Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: cran: BioVenn
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/BioVenn
Create Area-Proportional Venn Diagrams from Biological Lists
10 versions
Latest release: over 3 years ago
382 downloads last month
Papers Mentioning BioVenn 247
10.1371/journal.pone.0141171
T Cell Transcriptomes Describe Patient Subtypes in Systemic Lupus ErythematosusCited by: 43
Author(s): Sean J. Bradley, Abel Suárez‐Fueyo, David Moss, Vasileios C. Kyttaris, George C. Tsokos
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0221837
Integrative proteomic and glycoproteomic profiling of Mycobacterium tuberculosis culture filtrateCited by: 18
Author(s): Paula Tucci, Madelón Portela, Carlos Rivas Chetto, Gualberto González‐Sapienza, Mónica Marı́n
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0135143
Large-Scale Transcriptome Analysis in Faba Bean (Vicia faba L.) under Ascochyta fabae InfectionCited by: 39
Author(s): Sara Ocaña, Pedro Seoane, Rocío Bautista, Carmen Palomino, M. Gonzalo Claros, A. M. Torres, Eva Madrid
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0156018
Proteomic Study of Entamoeba histolytica Trophozoites, Cysts, and Cyst-Like StructuresCited by: 17
Author(s): Milka Luna-Nácar, José Navarrete-Perea, Bárbara Moguel, Raúl J. Bobes, Juan Pedro Laclette, Julio César Carrero
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pone.0100930
Response of the Hepatic Transcriptome to Aflatoxin B1 in Domestic Turkey (Meleagris gallopavo)Cited by: 28
Author(s): Melissa S. Monson, Robert E. Settlage, K. Wyatt McMahon, Kristelle M. Mendoza, Sumit Rawal, Hani El-Nezami, Roger A. Coulombe, Kent M. Reed
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0101717
eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using EllipsesCited by: 434
Author(s): Luana Micallef, Peter Rodgers
Software Mentions: 3
Published: over 10 years ago
10.1371/journal.pone.0172220
Can milk cell or skim milk miRNAs be used as biomarkers for early pregnancy detection in cattle?Cited by: 27
Author(s): Corina I. Schanzenbach, Benedikt Kirchner, Susanne E. Ulbrich, Michael W. Pfaffl
Software Mentions: 3
Published: over 7 years ago
10.1371/journal.pone.0197548
ILDR2 has a negligible role in hepatic steatosisCited by: 0
Author(s): Elizabeth J. Millings, Maria Caterina De Rosa, Sarah Fleet, Kazuhisa Watanabe, Richard Rausch, Dieter Egli, Gen Li, Charles A. LeDuc, Yiying Zhang, Stuart G. Fischer, Rudolph L. Leibel
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.pone.0086787
Effects of Sulforaphane and 3,3′-Diindolylmethane on Genome-Wide Promoter Methylation in Normal Prostate Epithelial Cells and Prostate Cancer CellsCited by: 90
Author(s): Carmen P. Wong, Anna Hsu, Alex Buchanan, Zoraya Palomera-Sánchez, Laura M. Beaver, E. Andrés Houseman, David E. Williams, Roderick H. Dashwood, Emily Ho
Software Mentions: 3
Published: almost 11 years ago
10.1371/journal.pone.0164533
Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for WheatCited by: 178
Author(s): Akitomo Kawasaki, Suzanne Donn, Peter R. Ryan, Ulrike Mathesius, Rosangela Devilla, Amanda Jones, Michelle Watt
Software Mentions: 3
Published: about 8 years ago
10.1371/journal.pone.0188441
Transcriptome-wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of controlCited by: 15
Author(s): Santiago Solís Chávez, Guillermo Eastman, Pablo Smircich, Lorena Becco, Carolina Oliveira-Rizzo, Rafael Sebastián Fort, Mariana Potenza, Beatríz Garat, José Sotelo‐Silveira, Marı́a Ana Duhagon
Software Mentions: 3
Published: almost 7 years ago
10.1038/celldisc.2015.35
Discovery of a highly potent glucocorticoid for asthma treatmentCited by: 8
Author(s): Yuanzheng He, Jingjing Shi, Wei Yi, Xin Ren, Xiang Gao, Jianshuang Li, Nanyan Wu, Kevin Weaver, Qian Xie, Sok Kean Khoo, Tao Yang, Xiaozhu Huang, Karsten Melcher, H. Eric Xu
Software Mentions: 3
Published: almost 9 years ago
10.1186/s12014-019-9229-1
Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverageCited by: 23
Author(s): Eliska Jankovska, Marek Svitek, Karel Holada, Jiřı́ Petrák
Software Mentions: 3
Published: over 5 years ago
10.1016/j.dib.2019.104587
