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10.3389/fcell.2020.613583

Extracellular Vesicles From Liver Progenitor Cells Downregulates Fibroblast Metabolic Activity and Increase the Expression of Immune-Response Related Molecules
Cited by: 0
Author(s): Félix Royo, Mikel Azkargorta, José Luis Lavín, Marc Clos-García, Ana R. Cortázar, Monika Gonzalez-Lopez, Laura Bárcena, Hernando A. del Portillo, María Yáñez‐Mó, Antonio Marcilla, Francesc E. Borràs, Héctor Peinado, Isabel Guerrero, Mar Valés‐Gómez, Unai Cereijo, Teresa Sardón, Ana M. Aransay, Félix Elortza, Juan Manuel Falcón‐Pérez
Software Mentions: 3
Published: almost 4 years ago

10.3389/fcell.2021.683861

Deletion of the Wilms’ Tumor Suppressor Gene in the Cardiac Troponin-T Lineage Reveals Novel Functions of WT1 in Heart Development
Cited by: 7
Author(s): Sandra Díaz Del Moral, Silvia Barrena, Francisco Hernández-Torres, Amelia Aránega, José Manuel Villaescusa, Juan José Gómez Doblas, Diego Franco, Manuel Jiménez‐Navarro, Ramón Muñoz‐Chápuli, Rita Carmona
Software Mentions: 3
Published: over 3 years ago

10.3389/fimmu.2020.01785

Pregnancy Downregulates Plasmablast Metabolic Gene Expression Following Influenza Without Altering Long-Term Antibody Function
Cited by: 5
Author(s): Dominika Swieboda, Elizabeth Q. Littauer, Jacob Beaver, Lisa K. Mills, Katherine M. Bricker, E. Stein Esser, Olivia Q Antao, Dahnide T Williams, Ioanna Skountzou
Software Mentions: 3
Published: over 4 years ago

10.3389/fimmu.2018.01344

Common Features of Regulatory T Cell Specialization During Th1 Responses
Cited by: 37
Author(s): Katharina Littringer, Claudia Moresi, Nikolas Rakebrandt, Xiaobei Zhou, Michelle Schorer, Tamas Dolowschiak, Florian Kirchner, Felix Rost, Christian W. Keller, Donal McHugh, Salomé LeibundGut‐Landmann, Mark D. Robinson, Nicole Joller
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2020.01968

Cytoplasmic Citrate Flux Modulates the Immune Stimulatory NKG2D Ligand MICA in Cancer Cells
Cited by: 10
Author(s): Sofie Hedlund Møller, Maiken Mellergaard, Mikkel Madsen, Amaia Vergara Bermejo, Stine Dam Jepsen, Marie Haugsten Hansen, Rikke Illum Høgh, Blanca I. Aldana, Claus Desler, Lene Juel Rasmussen, Elahu G. Sustarsic, Zachary Gerhart-Hines, Evangelia Daskalaki, Craig E. Wheelock, Thomas K. Hiron, Dazhen Lin, Christopher A. O’Callaghan, Hans H. Wandall, Lars Ole Andresen, Søren Skov
Software Mentions: 3
Published: over 4 years ago

10.3389/fmicb.2019.02610

Genetic, Epigenetic and Phenotypic Diversity of Four Bacillus velezensis Strains Used for Plant Protection or as Probiotics
Cited by: 29
Author(s): Oleg N. Reva, Dirk Swanevelder, Liberata Mwita, Aneth David Mwakilili, Dillon Muzondiwa, Monique Joubert, Wai Chan, Stefanie Lutz, Christian H. Ahrens, Lylia V. Avdeeva, М. А. Хархота, Donatha Damian Tibuhwa, Sylvester Leonard Lyantagaye, Joachim Vater, Rainer Borriss, Johan Meijer
Software Mentions: 3
Published: about 5 years ago

10.3389/fneur.2020.573575

Differential Glial Activation in Early Epileptogenesis—Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus
Cited by: 4
Author(s): Toni Berger, Magnus Dehli Vigeland, Hanne Sagsveen Hjorthaug, Cecilie G. Nome, Erik Taubøll, Kaja Kristine Selmer, Kjell Heuser
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2016.01692

A Developmental and Molecular View of Formation of Auxin-Induced Nodule-Like Structures in Land Plants
Cited by: 19
Author(s): Ryan Hiltenbrand, Jacklyn Thomas, Hannah McCarthy, Karl Dykema, Ashley Spurr, Hamilton Newhart, Mary E. Winn, Arijit Mukherjee
Software Mentions: 3
Published: about 8 years ago

10.3390/genes12030417

Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)
Cited by: 9
Author(s): Fulei Mo, Nian Zhang, Yefeng Qiu, Lingjun Meng, Mozhen Cheng, Jiayin Liu, Lanning Yao, Rui Lv, Yuxin Liu, Yao Zhang, Xiuling Chen, Aoxue Wang
Software Mentions: 3
Published: over 3 years ago

10.1016/j.gdata.2015.12.027

Transcriptional profiling of the epigenetic regulator Smchd1
Cited by: 12
Author(s): Ruijie Liu, Kelan Chen, Natasha Jansz, Marnie E. Blewitt, Matthew E. Ritchie
Software Mentions: 3
Published: over 8 years ago

