cran: BioVenn | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0141171

T Cell Transcriptomes Describe Patient Subtypes in Systemic Lupus Erythematosus
Cited 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 filtrate
Cited 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 Infection
Cited by: 39
Author(s): Sara Ocaña, Pedro Seoane, Rocío Bautista, Carmen Palomino, M. Gonzalo Claros, A. M. Torres, Eva Madrid
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0156018

Proteomic Study of Entamoeba histolytica Trophozoites, Cysts, and Cyst-Like Structures
Cited 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 Ellipses
Cited 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 steatosis
Cited 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 Cells
Cited 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 Wheat
Cited 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 control
Cited 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 treatment
Cited 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 coverage
Cited 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 dataset
Cited 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 Transcription
Cited 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 Nerves
Cited 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 Delay
Cited 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: about 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 model
Cited 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 Cells
Cited 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 Response
Cited 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 Cancer
Cited 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 Cells
Cited 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 Workflows
Cited 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 Manner
Cited 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 tool
Cited 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 Networks
Cited 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 Arabidopsis
Cited 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 Pathogenic
Cited by: 35
Author(s): Simon Kelly, Terry Mun, Jens Stougaard, Cécile Ben, Stig Uggerhøj Andersen
Software Mentions: 3
Published: about 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 Profiling
Cited 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 Genes
Cited by: 6
Author(s): Yiheng Chen, Luis B. Agellon
Software Mentions: 3
Published: about 4 years ago

10.1038/s41438-018-0087-1

Genotype-specific suppression of multiple defense pathways in apple root during infection by Pythium ultimum
Cited 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 proteomics
Cited 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 baumannii
Cited 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 tuberculosis
Cited 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 fibroblasts
Cited 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 disease
Cited 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 Kernels
Cited 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 Escherichia coli K-12
Cited 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. elegans
Cited 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 library
Cited 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: about 4 years ago

10.7554/eLife.28129

CRISPR-mediated genetic interaction profiling identifies RNA binding proteins controlling metazoan fitness
Cited 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 adhesion
Cited 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 T4
Cited 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 therapy
Cited 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 sequencing
Cited 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 Thermotherapy
Cited by: 7
Author(s): Mustafa Düzgün, Konstantinos Theofilatos, Alexandros G. Georgakilas, Athanasia Pavlopoulou
Software Mentions: 3
Published: almost 5 years ago

10.3390/nu12020544

Consumption of the Total Western Diet Promotes Colitis and Inflammation-Associated Colorectal Cancer in Mice
Cited 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: over 4 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 Lupus
Cited 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 conditions
Cited 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 Cells
Cited 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 rats
Cited 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 Production
Cited 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 Lake
Cited 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: almost 9 years ago

10.3389/fmolb.2021.643178

In vivo N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix Building
Cited 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 Analysis
Cited 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 thaliana
Cited 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 chlortetracycline
Cited 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 formation
Cited 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 cells
Cited 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 Response
Cited 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 failure
Cited 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 Interactions
Cited 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 Accumulation
Cited 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 Stress
Cited by: 4
Author(s): Erin M. Arms, Zhanghang Yan, Dina A. St. Clair
Software Mentions: 2
Published: over 7 years ago

10.1186/s12862-019-1476-2

Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora
Cited 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 inhibitors
Cited 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 Treatment
Cited 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 Genes
Cited 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 Deficiency
Cited 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 immunopeptidome
Cited 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 Tissues
Cited 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 terms
Cited 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 Disease
Cited 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 homeostasis
Cited 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 diagrams
Cited 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 lists
Cited by: 39
Author(s): Alexander Lachmann, Avi Ma’ayan
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0071084

Genomic Profiling Reveals That Transient Adipogenic Activation Is a Hallmark of Mouse Models of Skeletal Muscle Regeneration
Cited by: 61
Author(s): Laura Lukjanenko, Sophie Brachat, Eliane Pierrel, Estelle Lach-Trifilieff, Jérôme N. Feige
Software Mentions: 2
Published: about 11 years ago

10.1073/pnas.1911622116

Contribution of proteasome-catalyzed peptide cis -splicing to viral targeting by CD8 + T cells in HIV-1 infection
Cited 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: almost 5 years ago

10.1186/1477-5956-10-40

Comparative proteomic analysis of transition of saccharomyces cerevisiae from glucose-deficient medium to glucose-rich medium
Cited 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 cerevisiae
Cited by: 41
Author(s): Bennett J. Giardina, Bruce A. Stanley, Hung‐Lung Chiang
Software Mentions: 2
Published: over 10 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 serum
Cited 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 Samples
Cited 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 Conditions
Cited 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 hallmarks
Cited 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 cerevisiae
Cited 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 103
Cited 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 neurons
Cited 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 Monolayers
Cited 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 Interactions
Cited 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 data
Cited 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 risk
Cited 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 strawberry
Cited 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 quiescence
Cited 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 offspring
Cited 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 undulatus
Cited 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 cancers
Cited 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 Cultures
Cited 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 Streptococcus pyogenes secretome
Cited 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

Projects: cran: BioVenn

Papers Mentioning BioVenn 247