Estradiol and genistein effects on the sea bass (Dicentrarchus labrax) scales: Transcriptome datasetCited by: 4
Author(s): Patrícia I. S. Pinto, André R. Andrade, Michael A. S. Thorne, M. Dulce Estêvão, Adelino V.M. Canário, Deborah M. Power
Software Mentions: 3
Published: almost 5 years ago
10.3389/fcell.2020.00678
Cofilin-1 Is a Mechanosensitive Regulator of TranscriptionCited by: 3
Author(s): Catarina Domingues, Argemiro Geraldo, Sandra I. Anjo, Ana Catarina Matos, Cláudio M.R. Almeida, Inês Caramelo, José A. Lopes‐da‐Silva, Artur Paiva, J. Carvalho, Rita Neves, Bruno Manadas, Mário Grãos
Software Mentions: 3
Published: over 4 years ago
10.3389/fncel.2020.00185
Absence of Plekhg5 Results in Myelin Infoldings Corresponding to an Impaired Schwann Cell Autophagy, and a Reduced T-Cell Infiltration Into Peripheral NervesCited by: 3
Author(s): Patrick Lüningschrör, Carsten Slotta, Peter Heimann, Michael Briese, Ulrich M. Weikert, Bita Massih, Silke Appenzeller, Michael Sendtner, Christian Kaltschmidt, Barbara Kaltschmidt
Software Mentions: 3
Published: over 4 years ago
10.3389/fncel.2020.00239
The CNS Myelin Proteome: Deep Profile and Persistence After Post-mortem DelayCited by: 46
Author(s): Olaf Jahn, Sophie B Siems, Kathrin Kusch, Dörte Hesse, Ramona B. Jung, Thomas Liepold, Marina Uecker, Ting Sun, Hauke Werner
Software Mentions: 3
Published: over 4 years ago
10.3389/fncel.2014.00148
Deregulated expression of cytoskeleton related genes in the spinal cord and sciatic nerve of presymptomatic SOD1G93A Amyotrophic Lateral Sclerosis mouse modelCited by: 24
Author(s): Jéssica Ruivo Maximino, Gilson Pereira de Oliveira, Chrystian Junqueira Alves, Gerson Chadi
Software Mentions: 3
Published: over 10 years ago
10.3389/fimmu.2019.02708
TcellSubC: An Atlas of the Subcellular Proteome of Human T CellsCited by: 13
Author(s): Rubin Narayan Joshi, Charlotte Stadler, Robert Lehmann, Janne Lehtiö, Jesper Tegnér, Angelika Schmidt, Mattias Vesterlund
Software Mentions: 3
Published: almost 5 years ago
10.3389/fimmu.2019.01019
IRF1 Maintains Optimal Constitutive Expression of Antiviral Genes and Regulates the Early Antiviral ResponseCited by: 67
Author(s): Debasis Panda, Erisa Gjinaj, Mahesh Bachu, Erica Squire, Hilary Novatt, Keiko Ozato, Ronald L. Rabin
Software Mentions: 3
Published: over 5 years ago
10.3389/fimmu.2021.707298
Effects of Combinatorial Ubiquitinated Protein-Based Nanovaccine and STING Agonist in Mice With Drug-Resistant and Metastatic Breast CancerCited by: 4
Author(s): Fang Huang, Ning Pan, Yi-ting Wei, Jinjin Zhao, Mohanad Aldarouish, Xuru Wang, Xiaotong Sun, Wen Zhang, Yongqiang Chen, Lixin Wang
Software Mentions: 3
Published: about 3 years ago
10.3389/fimmu.2021.535039
Complex Interplay Between MAZR and Runx3 Regulates the Generation of Cytotoxic T Lymphocyte and Memory T CellsCited by: 3
Author(s): Alexandra Franziska Gülich, Ramona Rica, Caroline Tizian, Csilla Viczenczová, Kseniya Khamina, Thomas Faux, Daniela Hainberger, Thomas Penz, Rémy Bosselut, Christoph Bock, Asta Laiho, Laura L. Elo, Andréas Bergthaler, Wilfried Ellmeier, Shoji Sakaguchi
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2018.00912
Discrimination Between Human Leukocyte Antigen Class I-Bound and Co-Purified HIV-Derived Peptides in Immunopeptidomics WorkflowsCited by: 38
Author(s): Thomas Partridge, Annalisa Nicastri, Anna E. Kliszczak, L M Yindom, Benedikt M. Kessler, Nicola Ternette, Persephone Borrow
Software Mentions: 3
Published: over 6 years ago
10.3389/fimmu.2020.01430
Characterization of a Novel Compound That Stimulates STING-Mediated Innate Immune Activity in an Allele-Specific MannerCited by: 6
Author(s): Jinu Abraham, Sara Botto, Nobuyo Mizuno, Kara Pryke, Bryan Gall, Dylan T. Boehm, Tina Sali, Haihong Jin, Aaron Nilsen, Michael Gough, Jason R. Baird, Marita Chakhtoura, Caroline Subra, Lydie Trautmann, Elias K. Haddad, Victor R. DeFilippis
Software Mentions: 3
Published: over 4 years ago
10.3389/fphar.2020.612573
miRNome profiling of LSC-enriched CD34+CD38−CD26+ fraction in Ph+ CML-CP samples from Argentinean patients: a potential new pharmacogenomic toolCited by: 9