10.1186/s13742-015-0091-4

Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
Cited by: 52
Author(s): Liang Wu, Xiaolong Zhang, Zhikun Zhao, Ling Wang, Bo Li, Guibo Li, Michael Dean, Qichao Yu, Yanhui Wang, Xinxin Lin, Weijian Rao, Zhanlong Mei, Yang Li, Runze Jiang, Huan Yang, Fuqiang Li, Guoyun Xie, Liqin Xu, Kui Wu, Jie Zhang, Jianghao Chen, Ting Wang, Karsten Kristiansen, Xiuqing Zhang, Yingrui Li, Huanming Yang, Jian Wang, Yong Hou, Xun Xu
Software Mentions: 3
Published: about 9 years ago

10.1093/gigascience/giy027

Whole-genome resequencing reveals signatures of selection and timing of duck domestication
Cited by: 70
Author(s): Zebin Zhang, Yaxiong Jia, Pedro Almeida, Judith E. Mank, Marcel van Tuinen, Qiong Wang, Zhihua Jiang, Yu Chen, Kai Zhan, Shuisheng Hou, Zhengkui Zhou, Huifang Li, Fan Yang, Yong He, Zhonghua Ning, Ning Yang, Lujiang Qu
Software Mentions: 3
Published: over 6 years ago

10.1080/19490976.2021.1939598

The commensal bacterium Lactiplantibacillus plantarum imprints innate memory-like responses in mononuclear phagocytes
Cited by: 5
Author(s): Aize Pellón, Diego Barriales, Ainize Peña‐Cearra, Janire Castelo-Careaga, Ainhoa Palacios, Nerea Lopez, Estíbaliz Atondo, Miguel Ángel Pascual-Itoiz, Itziar Martín-Ruiz, Leticia Sampedro, Monika Gonzalez-Lopez, Laura Bárcena, Teresa Martín-Mateos, José María Landete, Rafael Prados-Rosales, Laura Plaza-Vinuesa, Rosario Múñoz, Blanca de las Rivas, Juan Miguel Díaz Rodríguez, Edurne Berra, Ana M. Aransay, Leticia Abecia, José Luis Lavín, Héctor Rodríguez, Juan Anguíta
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41437-018-0181-z

Single-cell expression noise and gene-body methylation in Arabidopsis thaliana
Cited by: 30
Author(s): Róbert Horváth, Benjamin Laenen, Shohei Takuno, Tanja Slotte
Software Mentions: 3
Published: almost 6 years ago

10.1038/srep45560

Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle
Cited by: 54
Author(s): Lingzhao Fang, Goutam Sahana, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-017-15420-7

Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans
Cited by: 47
Author(s): Rhianna C. Laker, Christian Garde, Donny M. Camera, William J. Smiles, Juleen R. Zierath, John A. Hawley, Romain Barrès
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-018-34191-3

Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
Cited by: 12
Author(s): P. R. Brochmann, Andrew Hesketh, Bimal Jana, G. H. Brodersen, Luca Guardabassi
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-019-46948-5

Disruption of NOTCH signaling by a small molecule inhibitor of the transcription factor RBPJ
Cited by: 34
Author(s): Cecilia Hurtado, A. G. Safarova, Michael P. Smith, Raeeun Chung, Arne A.N. Bruyneel, Jorge Gómez-Galeno, Franz Oswald, Christopher J. Larson, John R. Cashman, Pilar Ruiz‐Lozano, Philip Janiak, Teri Suzuki, Mark Mercola
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-49440-2

Transgenerational Self-Reconstruction of Disrupted Chromatin Organization After Exposure To An Environmental Stressor in Mice
Cited by: 23
Author(s): Carlos Díaz-Castillo, Raquel Chamorro-García, Toshihiro Shioda, Bruce Blumberg
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-69758-6

Regulated expression and function of the GABAB receptor in human pancreatic beta cell line and islets
Cited by: 19
Author(s): Latif Rachdi, Alicia Maugein, Séverine Pechberty, Mathieu Armanet, Juliette Hamroune, Philippe Ravassard, Stéfano Marullo, Olivier Albagli, Raphaël Scharfmann
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-020-77606-w

The absence of (TCAGGG)n repeats in some telomeres, combined with variable responses to NR2F2 depletion, suggest that this nuclear receptor plays an indirect role in the alternative lengthening of telomeres
Cited by: 5
Author(s): Ahmed S. N. Alhendi, Nicola J. Royle
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-021-90412-2

Axonopathy precedes cell death in ocular damage mediated by blast exposure
Cited by: 9
Author(s): Nickolas Boehme, Adam Hedberg-Buenz, Nicole Tatro, Michael Bielecki, William C Castonguay, Todd E. Scheetz, Michael G. Anderson, Laura M. Dutca
Software Mentions: 3
Published: over 3 years ago

