cran: gplots | Projects | Ecosyste.ms: Papers

10.3390/microorganisms9071495

Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
Cited by: 15
Author(s): Tim Piel, Giovanni Sandrini, Gerard Muyzer, Corina P. D. Brussaard, Pieter C. Slot, Maria J. van Herk, Jef Huisman, P. Visser
Software Mentions: 4
Published: over 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 6 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: almost 7 years ago

10.3390/microorganisms9020294

Potential Association between Vaginal Microbiota and Cervical Carcinogenesis in Korean Women: A Cohort Study
Cited by: 23
Author(s): Gi-Ung Kang, Da-Ryung Jung, Yoon Hee Lee, Se Young Jeon, Hyung Soo Han, Gun Oh Chong, Jae‐Ho Shin
Software Mentions: 4
Published: over 5 years ago

10.1172/jci.insight.141341

Shear stress associated with cardiopulmonary bypass induces expression of inflammatory cytokines and necroptosis in monocytes
Cited by: 17
Author(s): Lan N. Tu, Lance Hsieh, Masaki Kajimoto, Kevin Charette, Nataliya Kibiryeva, Adriana Forero, Sarah E. Hampson, Jennifer Marshall, James E. O’Brien, Marta Scatena, Michael A. Portman, Ram Savan, Christopher Benner, Alberto Aliseda, Muhammad Nuri, Douglas C. Bittel, Peter Pastuszko, Vishal Nigam
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12974-020-01797-2

Glioblastoma hijacks microglial gene expression to support tumor growth
Cited by: 63
Author(s): Sybren L. N. Maas, Erik R. Abels, Lieke L van de Haar, Xuan Zhang, Liza M. Morsett, Srinjoy Sil, Joana Guedes, Pritha Sen, Shilpa Prabhakar, Suzanne E. Hickman, Charles P. Lai, David T. Ting, Xandra O. Breakefield, Marike L. D. Broekman, Joseph El Khoury
Software Mentions: 4
Published: over 6 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 10 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 15 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 11 years ago

10.3390/microorganisms9081585

Whole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System
Cited by: 11
Author(s): Ana C. Reis, Liliana C. M. Salvador, Suelee Robbe‐Austerman, Rogério Tenreiro, Ana Botelho, Teresa Albuquerque, Mónica V. Cunha
Software Mentions: 4
Published: about 5 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: over 7 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: over 7 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: almost 7 years ago

10.1007/s00251-014-0819-9

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires
Cited by: 79
Author(s): Elin Bergseng, Siri Dørum, Magnus Ø. Arntzen, Morten Nielsen, Ståle Nygård, Søren Buus, Gustavo Souza, Ludvig M. Sollid
Software Mentions: 4
Published: almost 12 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 5 years ago

10.1186/s12864-018-4564-6

Characterization of the human RFX transcription factor family by regulatory and target gene analysis
Cited by: 57
Author(s): Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Santosh Misra, Carsten O. Daub, Juha Kere, Peter Swoboda
Software Mentions: 4
Published: over 8 years ago

10.1093/gigascience/giz102

Metabolic responses of rice source and sink organs during recovery from combined drought and heat stress in the field
Cited by: 13
Author(s): Lovely Mae F Lawas, Alexander Erban, Joachim Kopka, S. V. Krishna Jagadish, Ellen Zuther, Dirk K. Hincha
Software Mentions: 4
Published: about 7 years ago

10.1186/s12711-020-00553-7

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems
Cited by: 38
Author(s): Samuele Bovo, Anisa Ribani, María Muñoz, E. Alves, J. P. Araújo, Rıccardo Bozzi, Marjeta Čandek-Potokar, Rui Charneca, Federica Di Palma, Graham Etherington, Ana Fernández, Fabián García, Juan García‐Casco, Danijel Karolyi, M. Gallo, Vladimir Margeta, J.M. Martins, Marie J. Mercat, Giulia Moscatelli, Yolanda Núñez, Raquel Quintanilla, Čedomir Radović, Violeta Razmaitė, Juliette Riquet, Radomir Savić, Giuseppina Schiavo, G. Usai, Valerio Joe Utzeri, Christoph Zimmer, Cristina Óvilo, Luca Fontanesi
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms9010149

Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species
Cited by: 21
Author(s): Niranjan P. Sahu, Zsolt Merényi, Balázs Bálint, Brigitta Kiss, György Sipos, Rebecca A. Owens, László G. Nagy
Software Mentions: 4
Published: almost 6 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 7 years ago

10.1186/1471-2164-15-884

A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions
Cited by: 46
Author(s): Beatrix Bicskei, James E. Bron, Kevin A. Glover, John B. Taggart
Software Mentions: 4
Published: almost 13 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 10 years ago

