111/1462-2920.14808

Volatile‐mediated antagonism of soil bacterial communities against fungi
Cited by: 39
Author(s): Yong Li, Paolina Garbeva, Xiaojiao Liu, Paulien J. A. Klein Gunnewiek, Anna Clocchiatti, Maria P. J. Hundscheid, Xingxiang Wang, Wietse de Boer
Software Mentions: 4
Published: about 5 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

10.1038/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/s41598-019-40992-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/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

10.1186/s13148-020-00990-7

DNA methylation epi-signature is associated with two molecularly and phenotypically distinct clinical subtypes of Phelan-McDermid syndrome
Cited by: 25
Author(s): Laila C. Schenkel, Erfan Aref‐Eshghi, Kathleen Rooney, Jennifer Kerkhof, Michael A. Levy, Haley McConkey, R. Curtis Rogers, Katy Phelan, Sara M. Sarasua, Lavanya Jain, Rini Pauly, Luigi Boccuto, Barbara R. DuPont, Gerarda Cappuccio, Nicola Brunetti‐Pierri, Charles E. Schwartz, Bekim Sadiković
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0134168

Comparative Proteomics of Activated THP-1 Cells Infected with Mycobacterium tuberculosis Identifies Putative Clearance Biomarkers for Tuberculosis Treatment
Cited by: 19
Author(s): Benjawan Kaewseekhao, Vivek Naranbhai, Sittiruk Roytrakul, Wises Namwat, Atchara Paemanee, Viraphong Lulitanond, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 4
Published: over 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

10.1371/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

10.1371/journal.pone.0111637

miR-27 Negatively Regulates Pluripotency-Associated Genes in Human Embryonal Carcinoma Cells
Cited by: 14
Author(s): Heiko Fuchs, Matthias Theuser, Wasco Wruck, James Adjaye
Software Mentions: 4
Published: about 10 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

10.1371/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

10.1155/2020/3968279

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

10.1186/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

10.1016/j.cels.2017.11.002

Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines
Cited by: 18
Author(s): Peter Blattmann, David Henriques, Michael Zimmermann, Fabian Frommelt, Uwe Sauer, Julio Sáez-Rodríguez, Ruedi Aebersold
Software Mentions: 4
Published: almost 7 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

10.6026/97320630016567

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

10.1371/journal.pone.0212577

Developmental fluoxetine exposure in zebrafish reduces offspring basal cortisol concentration via life stage-dependent maternal transmission
Cited by: 15
Author(s): Rubén Martínez, Marilyn N. Vera-Chang, Majd Haddad, J.B.A. van Zon, Laia Navarro‐Martín, Vance L. Trudeau, Jan A. Mennigen
Software Mentions: 4
Published: almost 6 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

10.1111/cpr.12885

NUP98‐HOXA10hd fusion protein sustains multi‐lineage haematopoiesis of lineage‐committed progenitors in transplant setting
Cited by: 2
Author(s): Yong Dong, Kaitao Wang, Qitong Weng, Tongjie Wang, Pingwei Zhou, Xiaofei Liu, Geng Yang, Lijuan Liu, Hongling Wu, Jinyong Wang, Juan Du
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2021.619634

Comparative Metabolite and Gene Expression Analyses in Combination With Gene Characterization Revealed the Patterns of Flavonoid Accumulation During Cistus creticus subsp. creticus Fruit Development
Cited by: 6
Author(s): Neda Aničić, Efstathia Patelou, Antigoni Papanikolaou, Anthi Kanioura, Camilla Valdesturli, Panagiotis Arapitsas, Marijana Škorić, Milan Dragićević, Uroš Gašić, Αθανάσιος Κουκουνάρας, Stefanos Kostas, Eirini Sarrou, Stefan Martens, Danijela Mišić, Angelos K. Kanellis
Software Mentions: 4
Published: over 3 years ago

10.3389/fpls.2018.01209

Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses
Cited by: 39
Author(s): Jérémie Bazin, Natali Romero, Richard Rigo, Céline Charon, Thomas Blein, Federico Ariel, Martín Crespi
Software Mentions: 4
Published: over 6 years ago

10.1038/s41421-018-0030-5

Sea cucumber genome provides insights into saponin biosynthesis and aestivation regulation
Cited by: 64
Author(s): Yuli Li, Ruijia Wang, Xiaogang Xun, Jing Wang, Lisui Bao, Ramesha Thimmappa, Jun Ding, Jingwei Jiang, Liheng Zhang, Tianqi Li, Jia Lv, Chuang Mu, Xiaoli Hu, Lingling Zhang, Jing Liu, Yuqiang Li, Lijie Yao, Wenqian Jiao, Yangfan Wang, Shanshan Lian, Zelong Zhao, Yaoyao Zhan, Xiaoting Huang, Huan Liao, Wang Jia, Hongzhen Sun, Xue Mi, Yu Xia, Qiang Xing, Wei Lü, Anne Osbourn, Zunchun Zhou, Yaqing Chang, Zhenmin Bao, Shi Wang
Software Mentions: 4
Published: over 6 years ago

Projects: cran: gplots

Papers Mentioning gplots 2,122