10.7150/thno.57237

The metabesity factor HMG20A potentiates astrocyte survival and reactive astrogliosis preserving neuronal integrity
Cited by: 14
Author(s): Petra I. Lorenzo, Eugenia Martin Vázquez, Livia López-Noriega, Esther Fuente-Martín, José Manuel Mellado-Gil, Jaime M. Franco, Nadia Cobo-Vuilleumier, José A. Guerrero-Martínez, Silvana Y. Romero-Zerbo, Jesús A Perez-Cabello, Sabrina Rivero, Antonio Campos‐Caro, Christian Claude Lachaud, Alejandra Crespo Barreda, Manuel Aguilar‐Diosdado, Esther Fuentes, Aléjandro Martín-Montalvo, Manuel Álvarez‐Dolado, Franz Martı́n, Gemma Rojo‐Martínez, David Pozo, Francisco Javier Bermúdez‐Silva, Valentine Comaills, José Carlos Castañeda Reyes, Benoît Gauthier
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41398-018-0223-6

Common and differential transcriptional responses to different models of traumatic stress exposure in rats
Cited by: 2
Author(s): Moriah L. Jacobson, Lydia A. Kim, Rob Patro, Barbara Rosati, David McKinnon
Software Mentions: 3
Published: about 6 years ago

10.3906/biy-2005-21

Signature changes in the expressions of protein-coding genes, lncRNAs, and repeat elements in early and late cellular senescence
Cited by: 4
Author(s): Gökhan Karakülah, Cihangir Yandım
Software Mentions: 3
Published: almost 4 years ago

10.1128/mBio.00301-18

TgTKL1 Is a Unique Plant-Like Nuclear Kinase That Plays an Essential Role in Acute Toxoplasmosis
Cited by: 15
Author(s): Joseph M. Varberg, Isabelle Coppens, Gustavo Arrizabalaga, Rajshekhar Y. Gaji
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00612-20

A Mutation Upstream of the rplN-rpsD Ribosomal Operon Downregulates Bordetella pertussis Virulence Factor Production without Compromising Bacterial Survival within Human Macrophages
Cited by: 4
Author(s): Jakub Novák, David Jurnečka, Irena Linhartová, Jana Holubová, Ondřej Staněk, Daniel Štipl, Ana Dienstbier, Branislav Večerek, Nayara Azevedo, Jan Provazník, Vladimı́r Beneš, Peter Šebo
Software Mentions: 3
Published: almost 4 years ago

10.1128/mSystems.00610-21

Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa
Cited by: 2
Author(s): Raimo Franke, Heike Overwin, Susanne Häußler, Mark Brönstrup
Software Mentions: 3
Published: about 3 years ago

10.3390/jof7030198

Innate Resistance and Phosphite Treatment Affect Both the Pathogen’s and Host’s Transcriptomes in the Tanoak-Phytophthora ramorum Pathosystem
Cited by: 9
Author(s): Takao Kasuga, Katherine J. Hayden, Catherine A. Eyre, Peter J.P. Croucher, Shannon Schechter, Jessica W. Wright, Matteo Garbelotto
Software Mentions: 3
Published: over 3 years ago

10.1016/j.jlr.2021.100056

Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells
Cited by: 6
Author(s): Stacey L. Borrego, Johannes F. Fahrmann, Jue Hou, Dawei Lin, Bruce J. Tromberg, Oliver Fiehn, Peter Kaiser
Software Mentions: 3
Published: almost 4 years ago

10.7554/eLife.58591

Transcriptional profiling of mouse peripheral nerves to the single-cell level to build a sciatic nerve ATlas (SNAT)
Cited by: 74
Author(s): Daniel Gerber, Jorge A. Pereira, Joanne Gerber, Ge Tan, Slavica Dimitrieva, Emilio Yángüez, Ueli Suter
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.46711

Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms
Cited by: 23
Author(s): Yoseop Yoon, Jeff Klomp, Inés Martín-Martín, Frank Criscione, Eric Calvo, José M. C. Ribeiro, Urs Schmidt‐Ott
Software Mentions: 3
Published: about 5 years ago

10.1186/s12967-016-1083-6

Targeted myocardial gene expression in failing hearts by RNA sequencing
Cited by: 20
Author(s): Kajari Dhar, Anthony L. Moulton, Eric Rome, Fang Qiu, Jeff Kittrell, Eugenia Raichlin, Ronald Zolty, J. Um, Michael J. Moulton, Hesham Basma, Daniel R. Anderson, James D. Eudy, Brian D. Lowes
Software Mentions: 3
Published: almost 8 years ago

10.7554/eLife.27596

Maturation of selected human mitochondrial tRNAs requires deadenylation
Cited by: 68
Author(s): Sarah F Pearce, Joanna Rorbach, Lindsey Van Haute, Aaron R. D’Souza, Pedro Rebelo-Guiomar, Christopher A. Powell, Ian Brierley, Andrew E. Firth, Michal Minczuk
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.52473

Rejuvenating conventional dendritic cells and T follicular helper cell formation after vaccination
Cited by: 46
Author(s): Marisa Stebegg, Alexandre Bignon, Danika L. Hill, Alyssa Silva-Cayetano, Christel Krueger, Ine Vanderleyden, Silvia Innocentin, Louis Boon, Jiong Wang, Martin S. Zand, James Dooley, Jonathan Clark, Adrian Liston, Edward J Carr, Michelle A. Linterman
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms22073611