Author(s): María Sol Ruiz, María Belén Sánchez, Simone Bonecker, Carolina Furtado, Daniel Koile, Patricio Yankilevich, Santiago Cranco, Maria Del Rosario Custidiano, Josefina Freitas, Beatriz Moiraghi, Mariel Ana Pérez, Carolina Pavlovsky, Ana Inés Varela, Verónica Ventriglia, Julio César Sánchez Ávalos, Irene Larripa, Ilana Zalcberg, José Mordoh, Peter Valent, Michele Bianchini
Software Mentions: 3
Published: almost 4 years ago
10.3389/fpls.2021.641232
Management After Windstorm Affects the Composition of Ectomycorrhizal Symbionts of Regenerating Trees but Not Their Mycorrhizal NetworksCited by: 0
Author(s): Petra Veselá, Martina Vašutová, Magda Edwards‐Jonášová, Filip Holub, Peter Fleischer, Pavel Cudlín
Software Mentions: 3
Published: over 3 years ago
10.3389/fpls.2021.691790
Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in ArabidopsisCited by: 7
Author(s): Anna‐Lisa Paul, Natasha J. Haveman, Brandon Califar, Robert J. Ferl
Software Mentions: 3
Published: about 3 years ago
10.3389/fpls.2018.01218
Distinct Lotus japonicus Transcriptomic Responses to a Spectrum of Bacteria Ranging From Symbiotic to PathogenicCited by: 35
Author(s): Simon Kelly, Terry Mun, Jens Stougaard, Cécile Ben, Stig Uggerhøj Andersen
Software Mentions: 3
Published: over 6 years ago
10.3389/fpls.2016.01020
Low Temperature and Short-Term High-CO2 Treatment in Postharvest Storage of Table Grapes at Two Maturity Stages: Effects on Transcriptome ProfilingCited by: 30
Author(s): Raquel Rosales, Irene Romero, Carlos Fernández-Caballero, M. Isabel Escribano, Carmen Merodio, Marı́a T. Sanchez-Ballesta
Software Mentions: 3
Published: over 8 years ago
10.3390/genes11080943
Distinct Alteration of Gene Expression Programs in the Small Intestine of Male and Female Mice in Response to Ablation of Intestinal Fabp GenesCited by: 6
Author(s): Yiheng Chen, Luis B. Agellon
Software Mentions: 3
Published: over 4 years ago
10.1038/s41438-018-0087-1
Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimumCited by: 16
Author(s): Yanmin Zhu, Jonathan Shao, Zhe Zhou, Robert E. Davis
Software Mentions: 3
Published: almost 6 years ago
10.1242/jcs.221606
The N-cadherin interactome in primary cardiomyocytes as defined by quantitative proximity proteomicsCited by: 39
Author(s): Li Yang, Chelsea D. Merkel, Xuemei Zeng, Jonathon A. Heier, Pamela S. Cantrell, Mai Sun, Donna B. Stolz, Simon C. Watkins, Nathan A. Yates, Adam V. Kwiatkowski
Software Mentions: 3
Published: almost 6 years ago
10.1371/journal.ppat.1007030
A global regulatory system links virulence and antibiotic resistance to envelope homeostasis in Acinetobacter baumanniiCited by: 70
Author(s): Edward Geisinger, Nadav J. Mortman, Germán Vargas-Cuebas, Albert Tai, Ralph R. Isberg
Software Mentions: 3
Published: over 6 years ago
10.1371/journal.ppat.1008621
CD11cHi monocyte-derived macrophages are a major cellular compartment infected by Mycobacterium tuberculosisCited by: 30
Author(s): Jin‐Hee Lee, Shayla Boyce, Jennifer Powers, Christina E. Baer, Christopher M. Sassetti, Samuel M. Behar
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-019-44574-9
Vitamin D and Wnt3A have additive and partially overlapping modulatory effects on gene expression and phenotype in human colon fibroblastsCited by: 19
Author(s): Gemma Ferrer-Mayorga, Núria Niell, Ramón Cantero, José Manuel González‐Sancho, Luis del Peso, Alberto Múñoz, María Jesús Larriba
Software Mentions: 3
Published: over 5 years ago
10.1126/scitranslmed.abg7673
Exaggerated IL-17A activity in human in vivo recall responses discriminates active tuberculosis from latent infection and cured diseaseCited by: 27
Author(s): Gabriele Pollara, Chris Turner, Joshua Rosenheim, Aneesh Chandran, Lucy Bell, Ayesha Khan, Amit A. Patel, Luis Felipe Peralta, Anna Folino, Ayse U. Akarca, Cristina Venturini, Tina Baker, Simone Ecker, Fabio Luigi Massimo Ricciardolo, Teresa Marafioti, César Ugarte-Gil, David Moore, Benjamin M. Chain, Gillian S. Tomlinson, Mahdad Noursadeghi
Software Mentions: 3
Published: over 3 years ago
10.3390/toxins10010005
Carbon Dioxide Mediates the Response to Temperature and Water Activity Levels in Aspergillus flavus during Infection of Maize KernelsCited by: 29