10.1371/journal.pone.0050267

Multivariate Approach for Studying Interactions between Environmental Variables and Microbial Communities
Cited by: 21
Author(s): Xinhui Wang, Marinus J.C. Eijkemans, Jacco Wallinga, Giske Biesbroek, Krzysztof Trzciński, Elisabeth A. M. Sanders, Debby Bogaert
Software Mentions: 4
Published: almost 14 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: over 12 years ago

10.3390/microorganisms8070987

Analysis of Tick Surface Decontamination Methods
Cited by: 13
Author(s): Angeline Hoffmann, Volker Fingerle, Matthias Noll
Software Mentions: 4
Published: over 6 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 5 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: about 6 years ago

10.1371/journal.pone.0149171

RNA-Seq Reveals the Angiogenesis Diversity between the Fetal and Adults Bone Mesenchyme Stem Cell
Cited by: 2
Author(s): Xin Zhao, Yingmin Han, Yu Liang, Chao Nie, Jian Wang
Software Mentions: 4
Published: over 10 years ago

10.3390/microorganisms7020035

The Purple Sea Urchin Strongylocentrotus purpuratus Demonstrates a Compartmentalization of Gut Bacterial Microbiota, Predictive Functional Attributes, and Taxonomic Co-Occurrence
Cited by: 17
Author(s): Joseph A. Hakim, Julie B. Schram, Aaron W. E. Galloway, Casey D. Morrow, Michael R. Crowley, Stephen A. Watts, Asim K. Bej
Software Mentions: 4
Published: over 7 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 7 years ago

10.18632/oncotarget.15068

Genome-scale analysis identifies GJB2 and ERO1LB as prognosis markers in patients with pancreatic cancer
Cited by: 39
Author(s): Tao Zhu, Yuanfeng Gao, Yixin Chen, Zhibin Wang, Ji‐Ye Yin, Xiao‐Yuan Mao, Xi Li, Wei Zhang, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 4
Published: over 9 years ago

10.1186/s13059-015-0825-8

Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells
Cited by: 26
Author(s): Christelle Etard, Olivier Armant, Urmas Roostalu, Victor Gourain, Marco Ferg, Uwe Strähle
Software Mentions: 4
Published: almost 11 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 9 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 5 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 6 years ago

10.3390/ijms21020440

Anisotropic Platinum Nanoparticle-Induced Cytotoxicity, Apoptosis, Inflammatory Response, and Transcriptomic and Molecular Pathways in Human Acute Monocytic Leukemia Cells
Cited by: 24
Author(s): Sangiliyandi Gurunathan, M. Jeyaraj, Hyeonwoo La, Hyunjin Yoo, Youngsok Choi, Jeong Tae, Chankyu Park, Jin‐Hoi Kim, Kwonho Hong
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0251121

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

10.6026/97320630016567

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 6 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 11 years ago

10.3390/microorganisms9071378

Effects of Wine and Its Microbial-Derived Metabolites on Intestinal Permeability Using Simulated Gastrointestinal Digestion/Colonic Fermentation and Caco-2 Intestinal Cell Models
Cited by: 11
Author(s): Irene Zorraquín‐Peña, Diego Taladrid, Alba Tamargo, Mariana Silva, Natalia Molinero, Dolores González de Llano, Begoňa Bartolomé, M. Victoria Moreno‐Arribas
Software Mentions: 4
Published: over 5 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 5 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 8 years ago

10.1371/journal.pone.0061736

Gene Expression Signatures of Energetic Acclimatisation in the Reef Building Coral Acropora millepora
Cited by: 30
Author(s): Line K. Bay, Aurélie Guérécheau, Nikos Andreakis, Karin E. Ulstrup, Mikhail V. Matz
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0224644

Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA- PCG pairs involved in intermediary metabolism
Cited by: 5
Author(s): Angela Zhang, Cindy Yanfei Li, Edward J. Kelly, Lianne Sheppard, Julia Yue Cui
Software Mentions: 4
Published: over 6 years ago

10.3390/cancers7040887

Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics
Cited by: 27
Author(s): Janet Doolittle-Hall, Danielle L. Cunningham Glasspoole, William T. Seaman, Jennifer Webster‐Cyriaque
Software Mentions: 4
Published: almost 11 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 6 years ago

10.1016/j.cell.2017.03.040

Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans
Cited by: 175
Author(s): Timothy A. Scott, Leonor M. Quintaneiro, Povilas Norvaišas, Prudence PokWai Lui, Matthew P. Wilson, Kit‐Yi Leung, Lucía Herrera-Domínguez, Sonia Sudiwala, Alberto Pessia, Peter T. Clayton, Kevin Bryson, Vidya Velagapudi, Philippa B. Mills, Athanasios Typas, Nicholas D. E. Greene, Filipe Cabreiro
Software Mentions: 4
Published: over 9 years ago

