cran: gplots | Projects | Ecosyste.ms: Papers

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

10.1186/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.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: about 13 years ago

10.1186/s12866-020-01771-1

Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia
Cited by: 6
Author(s): Leah J Radeke, Michael A. Herman
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms22157804

Skin Wound Healing Rate in Fish Depends on Species and Microbiota
Cited by: 9
Author(s): Tery Yun, Soeun Shin, Kyungwon Bang, Mugeun Lee, Jung-Ah Cho, Min Won Baek
Software Mentions: 4
Published: about 5 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: over 5 years ago

10.3390/v10120715

Seasonality Drives Microbial Community Structure, Shaping both Eukaryotic and Prokaryotic Host–Viral Relationships in an Arctic Marine Ecosystem
Cited by: 23
Author(s): Ruth‐Anne Sandaa, Julia E. Storesund, Emily Olesin, Maria Lund Paulsen, Aud Larsen, Gunnar Bratbak, Jessica L. Ray
Software Mentions: 4
Published: over 7 years ago

10.3390/ijms21155265

New Methodology for the Identification of Metabolites of Saccharides and Cyclitols by Off-Line EC-MALDI-TOF-MS
Cited by: 3
Author(s): Gulyaim Sagandykova, Justyna Walczak-Skierska, Fernanda Monedeiro, Paweł Pomastowski
Software Mentions: 4
Published: about 6 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: about 5 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: over 6 years ago

10.3390/ijms21062252

Vesicles Shed by Pathological Murine Adipocytes Spread Pathology: Characterization and Functional Role of Insulin Resistant/Hypertrophied Adiposomes
Cited by: 25
Author(s): Tamara Camino, Nerea Lago-Baameiro, Susana B. Bravo, Aurelio M. Sueiro, Iván Couto, F. De Toro Santos, Javier Baltar, Felipe Casanueva Freijó, María Pardo
Software Mentions: 4
Published: over 6 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: almost 11 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 8 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: about 5 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: almost 11 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: almost 9 years ago

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: almost 8 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: over 12 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

10.3390/microorganisms8070987

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

10.1186/1471-2164-15-474

The human miRNA repertoire of different blood compounds
Cited by: 56
Author(s): Petra Leidinger, Christina Backes, Benjamin Meder, Eckart Meese, Andreas Keller
Software Mentions: 4
Published: about 12 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: over 5 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

10.3390/ijms22116101

Loss of Nnt Increases Expression of Oxidative Phosphorylation Complexes in C57BL/6J Hearts
Cited by: 4
Author(s): Jack Williams, Charlotte Hall, Eirini Meimaridou, Louise A. Metherell
Software Mentions: 4
Published: about 5 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: over 10 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

10.1186/s12864-016-2801-4

RNA-Seq analysis of Gtf2ird1 knockout epidermal tissue provides potential insights into molecular mechanisms underpinning Williams-Beuren syndrome
Cited by: 8
Author(s): Susan M. Corley, Cesar P Canales, Paulina Carmona-Mora, Veronica Mendoza-Reinosa, Annemiek Beverdam, Edna C. Hardeman, Marc R. Wilkins, Steve Palmer
Software Mentions: 4
Published: about 10 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

10.3390/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: about 5 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: about 6 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

10.1186/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: almost 8 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: over 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: about 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 10 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: almost 8 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: over 10 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: almost 9 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: about 6 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

10.1186/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: about 9 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: about 5 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

10.3389/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: almost 6 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

10.1007/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/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

10.1128/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: about 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: almost 9 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: about 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: about 7 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: over 6 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/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: over 6 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: almost 7 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: 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

10.1111/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: over 11 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: almost 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: 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: about 5 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: over 8 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: about 12 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: almost 7 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

10.1038/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: almost 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/s41598-021-87805-8

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/s41598-021-90250-2

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: 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: over 10 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: 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 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: about 5 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: almost 5 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: about 10 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: about 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: about 5 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 13 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 7 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: over 6 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: almost 11 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

10.1038/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: about 9 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: almost 13 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: about 9 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: over 10 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: about 5 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

10.15252/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: about 6 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 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

10.1186/1471-2164-14-320

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 13 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: over 9 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: almost 10 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 7 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

10.1371/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: almost 15 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

Projects: cran: gplots

Enhanced Analysis

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning gplots 2,122