Author(s): Matthew K. Gilbert, Ángel Medina, Brian M. Mack, Matthew D. Lebar, Alicia Rodríguez, Deepak Bhatnagar, Naresh Magan, Gregory R. OBrian, Gary A. Payne
Software Mentions: 3
Published: almost 7 years ago
10.1128/mBio.02096-17
The Essential Genome of <i>Escherichia coli</i> K-12Cited by: 204
Author(s): Emily C. A. Goodall, Ashley Robinson, Iain G. Johnston, Sara Jabbari, A. Keith Turner, Adam F. Cunningham, Peter A. Lund, Jeffrey A. Cole, Ian R. Henderson
Software Mentions: 3
Published: over 6 years ago
10.7554/eLife.56731
A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegansCited by: 36
Author(s): Kevin I. Manage, Alicia K. Rogers, Dylan C Wallis, Celja J Uebel, Dorian C. Anderson, Dieu An H Nguyen, Katerina Arca, Kristen C. Brown, Ricardo J. Cordeiro Rodrigues, Bruno F.M. de Albuquerque, René F. Ketting, Taiowa A. Montgomery, Carolyn M. Phillips
Software Mentions: 3
Published: over 4 years ago
10.7554/eLife.54572
Building the vertebrate codex using the gene breaking protein trap libraryCited by: 10
Author(s): Noriko Ichino, MaKayla R Serres, Rhianna Urban, Mark D. Urban, Anthony J. Treichel, Kyle Schaefbauer, Lauren E Greif, Gaurav K. Varshney, Kimberly J. Skuster, Melissa McNulty, Camden L Daby, Ying Wang, Hsin-Kai Liao, Suzan El‐Rass, Yonghe Ding, Weibin Liu, Jennifer L. Anderson, Mark D Wishman, Ankit Sabharwal, Lisa A. Schimmenti, Sridhar Sivasubbu, Darius Balciunas, Matthias Hammerschmidt, Steven A. Farber, Xiang Wen, Xiaolei Xu, Maura McGrail, Jeffrey J. Essner, Shawn M. Burgess, Karl J. Clark, Stephen C. Ekker
Software Mentions: 3
Published: over 4 years ago
10.7554/eLife.28129
CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitnessCited by: 32
Author(s): Adam Norris, Xicotencatl Gracida, John A. Calarco
Software Mentions: 3
Published: over 7 years ago
10.7554/eLife.44597
The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell–cell adhesionCited by: 25
Author(s): Gareth W. Fearnley, Kung Chia Young, James R. Edgar, Robin Antrobus, Iain M. Hay, Wei‐Ching Liang, Nadia Martínez‐Martín, Wei‐Yu Lin, Janet E. Deane, Hayley J. Sharpe
Software Mentions: 3
Published: over 5 years ago
10.3390/ijms21114070
Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4Cited by: 7
Author(s): Rui Shi, Dilip R. Panthee
Software Mentions: 3
Published: over 4 years ago
10.18632/oncotarget.18910
Integrated analysis of the molecular action of Vorinostat identifies epi-sensitised targets for combination therapyCited by: 3
Author(s): Jodie Hay, Katrina M. Lappin, Fabio G. Liberante, Laura M. Kettyle, Kyle B. Matchett, Alexander Thompson, Ken Mills
Software Mentions: 3
Published: over 7 years ago
10.18632/oncotarget.25764
Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencingCited by: 5
Author(s): Lilla Ozgyin, Attila Horváth, Bálint László Bálint
Software Mentions: 3
Published: over 6 years ago
10.1155/2019/4606219
A Bioinformatic Approach for the Identification of Molecular Determinants of Resistance/Sensitivity to Cancer ThermotherapyCited by: 7
Author(s): Mustafa Düzgün, Konstantinos Theofilatos, Alexandros G. Georgakilas, Athanasia Pavlopoulou
Software Mentions: 3
Published: about 5 years ago
10.3390/nu12020544
Consumption of the Total Western Diet Promotes Colitis and Inflammation-Associated Colorectal Cancer in MiceCited by: 29
Author(s): Abby D. Benninghoff, Korry Hintze, Stephany P. Monsanto, Daphne Rodriguez, Ashli Hunter, Sumira Phatak, James J. Pestka, Arnaud J. Van Wettere, Robert E. Ward
Software Mentions: 3
Published: almost 5 years ago
10.3389/fimmu.2019.02851
Docosahexaenoic Acid Consumption Impedes Early Interferon- and Chemokine-Related Gene Expression While Suppressing Silica-Triggered Flaring of Murine LupusCited by: 17
Author(s): Abby D. Benninghoff, Melissa A. Bates, Preeti Chauhan, Kathryn A. Wierenga, Kristen N. Gilley, Andrij Holian, Jack R. Harkema, James J. Pestka
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2164-10-410
Transcriptional response of the model planctomycete Rhodopirellula baltica SH1T to changing environmental conditionsCited by: 47