10.1080/15384101.2016.1261765

Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion
Cited by: 24
Author(s): Maria Sokolova, Mikko Turunen, Oliver Mortusewicz, Teemu Kivioja, Patrick Herr, Anna Vähärautio, Mikael Björklund, Minna Taipale, Thomas Helleday, Jussi Taipale
Software Mentions: 4
Published: almost 10 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: about 6 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 9 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 6 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 7 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 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 5 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 10 years ago

10.3389/fmicb.2021.681185

Evaluation of the Relationships Between Microbiota and Metabolites in Soft-Type Ripened Cheese Using an Integrated Omics Approach
Cited by: 9
Author(s): Ryosuke Unno, Toshihiro Suzuki, Minenosuke Matsutani, Morio Ishikawa
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.00699

Tillage Changes Vertical Distribution of Soil Bacterial and Fungal Communities
Cited by: 112
Author(s): Run‐Cang Sun, Wenyan Li, Wenxu Dong, Yinping Tian, Chunsheng Hu, Binbin Liu
Software Mentions: 4
Published: over 8 years ago

10.3389/fonc.2013.00184

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways
Cited by: 13
Author(s): Alexander J. Trevarton, Michael B. Mann, Christoph Knapp, Hiromitsu Araki, Jonathan D. Wren, Steven Stones-Havas, Michael A. Black, Cristin G. Print
Software Mentions: 4
Published: almost 14 years ago

10.3389/fphys.2018.00019

Comparison of Fatty Acid and Gene Profiles in Skeletal Muscle in Normal and Obese C57BL/6J Mice before and after Blunt Muscle Injury
Cited by: 6
Author(s): Jens-Uwe Werner, Klaus Tödter, Pengfei Xu, Lydia Lockhart, Markus Jähnert, Pascal Gottmann, Annette Schürmann, Ludger Scheja, Martin Wabitsch, Uwe Knippschild
Software Mentions: 4
Published: over 8 years ago

10.3389/fphys.2018.00674

Diet-Induced Obesity Affects Muscle Regeneration After Murine Blunt Muscle Trauma—A Broad Spectrum Analysis
Cited by: 19
Author(s): Pengfei Xu, Jens-Uwe Werner, Sebastian Milerski, Carmen M. Hamp, Tatjana Kuzenko, Markus Jähnert, Pascal Gottmann, Luisa de Roy, Daniela Warnecke, Alireza Abaei, Annette Palmer, Markus Huber‐Lang, Lutz Dürselen, Volker Rasche, Annette Schürmann, Martin Wabitsch, Uwe Knippschild
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2019.00473

Proteases Underground: Analysis of the Maize Root Apoplast Identifies Organ Specific Papain-Like Cysteine Protease Activity
Cited by: 15
Author(s): Jan Schulze Hüynck, Farnusch Kaschani, Karina van der Linde, Sebastian Ziemann, André N. Müller, Thomas Colby, Markus Kaiser, Johana C. Misas-Villamil, Gunther Doehlemann
Software Mentions: 4
Published: over 7 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 5 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: about 8 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 11 years ago

10.1038/srep16238

IDH mutation status is associated with a distinct hypoxia/angiogenesis transcriptome signature which is non-invasively predictable with rCBV imaging in human glioma
Cited by: 243
Author(s): Philipp Kickingereder, Felix Sahm, Alexander Radbruch, Wolfgang Wick, Sabine Heiland, Andreas von Deimling, Martin Bendszus, Benedikt Wiestler
Software Mentions: 4
Published: almost 11 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: over 10 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 10 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 9 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 9 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 8 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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 5 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: almost 6 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 8 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 7 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 6 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: almost 6 years ago

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 9 years ago

10.1128/mSystems.00334-20

Human Milk Oligosaccharides Modulate the Risk for Preterm Birth in a Microbiome-Dependent and -Independent Manner
Cited by: 9
Author(s): Manuela-Raluca Pausan, V Kolovetsiou-Kreiner, Gesa Richter, Tobias Madl, Elisabeth Giselbrecht, Barbara Obermayer‐Pietsch, Eva-Christine Weiss, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger
Software Mentions: 4
Published: over 6 years ago

10.1038/s41396-020-0676-5

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium
Cited by: 27
Author(s): Hwee Sze Tee, David W. Waite, Leo S. Payne, Martin Middleditch, Susie Wood, Kim M. Handley
Software Mentions: 4
Published: over 6 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 7 years ago

10.1038/s41368-018-0037-7

Increased virulence of the oral microbiome in oral squamous cell carcinoma revealed by metatranscriptome analyses
Cited by: 74
Author(s): Susan Yost, Philip Stashenko, Yoon-Hee Choi, Maria A. Kukuruzinska, Caroline A. Genco, Andrew Salama, Ellen O. Weinberg, Carolyn D. Kramer, Jorge Frias-Lopez
Software Mentions: 4
Published: almost 8 years ago