Analysis of Gene Expression Changes in Plants Grown in Salty Soil in Response to Inoculation with Halophilic Bacteria
Cited by: 2
Author(s): Ashley Miller, Brent L. Nielsen
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22137212

Isolation and Characterization of Barley (Hordeum vulgare) Extracellular Vesicles to Assess Their Role in RNA Spray-Based Crop Protection
Cited by: 7
Author(s): Timo Schlemmer, Patrick Barth, Weipert Lisa, Preußer Christian, Martin Hardt, Möbus Anna, Tobias Busche, Aline Koch
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22147576

Expression of RUNX1-JAK2 in Human Induced Pluripotent Stem Cell-Derived Hematopoietic Cells Activates the JAK-STAT and MYC Pathways
Cited by: 3
Author(s): Klaus Fortschegger, Anna-Maria Husa, Dagmar Schinnerl, Karin Nebral, Sabine Strehl
Software Mentions: 3
Published: over 3 years ago

10.1523/ENEURO.0143-21.2021

Sex Differences in Behavioral and Brainstem Transcriptomic Neuroadaptations following Neonatal Opioid Exposure in Outbred Mice
Cited by: 15
Author(s): Kristyn N. Borrelli, Emily J Yao, William Yen, Rhushikesh A. Phadke, Qiu T. Ruan, Melanie M Chen, Julia C Kelliher, Carly R. Langan, Julia L. Scotellaro, R.K. Babbs, Jacob A Beierle, Ryan W. Logan, William Johnson, Elisha M. Wachman, Alberto Cruz-Martín, Camron D. Bryant
Software Mentions: 3
Published: about 3 years ago

10.18632/oncotarget.9037

Integrative analysis reveals clinical phenotypes and oncogenic potentials of long non-coding RNAs across 15 cancer types
Cited by: 16
Author(s): Zelin Wang, Bin Li, Stephen R. Piccolo, Xiaoqin Zhang, Junhao Li, Hui Zhou, Jianhua Yang, Liang‐Hu Qu
Software Mentions: 3
Published: over 8 years ago

10.1186/s12867-017-0099-7

An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing
Cited by: 42
Author(s): Parisa Amini, Julia Ettlin, Lennart Opitz, Elena Clementi, Alexandra Malbon, Enni Markkanen
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.ppat.1009350

The purine nucleoside phosphorylase pnp-1 regulates epithelial cell resistance to infection in C. elegans
Cited by: 31
Author(s): Eillen Tecle, Crystal B. Chhan, Latisha Franklin, Ryan Underwood, Wendy Hanna-Rose, Emily R. Troemel
Software Mentions: 2
Published: over 3 years ago

10.1038/sdata.2018.287

Polysome profiling followed by RNA-seq of cardiac differentiation stages in hESCs
Cited by: 11
Author(s): Isabela Tiemy Pereira, Lucía Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya, Bruno Dallagiovanna
Software Mentions: 2
Published: almost 6 years ago

10.1113/JP280652

The mechanisms of skeletal muscle atrophy in response to transient knockdown of the vitamin D receptor in vivo
Cited by: 30
Author(s): Joseph J. Bass, Abid A. Kazi, Colleen S. Deane, Asif Nakhuda, Stephen P. Ashcroft, Matthew S. Brook, Daniel J. Wilkinson, Bethan E. Phillips, Andrew Philp, Janelle Tarum, Fawzi Kadi, Ditte Andersen, Amadeo Muñoz García, Kyle Smith, Iain J. Gallagher, Nathaniel J. Szewczyk, Mark E. Cleasby, Philip J. Atherton
Software Mentions: 2
Published: almost 4 years ago

10.1093/molbev/msz212

Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs
Cited by: 26
Author(s): Fabrice Darbellay, Anamaria Necşulea
Software Mentions: 2
Published: about 5 years ago

10.3390/ijms21113989

Characterization of miRNAs in Cultured Atlantic Salmon Head Kidney Monocyte-Like and Macrophage-Like Cells
Cited by: 12
Author(s): Nicole C. Smith, Sherri L. Christian, Nardos Tesfaye Woldemariam, Kathy A. Clow, Matthew L. Rise, Rune Andreassen
Software Mentions: 2
Published: over 4 years ago

10.3390/toxins13080520

Escherichia coli Alpha-Hemolysin HlyA Induces Host Cell Polarity Changes, Epithelial Barrier Dysfunction and Cell Detachment in Human Colon Carcinoma Caco-2 Cell Model via PTEN-Dependent Dysregulation of Cell Junctions
Cited by: 8
Author(s): Emanuel Schulz, Michael Schümann, Martina Schneemann, Violaine Dony, Anja Fromm, Oliver Nagel, Jörg–Dieter Schulzke, Roland Bücker
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms21165633

The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation
Cited by: 5
Author(s): Benjamin Lenzen, Thilo Rühle, Marie-Kristin Lehniger, Ayako Okuzaki, Mathias Labs, Jose M. Muiño, Uwe Ohler, Dario Leister, Christian Schmitz‐Linneweber
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-017-18407-6

A RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer
Cited by: 79
Author(s): Atsushi Yamada, Pingjian Yu, Wei Lin, Yoshinaga Okugawa, C. Richard Boland, Ajay Goel
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-018-24976-x

Skeletal muscle phosphatidylcholine and phosphatidylethanolamine respond to exercise and influence insulin sensitivity in men
Cited by: 40
Author(s): Sindre Lee, Frode Norheim, Hanne Løvdal Gulseth, Torgrim M. Langleite, Andreas Aker, Thomas E. Gundersen, Torgeir Holen, Kåre I. Birkeland, Christian A. Drevon
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-5550-3

Cardiomyogenic differentiation is fine-tuned by differential mRNA association with polysomes
Cited by: 16
Author(s): Isabela Tiemy Pereira, Lucía Spangenberg, Anny Waloski Robert, Rocío Amorín, Marco Augusto Stimamiglio, Hugo Naya, Bruno Dallagiovanna
Software Mentions: 2
Published: over 5 years ago

10.1111/pcmr.12778

SOX10 regulates multiple genes to direct eumelanin versus pheomelanin production in domestic rock pigeon
Cited by: 7
Author(s): Eric T. Domyan, J Hardy, Tanner Wright, Cody Frazer, Jordan Daniels, Joshua Kirkpatrick, Jacob Kirkpatrick, Kazumasa Wakamatsu, John E. Hill
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.ppat.1009522

Plasmacytoid dendritic cells have divergent effects on HIV infection of initial target cells and induce a pro-retention phenotype
Cited by: 5
Author(s): Orion Tong, Gabriel Duette, Thomas R. O’Neil, Caroline Royle, Hafsa Rana, Blake Johnson, Nicole L. Popovic, Suat Dervish, Michelle A. E. Brouwer, Heeva Baharlou, Ellis Patrick, Grahame Ctercteko, Sarah Palmer, Eun-Ok Lee, Eric Hunter, Andrew N. Harman, Anthony L. Cunningham, Najla Nasr
Software Mentions: 2
Published: over 3 years ago

10.1186/s12711-020-00574-2

Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle
Cited by: 18
Author(s): Sara de las Heras‐Saldana, Bryan Irvine Lopez, Nasir Moghaddar, Woncheoul Park, Woncheoul Park, Ki Yong Chung, Dajeong Lim, Seung H. Lee, Donghyun Shin, J. H. J. van der Werf
Software Mentions: 2
Published: about 4 years ago

10.3389/fonc.2017.00252

Development of Novel Patient-Derived Xenografts from Breast Cancer Brain Metastases
Cited by: 30
Author(s): María José Contreras-Zárate, D. Ryan Ormond, Austin E. Gillen, Colton Hanna, Nicole L. Day, Natalie J. Serkova, Britta M. Jacobsen, Susan M. Edgerton, Ann D. Thor, Virginia F. Borges, Kevin O. Lillehei, Michael W. Graner, Peter Kabos, Diana M. Cittelly
Software Mentions: 2
Published: about 7 years ago

10.1128/mBio.01939-17

Functional Analysis of Mating Type Genes and Transcriptome Analysis during Fruiting Body Development of Botrytis cinerea
Cited by: 31
Author(s): Sander Y.A. Rodenburg, Razak Terhem, Javier Veloso, Joost H. M. Stassen, Jan A.L. van Kan
Software Mentions: 2
Published: over 6 years ago

10.1186/s12711-017-0319-0

Exploring the genetic architecture and improving genomic prediction accuracy for mastitis and milk production traits in dairy cattle by mapping variants to hepatic transcriptomic regions responsive to intra-mammary infection
Cited by: 51
Author(s): Lingzhao Fang, Goutam Sahana, Peipei Ma, Guosheng Su, Ying Yu, Shengli Zhang, Mogens Sandø Lund, Peter Sørensen
Software Mentions: 2
Published: over 7 years ago

10.3390/genes11091059

Characterization of Differentially Expressed miRNAs and Their Predicted Target Transcripts during Smoltification and Adaptation to Seawater in Head Kidney of Atlantic Salmon
Cited by: 12
Author(s): Alice Shwe, Tone-Kari K Østbye, Aleksei Krasnov, Sigmund Ramberg, Rune Andreassen
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms21197259

Streamlining Quantitative Analysis of Long RNA Sequencing Reads
Cited by: 1
Author(s): Sebastian Oeck, Alicia I. Tüns, Sebastian Hurst, Alexander Schramm
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-81226-3

A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity
Cited by: 6
Author(s): Laura Bernhardt, Marcus Dittrich, Rabih El‐Merahbi, Antoine‐Emmanuel Saliba, Tobias Müller, Grzegorz Sumara, Jörg Vogel, Stefanie Nichols-Burns, Megan Mitchell, Thomas Haaf, Nady El Hajj
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.656548

The Heat Shock Transcription Factor HsfA Is Essential for Thermotolerance and Regulates Cell Wall Integrity in Aspergillus fumigatus
Cited by: 9
Author(s): João Henrique Tadini Marilhano Fabri, Marina Campos Rocha, Caroline Mota Fernandes, Gabriela Félix Persinoti, Laure Nicolas Annick Ries, Anderson Ferreira da Cunha, Gustavo Henrique Goldman, Maurizio Del Poeta, Iran Malavazi
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.00202

Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Cited by: 11
Author(s): José Manuel Rubio-Gómez, Carlos Molina-Santiago, Zulema Udaondo, Mireia Tena-Garitaonaindia, Tino Krell, Juan L. Ramos, Abdelali Daddaoua
Software Mentions: 2
Published: almost 5 years ago

10.3389/fimmu.2021.630318

Adenylate Kinase 4 Promotes Inflammatory Gene Expression via Hif1α and AMPK in Macrophages
Cited by: 15
Author(s): Wei-Yao Chin, Chi-Ying He, Tsun Wai Chow, Qi-You Yu, Liang‐Chuan Lai, Shi‐Chuen Miaw
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-53504-8

Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation
Cited by: 5
Author(s): Tamara Zoran, Michael Weber, Jan Springer, P. Lewis White, Joachim Bauer, Annika Schober, Claudia Löffler, Bastian Seelbinder, Kerstin Hünniger, Oliver Kurzai, André Scherag, Sascha Schäuble, Oliver Morton, Hermann Einsele, Jörg Linde, Jürgen Löffler
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-019-54091-4

Carprofen-induced depletion of proton motive force reverses TetK-mediated doxycycline resistance in methicillin-resistant Staphylococcus pseudintermedius
Cited by: 7
Author(s): Zofia Magnowska, Bimal Jana, Rikke Prejh Brochmann, Andrew Hesketh, René Lametsch, Cristian De Gobba, Luca Guardabassi
Software Mentions: 2
Published: almost 5 years ago

10.1534/g3.118.200499

Bulked-Segregant Analysis Coupled to Whole Genome Sequencing (BSA-Seq) for Rapid Gene Cloning in Maize
Cited by: 49
Author(s): Harry Klein, Yuguo Xiao, Phillip A. Conklin, Rajanikanth Govindarajulu, Jacob A Kelly, Michael J. Scanlon, Clinton Whipple, Madelaine Bartlett
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.2791

Identifying stably expressed genes from multiple RNA-Seq data sets
Cited by: 12
Author(s): Bin Zhuo, Sarah C. Emerson, Jeff H. Chang, Yanming Di
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-016-1406-x

Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms
Cited by: 51
Author(s): Nicolas Cerveau, Daniel J. Jackson
Software Mentions: 2
Published: almost 8 years ago

10.1128/mSphere.00042-16

Transcriptome Sequencing Reveals Wide Expression Reprogramming of Basal and Unknown Genes in Leptospira biflexa Biofilms
Cited by: 26
Author(s): Gregorio Iraola, Lucía Spangenberg, Bruno Lopes Bastos, Martín Graña, Larissa Vasconcelos, Áurea Maria Alves Nunes Almeida, Gonzalo Greif, Carlos Robello, Paula Ristow, Hugo Naya
Software Mentions: 2
Published: over 8 years ago

10.3389/fcell.2021.629430

DAND5 Inactivation Enhances Cardiac Differentiation in Mouse Embryonic Stem Cells
Cited by: 1
Author(s): José Manuel Inácio, João von Gilsa Lopes, Ana Mafalda Silva, Fernando Cristo, Sara Marques, Matthias E. Futschik, José António Belo
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22157916

ZmFAR1 and ZmABCG26 Regulated by microRNA Are Essential for Lipid Metabolism in Maize Anther
Cited by: 19
Author(s): Yilin Jiang, Ziwen Li, Xinze Liu, Taotao Zhu, Kui Xie, Quancan Hou, Tingwei Yan, Canfang Niu, Shaowei Zhang, Mengbing Yang, Rongrong Xie, Jing Wang, Jinping Li, Xianghai An, Xiangyuan Wan
Software Mentions: 2
Published: over 3 years ago

10.1128/mSystems.00046-21

Proteomic and Transcriptomic Analysis of Microviridae φX174 Infection Reveals Broad Upregulation of Host Escherichia coli Membrane Damage and Heat Shock Responses
Cited by: 6
Author(s): Bradley W. Wright, Dominic Y. Logel, Mehdi Mirzai, Dana Pascovici, Mark P. Molloy, Paul R. Jaschke
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms22169086

Programmed Cell Death in Developing Brachypodium distachyon Grain
Cited by: 1
Author(s): Safia Saada, Charles U. Solomon, Sinéad Drea
Software Mentions: 2
Published: about 3 years ago

10.3390/antiox10020334

Signal Transducer and Activator of Transcription 3 (STAT3) Suppresses STAT1/Interferon Signaling Pathway and Inflammation in Senescent Preadipocytes
Cited by: 10
Author(s): Aisha Madani, Yasser Majeed, Houari Abdesselem, Maha Victor Agha, Muneera Vakayil, Nour K Al Sukhun, Najeeb Halabi, Pankaj Kumar, Shahina Hayat, Mohamed A. Elrayess, Arash Rafii, Karsten Suhre, Nayef Mazloum
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2021.671453