Author(s): Patricia Wecker, Christine Klockow, Andreas Ellrott, Christian Quast, Philipp Langhammer, Jens Harder, Frank Oliver Glöckner
Software Mentions: 2
Published: about 15 years ago
10.3389/fmed.2020.00568
Borrelia burgdorferi-Induced Changes in the Class II Self-Immunopeptidome Displayed on HLA-DR Molecules Expressed by Dendritic CellsCited by: 4
Author(s): Maria G. Gutierrez-Hoffmann, Robert N. O’Meally, Robert N. Cole, Eleni Tiniakou, Erika Darrah, Mark J. Soloski
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0189492
Impact of maternal high fat diet on hypothalamic transcriptome in neonatal Sprague Dawley ratsCited by: 22
Author(s): Sanna Barrand, Tamsyn M. Crowley, Ryan J Wood-Bradley, Kirstie A. De Jong, James A. Armitage
Software Mentions: 2
Published: almost 7 years ago
10.3389/fmicb.2016.00968
Flow Cytometric and 16S Sequencing Methodologies for Monitoring the Physiological Status of the Microbiome in Powdered Infant Formula ProductionCited by: 12
Author(s): Amir H. P. Anvarian, Yu Cao, Shabarinath Srikumar, Séamus Fanning, Kieran Jordan
Software Mentions: 2
Published: over 8 years ago
10.3389/fmicb.2012.00415
Comparative Molecular Microbial Ecology of the Spring Haptophyte Bloom in a Greenland Arctic Oligosaline LakeCited by: 16
Author(s): Susanna Theroux, Yongsong Huang, Linda Amaral‐Zettler
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0143261
Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Genotypes That Are Susceptible, Resistant, and Hypersensitive to Reniform Nematode (Rotylenchulus reniformis)Cited by: 16
Author(s): Ruijuan Li, Aaron M. Rashotte, Narendra K. Singh, Kathy Lawrence, David Weaver, Robert D. Locy
Software Mentions: 2
Published: about 9 years ago
10.3389/fmolb.2021.643178
In vivo N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix BuildingCited by: 14
Author(s): Cédric Leduc, Laura Dupont, Loïc Joannes, Christine Monseur, Dominique Baiwir, Gabriel Mazzucchelli, Christophe Deroanne, Alain Colige, Mourad Bekhouche
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0036911
VENNTURE–A Novel Venn Diagram Investigational Tool for Multiple Pharmacological Dataset AnalysisCited by: 64
Author(s): Bronwen Martin, Wayne Chadwick, Tie Yi, Sung Soo Park, Da Yong Lu, Bin Ni, Shekhar K. Gadkaree, Kathleen Farhang, Kevin G. Becker, Stuart Maudsley
Software Mentions: 2
Published: over 12 years ago
10.1186/s12864-016-3039-x
Allyl-isothiocyanate treatment induces a complex transcriptional reprogramming including heat stress, oxidative stress and plant defence responses in Arabidopsis thalianaCited by: 24
Author(s): Ralph Kissen, Anders Øverby, Per Winge, Atle M. Bones
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pone.0225697
Quantitative dynamics of Salmonella and E. coli in feces of feedlot cattle treated with ceftiofur and chlortetracyclineCited by: 11
Author(s): Naomi Ohta, Bo Norby, Guy H. Loneragan, Javier Vinasco, Henk C. den Bakker, Sara D. Lawhon, Keri N. Norman, H. M. Scott
Software Mentions: 2
Published: almost 5 years ago
10.7554/eLife.63886
A KDM5–Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formationCited by: 12
Author(s): Hayden A. M. Hatch, Helen M. Belálcazar, Owen J. Marshall, Julie Secombe
Software Mentions: 2
Published: over 3 years ago
10.18632/oncotarget.10701
Comparative study of whole genome amplification and next generation sequencing performance of single cancer cellsCited by: 55
Author(s): Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P. McMullin, Denis A. Smirnov, Weimin Liu, Maria Geffken, Klaus Pantel, Simon A. Joosse
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2021.637959
Differential Regulation of the Ribosomal Association of mRNA Transcripts in an Arabidopsis Mutant Defective in Jasmonate-Dependent Wound ResponseCited by: 7
Author(s): Athen Kimberlin, Rebekah E Holtsclaw, Abraham J. Koo
Software Mentions: 2
Published: over 3 years ago
10.1186/s12967-016-0926-5
Long noncoding RNA dysregulation in ischemic heart failureCited by: 164
Author(s): Simona Greco, Germana Zaccagnini, Alessandra Perfetti, Paola Fuschi, Rea Valaperta, Christine Voellenkle, Serenella Castelvecchio, Carlo Gaetano, Nicoletta Finato, Antonio Paolo Beltrami, Lorenzo Menicanti, Fabio Martelli