10.3390/ijerph16162913

Investigation of Relationship Between Spatial Distribution of Medical Equipment and Preventable Mortality
Cited by: 3
Author(s): Beata Gavurová, David Tuček, Viliam Kováč
Software Mentions: 4
Published: about 7 years ago

10.1007/s00442-018-4291-3

Immune function and blood parasite infections impact stopover ecology in passerine birds
Cited by: 31
Author(s): Arne Hegemann, Pablo Alcalde Abril, Rachel Muheim, Sissel Sjöberg, Thomas Alerstam, Jan Nilsson, Dennis Hasselquist
Software Mentions: 4
Published: almost 8 years ago

10.1038/onc.2016.242

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network
Cited by: 16
Author(s): Yan Zhou, Oliver Frings, Rui M. Branca, Jorrit Boekel, Carlos le Sage, Erik Fredlund, Reuven Agami, Lukas M. Orre
Software Mentions: 4
Published: about 10 years ago

10.7554/eLife.22536

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells
Cited by: 68
Author(s): Nicholas T Hogan, Michael B. Whalen, Lindsey K Stolze, Nizar K Hadeli, Michael T. Lam, James R. Springstead, Christopher K. Glass, Casey E. Romanoski
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-021-96331-6

Genetic homogeneity, lack of larvae recruitment, and clonality in absence of females across western Mediterranean populations of the starfish Coscinasterias tenuispina
Cited by: 1
Author(s): Rocío Pérez‐Portela, Álex García-Cisneros, Marta Campos-Canet, Creu Palacín
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers13102499

Expression of Cancer Testis Antigens in Tumor-Adjacent Normal Liver Is Associated with Post-Resection Recurrence of Hepatocellular Carcinoma
Cited by: 3
Author(s): Lisanne Noordam, Zhouhong Ge, Hadiye Özturk, Michail Doukas, Shanta Mancham, Patrick P.C. Boor, Lucia Campos Carrascosa, Guoying Zhou, Thierry van den Bosch, Qiuwei Pan, Jan N.M. IJzermans, Marco J. Bruno, Dave Sprengers, Jaap Kwekkeboom
Software Mentions: 3
Published: over 5 years ago

10.3390/nu9030233

Integration of Traditional and Metabolomics Biomarkers Identifies Prognostic Metabolites for Predicting Responsiveness to Nutritional Intervention against Oxidative Stress and Inflammation
Cited by: 15
Author(s): You Jin Kim, Iksoo Huh, Ji Yeon Kim, Saejong Park, Sung Ha Ryu, Kyu Bong Kim, Suhkmann Kim, Taesung Park, Oran Kwon
Software Mentions: 3
Published: over 9 years ago

10.1093/infdis/jiu615

Gene Expression and Cytokine Profile Correlate With Mycobacterial Growth in a Human BCG Challenge Model
Cited by: 29
Author(s): Magali Matsumiya, Iman Satti, Agnieszka Chomka, Stephanie A. Harris, Lisa Stockdale, Joel N. Meyer, Helen A. Fletcher, Helen McShane
Software Mentions: 3
Published: almost 12 years ago

10.7554/eLife.68466

LIN37-DREAM prevents DNA end resection and homologous recombination at DNA double-strand breaks in quiescent cells
Cited by: 10
Author(s): Bo-Ruei Chen, Yinan Wang, Anthony Tubbs, Dali Zong, Faith C Fowler, Nicholas Zolnerowich, Wei Wu, Amelia Bennett, Chun-Chin Chen, Wendy Feng, André Nussenzweig, Jessica K. Tyler, Barry P. Sleckman
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2018.00968

QTL Mapping and Validation of Adult Plant Resistance to Stripe Rust in Chinese Wheat Landrace Humai 15
Cited by: 38
Author(s): Fengping Yuan, Qingdong Zeng, Jianhui Wu, Qilin Wang, Zujun Yang, Bang-Ping Liang, Xinhong Chen
Software Mentions: 3
Published: over 8 years ago

10.1186/s40594-021-00306-y

Am I getting through? Surveying students on what messages they recall from the first day of STEM classes
Cited by: 6
Author(s): Clara L. Meaders, Lillian G. Senn, Brian A. Couch, A. Kelly Lane, Marilyne Stains, MacKenzie R. Stetzer, Erin Vinson, Michelle K. Smith
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2016.02064

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype
Cited by: 76
Author(s): Jakson Leite, Doreen Fischer, Luc Felicianus Marie Rouws, Paulo Ivan Fernandes‐Júnior, Andreas Hofmann, Susanne Kublik, Michael Schloter, Gustavo Ribeiro Xavier, Viviane Radl
Software Mentions: 3
Published: over 9 years ago

Projects: cran: gplots

Enhanced Analysis

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning gplots 2,122