A Single Nucleotide Polymorphism in lptG Increases Tolerance to Bile Salts, Acid, and Staining of Calcofluor-Binding Polysaccharides in Salmonella enterica Serovar Typhimurium E40
Cited by: 1
Author(s): Taylor A. Wahlig, Eliot Stanton, Jared J. Godfrey, Andrew J. Stasic, Amy C. Lee Wong, Charles W. Kaspar
Software Mentions: 2
Published: over 3 years ago

10.3389/fbioe.2018.00151

Gene Co-expression Network Reveals Potential New Genes Related to Sugarcane Bagasse Degradation in Trichoderma reesei RUT-30
Cited by: 19
Author(s): Gustavo Pagotto Borin, Marcelo Falsarella Carazzolle, Renato Augusto Corrêa dos Santos, Diego Mauricio Riaño‐Pachón, Juliana Velasco de Castro Oliveira
Software Mentions: 2
Published: about 6 years ago

10.1093/femsle/fnz081

In silico prediction and characterisation of secondary metabolite clusters in the plant pathogenic fungus Verticillium dahliae
Cited by: 14
Author(s): Xiaoqian Shi-Kunne, Roger de Pedro Jové, Jasper R L Depotter, Malaika K. Ebert, Michael Seidl, Bart P.H.J. Thomma
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-85290-7

Development of a rapid scabies immunodiagnostic assay based on transcriptomic analysis of Sarcoptes scabiei var. nyctereutis
Cited by: 4
Author(s): Teruo Akuta, Daisuke Minegishi, Nobuhide Kido, Keitaro Imaizumi, Shinji Nakaoka, Sanro Tachibana, Kenji Hikosaka, Fumi Hori, Masataka, Nakagawa, Chiaki Sakuma, Yuki Oouchi, Yu Nakajima, Sohei Tanaka, Tomoko Omiya, Kouki Morikaku, Minori Kawahara, Yutaka Tada, Hiroshi Tarui, Takafumi Ueda, Takane Kikuchi-Ueda, Yasuo Ono
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-5173-0

Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes
Cited by: 12
Author(s): Juan Carlos Higareda‐Almaraz, Michael Karbiener, Maude Giroud, Florian M. Pauler, Teresa Gerhalter, Stephan Herzig, Marcel Scheideler
Software Mentions: 2
Published: about 6 years ago

10.1210/endocr/bqab054

Endometrium On-a-Chip Reveals Insulin- and Glucose-induced Alterations in the Transcriptome and Proteomic Secretome
Cited by: 15
Author(s): Tiago Henrique Camara De, Haidee Tinning, Elton J. R. Vasconcelos, Dapeng Wang, Niamh Forde
Software Mentions: 2
Published: over 3 years ago

10.1002/ece3.7125

Juvenile hormone pathway in honey bee larvae: A source of possible signal molecules for the reproductive behavior ofVarroa destructor
Cited by: 4
Author(s): Cristian M. Aurori, Alexandru-Ioan Giurgiu, Benjamin H. Conlon, Chedly Kastally, Daniel Severus Dezmirean, Jarkko Routtu, Adriana Aurori
Software Mentions: 2
Published: almost 4 years ago

10.3390/nu11010010

Plasma Sulphur-Containing Amino Acids, Physical Exercise and Insulin Sensitivity in Overweight Dysglycemic and Normal Weight Normoglycemic Men
Cited by: 26
Author(s): Sindre Lee, Trond E. Olsen, Kathrine J. Vinknes, Helga Refsum, Hanne Løvdal Gulseth, Kåre I. Birkeland, Christian A. Drevon
Software Mentions: 2
Published: almost 6 years ago

10.1242/dev.122077

Repression of Igf1 expression by Ezh2 prevents basal cell differentiation in the developing lung
Cited by: 48
Author(s): Laura A. Galvis, Aliaksei Z. Holik, Kieran M. Short, Julie Pasquet, Aaron T. L. Lun, Marnie E. Blewitt, Ian Smyth, Matthew E. Ritchie, Marie Liesse Asselin-Labat
Software Mentions: 2
Published: almost 10 years ago

10.3389/fpls.2019.00827

Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope
Cited by: 36
Author(s): Sean E. Weise, Tiffany Liu, Kevin L. Childs, Alyssa L. Preiser, Hailey M Katulski, Christopher Perrin-Porzondek, Thomas D. Sharkey
Software Mentions: 2
Published: over 5 years ago

10.1093/database/baab007

bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses
Cited by: 72
Author(s): Pascal Jézéquel, Wilfried Gouraud, Fadoua Ben Azzouz, Catherine Guérin‐Charbonnel, Philippe Juin, Hamza Lasla, Mario Campone
Software Mentions: 2
Published: almost 4 years ago

10.1016/j.dib.2019.105053

Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis
Cited by: 5
Author(s): Bruna Hilzendeger Marcon, Lucía Spangenberg, Bernardo Bonilauri, Anny Waloski Robert, Addeli Bez Batti Angulski, Guillermo Cabrera Cabo, Axel R. Cofré, Paulo Sergio Loiacono Bettes, Bruno Dallagiovanna, Patrícia Shigunov
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.dib.2017.03.050

Data on RDM16 and STA1 regulate differential usage of exon/intron in RNA directed DNA Methylation pathway
Cited by: 1
Author(s): Ravi Datta Sharma, Bert Bogaerts, Neha Goyal
Software Mentions: 2
Published: over 7 years ago