Software Mentions: 2
Published: over 8 years ago
10.3389/fpls.2016.00251
Overlapping Yet Response-Specific Transcriptome Alterations Characterize the Nature of Tobacco–Pseudomonas syringae InteractionsCited by: 17
Author(s): Zoltán Bozsó, Péter G. Ott, Evelin Kámán-Tóth, Gábor Bognár, Miklós Pogány, Ágnes Szatmári
Software Mentions: 2
Published: over 8 years ago
10.3390/nu13051462
Hepatic Transcriptome Profiling Reveals Lack of Acsm3 Expression in Polydactylous Rats with High-Fat Diet-Induced Hypertriglyceridemia and Visceral Fat AccumulationCited by: 3
Author(s): Kristýna Junková, Lukáš F Mirchi, Blanka Chylíková, M Janků, Jan Šilhavý, Martina Hüttl, Irena Marková, Denisa Miklánková, Josef Včelák, Hana Malínská, Michal Pravenec, Ondřej Šeda, František Liška
Software Mentions: 2
Published: over 3 years ago
10.3389/fpls.2017.00166
Differential Transcriptional Regulation in Roots of Tomato Near-Isogenic Lines in Response to Rapid-Onset Water StressCited by: 4
Author(s): Erin M. Arms, Zhanghang Yan, Dina A. St. Clair
Software Mentions: 2
Published: almost 8 years ago
10.1186/s12862-019-1476-2
Rare coral under the genomic microscope: timing and relationships among Hawaiian MontiporaCited by: 14
Author(s): Regina L. Cunha, Zac H. Forsman, Roy Belderok, Ingrid S. Knapp, Rita Castilho, Robert J. Toonen
Software Mentions: 2
Published: over 5 years ago
10.1590/1678-4685-GMB-2017-0264
De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae)Cited by: 8
Author(s): Ana Lúcia Anversa Segatto, José Francisco Diesel, Élgion Lúcio da Silva Loreto, João Batista Teixeira da Rocha
Software Mentions: 2
Published: over 6 years ago
10.1186/gb-2010-11-8-r82
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitorsCited by: 161
Author(s): Steven J.M. Jones, Janessa Laskin, Yvonne Y. Li, Obi L. Griffith, Jianghong An, Mikhail Bilenky, Yaron S.N. Butterfield, Timothée Cézard, Eric Chuah, Richard Corbett, Anthony P. Fejes, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D. Morin, Trevor J. Pugh, Tesa Severson, Sohrab P. Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas A. Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A. Moore, David G. Huntsman, İnanç Birol, Martin Hirst, Robert A. Holt, Marco A. Marra
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pone.0132090
Yeast m6A Methylated mRNAs Are Enriched on Translating Ribosomes during Meiosis, and under Rapamycin TreatmentCited by: 71
Author(s): Zsuzsanna Bódi, Andrew Bottley, Nathan Archer, Sean May, Rupert G. Fray
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.pone.0076487
Transcriptomics of the Rice Blast Fungus Magnaporthe oryzae in Response to the Bacterial Antagonist Lysobacter enzymogenes Reveals Candidate Fungal Defense Response GenesCited by: 30
Author(s): Sandra M. Mathioni, Nrupali Patel, Bianca Riddick, James A. Sweigard, Kirk J. Czymmek, Jeffrey Caplan, Sridhara G. Kunjeti, Saritha Kunjeti, Vidhyavathi Raman, Bradley I. Hillman, Donald Y. Kobayashi, Nicole Donofrio
Software Mentions: 2
Published: about 11 years ago
10.3390/ijms17111824
Effect of High-Carbohydrate Diet on Plasma Metabolome in Mice with Mitochondrial Respiratory Chain Complex III DeficiencyCited by: 11
Author(s): Jayasimman Rajendran, Nikica Tomašić, Heike Kotarsky, Eva Ekvall Hansson, Vidya Velagapudi, Jukka Kallijärvi, Vineta Fellman
Software Mentions: 2
Published: about 8 years ago
10.1172/jci.insight.141264
Solving an MHC allele–specific bias in the reported immunopeptidomeCited by: 19
Author(s): Martin G. Klatt, Kyeara N. Mack, Yang Bai, Zita E.H. Aretz, Levy Nathan, Sung Soo Mun, Tao Dao, David A. Scheinberg
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0123661
A Protein Deep Sequencing Evaluation of Metastatic Melanoma TissuesCited by: 20
Author(s): Charlotte Welinder, Krzysztof Pawłowski, Y. Sugita, Maria Yakovleva, Göran Jönsson, Christian Ingvar, Lotta Lundgren, Bo Baldetorp, Håkan Olsson, Melinda Rezeli, Bo Jansson, Thomas Laurell, Thomas E. Fehniger, Balázs Döme, Johan Malm, Elisabet Wieslander, Toshihide Nishimura, György Markó-Varga
Software Mentions: 2
Published: over 9 years ago
10.1186/2041-1480-3-7
GO2PUB: Querying PubMed with semantic expansion of gene ontology termsCited by: 12
Author(s): Charles Bettembourg, Christian Diot, Anita Burgun, Olivier Dameron
Software Mentions: 2
Published: almost 13 years ago
10.3390/ijms20122998
Transcriptomic Insights into the Response of the Olfactory Bulb to Selenium Treatment in a Mouse Model of Alzheimer’s DiseaseCited by: 11
Author(s): Rui Zheng, Zhonghao Zhang, Yuxi Zhao, Chen Chen, Shi-Zheng Jia, Xian-Chun Cao, Liming Shen, Jiazuan Ni, Guo-Li Song
Software Mentions: 2
Published: over 5 years ago
10.1093/jxb/erx067
Differential gene expression and transport functionality in the bundle sheath versus mesophyll – a potential role in leaf mineral homeostasisCited by: 23
Author(s): Noa Wigoda, Metsada Pasmanik‐Chor, Ting Yang, Ling Yu, Menachem Moshelion, Nava Moran
Software Mentions: 2
Published: over 7 years ago
10.1186/s12859-015-0611-3
InteractiVenn: a web-based tool for the analysis of sets through Venn diagramsCited by: 1,336
Author(s): Henry Heberle, Gabriela Vaz Meirelles, Felipe Rodrigues da Silva, Guilherme P. Telles, Rosane Minghim
Software Mentions: 2
Published: over 9 years ago
10.1186/1471-2105-11-87
Lists2Networks: Integrated analysis of gene/protein listsCited by: 39
Author(s): Alexander Lachmann, Avi Ma’ayan
Software Mentions: 2
Published: almost 15 years ago
10.1371/journal.pone.0071084
Genomic Profiling Reveals That Transient Adipogenic Activation Is a Hallmark of Mouse Models of Skeletal Muscle RegenerationCited by: 61
Author(s): Laura Lukjanenko, Sophie Brachat, Eliane Pierrel, Estelle Lach-Trifilieff, Jérôme N. Feige
Software Mentions: 2
Published: over 11 years ago
10.1073/pnas.1911622116
Contribution of proteasome-catalyzed peptide <i>cis</i> -splicing to viral targeting by CD8 <sup>+</sup> T cells in HIV-1 infectionCited by: 44
Author(s): Wayne Paes, German Leonov, Thomas Partridge, Takayuki Chikata, Hayato Murakoshi, Anna Frangou, Simon Brackenridge, Annalisa Nicastri, Andrew G. Smith, Gerald H. Learn, Yingying Li, Robert Parker, Shinichi Oka, Pierre Pellegrino, Ian Williams, Barton F. Haynes, Andrew J. McMichael, George M. Shaw, Beatrice H. Hahn, Masafumi Takiguchi, Nicola Ternette, Persephone Borrow
Software Mentions: 2
Published: about 5 years ago
10.1186/1477-5956-10-40
Comparative proteomic analysis of transition of saccharomyces cerevisiae from glucose-deficient medium to glucose-rich mediumCited by: 18
Author(s): Bennett J. Giardina, Bruce A. Stanley, Hung‐Lung Chiang
Software Mentions: 2
Published: over 12 years ago
10.1186/1477-5956-12-9
Glucose induces rapid changes in the secretome of Saccharomyces cerevisiaeCited by: 41
Author(s): Bennett J. Giardina, Bruce A. Stanley, Hung‐Lung Chiang
Software Mentions: 2
Published: almost 11 years ago
10.1186/s12953-017-0119-z
Characterisation of the circulating acellular proteome of healthy sheep using LC-MS/MS-based proteomics analysis of serumCited by: 8
Author(s): Saul Chemonges, Rajesh Gupta, Paul C. Mills, Steven Kopp, Paweł Sadowski
Software Mentions: 2
Published: almost 8 years ago
10.3390/proteomes9010004
Targeted Quantification of the Lysosomal Proteome in Complex SamplesCited by: 12
Author(s): Peter Mosen, Anne Sanner, Jasjot Singh, Dominic Winter
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0012088
Sox6 Is Necessary for Efficient Erythropoiesis in Adult Mice under Physiological and Anemia-Induced Stress ConditionsCited by: 27
Author(s): Bogdan Dumitriu, Pallavi Bhattaram, Peter Dy, Yuanshuai Huang, Nayeem Quayum, Jan Jensen, Véronique Lefebvre
Software Mentions: 2
Published: over 14 years ago
10.1038/srep25756
Proteome-wide alterations on adipose tissue from obese patients as age-, diabetes- and gender-specific hallmarksCited by: 45
Author(s): María Gómez-Serrano, Emilio Camafeita, Eva García-Santos, Juan Antonio López, Miguel A. Rubio, Andrés Sánchez‐Pernaute, Antonio Torres, Jesús Vázquez, Belén Peral
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pgen.1004249
Widespread Use of Non-productive Alternative Splice Sites in Saccharomyces cerevisiaeCited by: 80