10.1038/s42003-021-02495-2

Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses
Cited by: 1
Author(s): Swetha Rajasekaran, Jalal K. Siddiqui, Jessica Rakijas, Brandon Nicolay, Chen‐Yu Lin, Eshan Khan, Rahi Patel, Robert T. Morris, Emanuel Wyler, Myriam Boukhali, Jayashree Balasubramanyam, Ranjith Kumar, Capucine Van Rechem, Christine Vogel, Sailaja Elchuri, Markus Landthaler, Benedikt Obermayer, Wilhelm Haas, Nicholas J. Dyson, Wayne Miles
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-021-07667-2

Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species
Cited by: 3
Author(s): Ruijie Liu, Rick Tearle, Wai Yee Low, Tong Chen, D. A. Thomsen, Timothy P. L. Smith, Stefan Hiendleder, J. L. Williams
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.01580

Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection
Cited by: 12
Author(s): Thrimendra Kaushika Dissanayake, Sascha Schäuble, Mohammad H. Mirhakkak, Wai-Lan Wu, Anthony Chin-Ki Ng, Cyril C. Y. Yip, Albert García López, Thomas Wolf, M.R. Yeung, Kwok‐Hung Chan, Kwok‐Yung Yuen, Gianni Panagiotou, Kelvin Kai‐Wang To
Software Mentions: 2
Published: over 4 years ago

10.1186/s13071-017-2585-7

Tissue-specific transcriptomes of Anisakis simplex (sensu stricto) and Anisakis pegreffii reveal potential molecular mechanisms involved in pathogenicity
Cited by: 37
Author(s): Serena Cavallero, Fabrizio Lombardo, Xiaopei Su, Marco Salvemini, Cinzia Cantacessi, Stefano D'Amélio
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41420-021-00479-z

The oncogenic E3 ligase TRIP12 suppresses epithelial–mesenchymal transition (EMT) and mesenchymal traits through ZEB1/2
Cited by: 4
Author(s): Kwok Kin Lee, Deepa Rajagopalan, Shreshtha Sailesh Bhatia, Roberto Tirado-Magallanes, Wee Joo Chng, Sudhakar Jha
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0129321

Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells
Cited by: 13
Author(s): Patsharaporn Techasintana, J. Wade Davis, Matthew M. Gubin, Joseph Magee, Ulus Atasoy
Software Mentions: 2
Published: over 9 years ago

10.7554/eLife.52558

Mitochondrial pyruvate carrier is required for optimal brown fat thermogenesis
Cited by: 41
Author(s): Vanja Panic, Stephanie Pearson, James Banks, Trevor S. Tippetts, Jesse N. Velasco-Silva, Sanghoon Lee, Judith Simcox, Gisela Geoghegan, Claire Bensard, Tyler Van Ry, Will L Holland, Scott A. Summers, James E. Cox, Gregory S. Ducker, Jared Rutter, Claudio J. Villanueva
Software Mentions: 2
Published: over 4 years ago

10.1016/j.molmet.2020.101059

Overexpression of the vitamin D receptor (VDR) induces skeletal muscle hypertrophy
Cited by: 51
Author(s): Joseph J. Bass, Asif Nakhuda, Colleen S. Deane, Matthew S. Brook, Daniel J. Wilkinson, Mathew Piasecki, Andrew Philp, Janelle Tarum, Fawzi Kadi, Ditte Andersen, Amadeo Muñoz García, Kyle Smith, Iain J. Gallagher, Nathaniel J. Szewczyk, Mark E. Cleasby, Philip J. Atherton
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2020.02002

Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes – Observing Strong Local Effects of Nucleoid Structure on Gene Regulation
Cited by: 5
Author(s): Thøger Jensen Krogh, André Franke, Jakob Møller‐Jensen, Christoph Kaleta
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0163986

RNA-Seq Transcriptome Analysis of Direction-Selective T4/T5 Neurons in Drosophila
Cited by: 23
Author(s): Katarina Pankova, Alexander Borst
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.23853

Selenium-binding protein 1 is down-regulated in malignant melanoma
Cited by: 26
Author(s): M. Schott, Miriam M. de Jel, Julia C. Engelmann, Philipp Renner, Edward K. Geissler, Anja‐Katrin Bosserhoff, Silke Kuphal
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.molmet.2019.05.008

Global transcriptomic analysis of the arcuate nucleus following chronic glucocorticoid treatment
Cited by: 13
Author(s): Jonathan R. Wray, Alison Davies, Charlotte Sefton, Tiffany-Jayne Allen, Antony Adamson, Phil Chapman, Brian Lam, Giles S.H. Yeo, Anthony P. Coll, Erika Harno, Anne White
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0157480

The Impact of Intramammary Escherichia coli Challenge on Liver and Mammary Transcriptome and Cross-Talk in Dairy Cows during Early Lactation Using RNAseq
Cited by: 25
Author(s): K.M. Moyes, Peter Sørensen, Massimo Bionaz
Software Mentions: 2
Published: over 8 years ago

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Papers Mentioning Rsubread 331