Author(s): Tadashi Kawashima, Stephen M. Douglass, Jason Gabunilas, Matteo Pellegrini, Guillaume Chanfreau
Software Mentions: 2
Published: over 10 years ago
10.1038/srep44786
Complete genome sequencing and antibiotics biosynthesis pathways analysis of Streptomyces lydicus 103Cited by: 14
Author(s): Jun Nan, Ming-Zhu Ding, Hao Luo, Feng Gao, Yuan Yang
Software Mentions: 2
Published: over 7 years ago
10.1038/srep45221
Veratridine produces distinct calcium response profiles in mouse Dorsal Root Ganglia neuronsCited by: 17
Author(s): Zainab A. Mohammed, Ciara Doran, David Grundy, Mohammed A. Nassar
Software Mentions: 2
Published: over 7 years ago
10.1038/s41598-017-05102-9
Directional Exosome Proteomes Reflect Polarity-Specific Functions in Retinal Pigmented Epithelium MonolayersCited by: 69
Author(s): Mikael Klingeborn, W. Michael Dismuke, Nikolai P. Skiba, Una Kelly, W. Daniel Stamer, Catherine Bowes Rickman
Software Mentions: 2
Published: over 7 years ago
10.3390/plants10091802
Transcriptome Analyses of Barley Roots Inoculated with Novel Paenibacillus sp. and Erwinia gerundensis Strains Reveal Beneficial Early-Stage Plant–Bacteria InteractionsCited by: 9
Author(s): Tongda Li, Ross Mann, Jatinder Kaur, Germán Spangenberg, Tim Sawbridge
Software Mentions: 2
Published: about 3 years ago
10.7717/peerj.4449
First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq dataCited by: 9
Author(s): Jan D Brüwer, Christian R. Voolstra
Software Mentions: 2
Published: over 6 years ago
10.1038/s41598-018-37856-1
Blood-based analysis of type-2 diabetes mellitus susceptibility genes identifies specific transcript variants with deregulated expression and association with disease riskCited by: 20
Author(s): Maria-Ioanna Christodoulou, Margaritis Avgeris, Ioanna Kokkinopoulou, Eirini Maratou, Panagiota Mitrou, Christos K. Kontos, Efthimios Pappas, Eleni Boutati, Andreas Scorilas, Emmanuel G. Fragoulis
Software Mentions: 2
Published: almost 6 years ago
10.1038/s41598-019-41210-4
The VQ motif-containing proteins in the diploid and octoploid strawberryCited by: 11
Author(s): José Garrido-Gala, José Javier Higuera, Juan Muñoz‐Blanco, Francisco Amil-Ruíz, José L. Caballero
Software Mentions: 2
Published: over 5 years ago
10.1007/s10456-015-9485-2
The decrease in histone methyltransferase EZH2 in response to fluid shear stress alters endothelial gene expression and promotes quiescenceCited by: 59
Author(s): Monika Maleszewska, Byambasuren Vanchin, Martin C. Harmsen, Guido Krenning
Software Mentions: 2
Published: about 9 years ago
10.1038/s41598-019-46638-2
Poorly controlled diabetes during pregnancy and lactation activates the Foxo1 pathway and causes glucose intolerance in adult offspringCited by: 6
Author(s): Yukihiro Inoguchi, Kenji Ichiyanagi, Hiroaki Ohishi, Yasutaka Maeda, Noriyuki Sonoda, Yoshihiro Ogawa, Toyoshi Inoguchi, Hidetada Sasaki
Software Mentions: 2
Published: over 5 years ago
10.7717/peerj.4615
miRNAome expression profiles in the gonads of adultMelopsittacus undulatusCited by: 7
Author(s): Lan Jiang, Qingqing Wang, Jie Yu, Vinita Gowda, Gabriel Johnson, Junli Yang, Xianzhao Kan, Xuefei Yang
Software Mentions: 2
Published: over 6 years ago
10.11604/pamj.2019.34.67.17993
Pathology of Senegalese breast cancersCited by: 10
Author(s): Megan B. Fitzpatrick, Mara H. Rendi, Nancy B. Kiviat, Pape Moussa Touré, Amadou Dem, Papa Salif Sow, Stephen E. Hawes, Qinghua Feng, Kimberly H. Allison
Software Mentions: 2
Published: about 5 years ago
10.3390/v13050797
Characterization of Extracellular Vesicles Secreted in Lentiviral Producing HEK293SF Cell CulturesCited by: 7
Author(s): Aline Do Minh, Alexandra T. Star, Jacek Stupak, Kelly M. Fulton, Arsalan S. Haqqani, Jean-François Gélinas, Jianjun Li, Susan M. Twine, Amine Kamen
Software Mentions: 2
Published: over 3 years ago
10.1080/21505594.2021.1982501
Unique virulence role of post-translocational chaperone PrsA in shaping <i>Streptococcus pyogenes</i> secretomeCited by: 5
Author(s): Zehua Wu, Anaamika Campeau, Chao-Hsien Liu, David J. Gonzalez, M. Yamaguchi, Shigetada Kawabata, Chieh-Hsien Lu, Chian-Yu Lai, Hao-Chieh Chiu, Yung-Chi Chang
Software Mentions: 2
Published: about 3 years ago