bioconductor: HTSFilter | Projects

10.1016/j.celrep.2019.06.037

Three-Dimensional Genomic Structure and Cohesin Occupancy Correlate with Transcriptional Activity during Spermatogenesis
Cited by: 99
Author(s): Covadonga Vara, Andreu Paytuví-Gallart, Yasmina Cuartero, François Le Dily, Francisca García, Judit Salvà-Castro, Laura Gómez-H, Eva Julià, Cátia Moutinho, Riccardo Aiese Cigliano, Walter Sanseverino, Òscar Fornas, Alberto M. Pendás, Holger Heyn, Paul D. Waters, Marc A. Martí‐Renom, Aurora Ruiz‐Herrera
Software Mentions: 14
Published: over 5 years ago

10.1186/s12920-020-0695-0

Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain
Cited by: 20
Author(s): Wesley L. Cai, Celeste B. Greer, Jocelyn F. Chen, Anna Arnal-Estapé, Jian Cao, Qin Yan, Don X. Nguyen
Software Mentions: 7
Published: over 4 years ago

10.1099/mgen.0.000445

Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase
Cited by: 12
Author(s): Domenico Giosa, Maria Rosa Felice, Letterio Giuffrè, Riccardo Aiese Cigliano, Andreu Paytuví-Gallart, Carla Lo Passo, Cinzia Barresi, Enrico D’Alessandro, Huaiqiu Huang, Giuseppe Criseo, Héctor M. Mora-Montes, Sybren de Hoog, Orazio Romeo
Software Mentions: 7
Published: about 4 years ago

10.3390/v13061059

Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses
Cited by: 5
Author(s): Roberto J. Cieza, Jonathan L. Golob, Justin A. Colacino, Christiane E. Wobus
Software Mentions: 7
Published: over 3 years ago

10.3389/fpls.2021.613059

Identification of ABA-Mediated Genetic and Metabolic Responses to Soil Flooding in Tomato (Solanum lycopersicum L. Mill)
Cited by: 24
Author(s): Vicent Arbona, Miguel González-Guzmán, Zara Pitarch, José Tomás Matus, Héctor Candela, José L. Rambla, Antonio Granell, Aurelio Gómez‐Cadenas
Software Mentions: 6
Published: over 3 years ago

10.1002/pld3.159

The <i>HAC1</i> histone acetyltransferase promotes leaf senescence and regulates the expression of <i>ERF022</i>
Cited by: 28
Author(s): Will E. Hinckley, Keykhosrow Keymanesh, Jaime Cordova, Judy A. Brusslan
Software Mentions: 6
Published: over 5 years ago

10.1038/s41419-021-04169-7

New insight into the catalytic -dependent and -independent roles of METTL3 in sustaining aberrant translation in chronic myeloid leukemia
Cited by: 16
Author(s): Zaira Ianniello, Melissa Sorci, Lavinia Ceci Ginistrelli, Alessia Iaiza, Marcella Marchioni, Claudia Tito, Ernestina Capuano, Silvia Masciarelli, Tiziana Ottone, Cristina Attrotto, Manuela Rizzo, Luca Franceschini, Stefano de Pretis, Maria Teresa Voso, Mattia Pelizzola, Francesco Fazi, Alessandro Fatica
Software Mentions: 5
Published: about 3 years ago

10.3390/ijms21176067

Long-Term Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Berry Transcriptome
Cited by: 7
Author(s): Raffaella Balestrini, Stefano Ghignone, Gabriela Quiroga, Valentina Fiorilli, Irene Romano, Giorgio Gambino
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-019-5428-4

New insights in the control of antioxidants accumulation in tomato by transcriptomic analyses of genotypes exhibiting contrasting levels of fruit metabolites
Cited by: 20
Author(s): Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone, Maria Manuela Rigano
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41375-021-01221-5

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia
Cited by: 5
Author(s): Cédric Schleiss, Raphaël Carapito, Luc‐Matthieu Fornecker, Leslie Muller, Nicodème Paul, Ouria Tahar, Angélique Pichot, Manuela Tavian, Alina Nicolae, Laurent Miguet, Laurent Mauvieux, Raoul Herbrecht, Sarah Cianférani, Jean–Noël Freund, Myriam Maumy-Bertrand, Seiamak Bahram, Frédèric Bertrand, Laurent Vallat
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0136765

In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq
Cited by: 35
Author(s): Guoqiang Yi, Jiahui Yuan, Huijuan Bi, Wei Yan, Ning Yang, Lujiang Qu
Software Mentions: 4
Published: about 9 years ago

10.1186/s13059-015-0735-9

Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population
Cited by: 39
Author(s): Joke Baute, Dorota Herman, Frederik Coppens, Jolien De Block, Bram Slabbinck, Matteo Dell’Acqua, Mario Enrico Pè, Steven Maere, Hilde Nelissen, Dirk Inzé
Software Mentions: 4
Published: about 9 years ago

10.1186/s12859-015-0859-7

Effects of Mecp2 loss of function in embryonic cortical neurons: a bioinformatics strategy to sort out non-neuronal cells variability from transcriptome profiling
Cited by: 9
Author(s): Marcella Vacca, Kumar Parijat Tripathi, Luisa Speranza, Riccardo Aiese Cigliano, Francesco Scalabrì, Federico Marracino, Michele Madonna, Walter Sanseverino, Carla Perrone-Capano, Mario Rosario Guarracino, Maurizio D’Esposito
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1007180

Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood-brain barrier integrity
Cited by: 11
Author(s): Montserrat Torres-Oliva, Júlia Schneider, Gordon Wiegleb, Felix Kaufholz, Nico Posnien
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-019-6237-5

Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. ‘Moscatel Galego’)
Cited by: 14
Author(s): Vanessa Ferreira, José Tomás Matus, Olinda Pinto-Carnide, David Carrasco, Rosa Arroyo-García, Isaura Castro
Software Mentions: 3
Published: almost 5 years ago

10.3389/fpls.2020.01208

Fruit Development in Ficus carica L.: Morphological and Genetic Approaches to Fig Buds for an Evolution From Monoecy Toward Dioecy
Cited by: 15
Author(s): Ilaria Marcotuli, Andrea Mazzeo, Pasqualina Colasuonno, Roberto Terzano, Domenica Nigro, Carlo Porfido, Annalisa Tarantino, Riccardo Aiese Cigliano, Walter Sanseverino, Ágata Gadaleta, Giuseppe Ferrara
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21114003

Dexfenfluramine and Pergolide Cause Heart Valve Disease via Valve Metabolic Reprogramming and Ongoing Matrix Remodeling
Cited by: 1
Author(s): Cécile Oury, Patrick Maréchal, Nathalie Donis, Alexia Hulin, Alexandre Hego, Julien Tridetti, Mai-Linh Nguyen, Raluca Dulgheru, Marianne Fillet, Alain Nchimi, Patrizio Lancellotti
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0114598

Impact of the Genetic Background on the Composition of the Chicken Plasma MiRNome in Response to a Stress
Cited by: 14
Author(s): Marie-Laure Endale Ahanda, Tatiana Zerjal, Sophie Dhorne–Pollet, Andrea Rau, Amanda M. Cooksey, Elisabetta Giuffra
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-019-46282-w

Actin stabilizing compounds show specific biological effects due to their binding mode
Cited by: 26
Author(s): Shuaijun Wang, Álvaro H. Crevenna, İlke Uǧur, Antoine Marion, Iris Antes, Uli Kazmaier, Maria Hoyer, Don C. Lamb, Florian Gegenfurtner, Zane Kliesmete, Christoph Ziegenhain, Wolfgang Enard, Angelika M. Vollmar, Stefan Zahler
Software Mentions: 3
Published: over 5 years ago

10.5966/sctm.2015-0401

Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress
Cited by: 12
Author(s): Rémy Bétous, Marie-Laure Renoud, Claire Hoede, Ignacio González, Natalie Jones, Michel Longy, Luc Sensebé, Christophe Cazaux, Jean-Sébastien Hoffmann
Software Mentions: 3
Published: over 8 years ago

10.3390/microorganisms9081680

A Genomic and Transcriptomic Study on the DDT-Resistant Trichoderma hamatum FBL 587: First Genetic Data into Mycoremediation Strategies for DDT-Polluted Sites
Cited by: 7
Author(s): Domenico Davolos, Fabiana Russo, Loredana Canfora, Eligio Malusà, Małgorzata Tartanus, Ewa M. Furmanczyk, Andrea Ceci, Oriana Maggi, Anna Maria Persiani
Software Mentions: 2
Published: over 3 years ago

10.3390/genes11080847

Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit
Cited by: 7
Author(s): Antonietta Aliberti, Fabrizio Olivieri, Salvatore Graci, Maria Manuela Rigano, Amalia Barone, Valentino Ruggieri
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-56690-7

Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities
Cited by: 16
Author(s): Sandrine Le Guillou, Arlette Leduc, Johann Laubier, Sarah Barbey, Marie Rossignol, Rachel Lefebvre, Sylvain Marthey, Dénis Laloë, Fabienne Le Provost
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-020-68600-3

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency
Cited by: 12
Author(s): Christopher B. Mulholland, Franziska R. Traube, Enes Ugur, Edris Parsa, Eva-Maria Eckl, Maximilian Schönung, Miha Modic, Michael D. Bartoschek, Paul Stolz, Joël Ryan, Thomas Carell, Heinrich Leonhardt, Sebastian Bultmann
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.ppat.1006044

Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum
Cited by: 37
Author(s): Anthony Perrier, Rémi Peyraud, David Rodrı́guez-Làzaro, Xavier Barlet, Emmanuel Lucasson, Jérôme Gouzy, Nemo Peeters, Stéphane Genin, Alice Guidot
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41598-017-07532-x

The hypothesis that Helicobacter pylori predisposes to Alzheimer’s disease is biologically plausible
Cited by: 23
Author(s): Felice Contaldi, Federico Capuano, Andrea Fulgione, Riccardo Aiese Cigliano, Walter Sanseverino, Domenico Iannelli, Chiara Medaglia, Rosanna Capparelli
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0140111

Food Deprivation Affects the miRNome in the Lactating Goat Mammary Gland
Cited by: 23
Author(s): Lenha Mobuchon, Sylvain Marthey, Sandrine Le Guillou, Dénis Laloë, Fabienne Le Provost, Christine Leroux
Software Mentions: 2
Published: about 9 years ago

10.3390/ijms21062136

A Compensatory U1snRNA Partially Rescues FAH Splicing and Protein Expression in a Splicing-Defective Mouse Model of Tyrosinemia Type I
Cited by: 12
Author(s): Dario Balestra, Daniela Scalet, Mattia Ferrarese, Silvia Lombardi, Nicole Ziliotto, Chrystal C. Croes, Naomi Petersen, Piter J. Bosma, Federico Riccardi, Franco Pagani, Mirko Pinotti, Stan F.J. van de Graaf
Software Mentions: 2
Published: over 4 years ago

10.1186/s12870-019-2156-5

Osa-miR7695 enhances transcriptional priming in defense responses against the rice blast fungus
Cited by: 30
Author(s): Ferran Sánchez-Sanuy, Cristina Peris-Peris, Shiho Tomiyama, Kazunori Okada, Yue‐Ie C. Hsing, Blanca San Segundo, Sonia Campo
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-018-5415-1

RNA-seq analysis of hepatic gene expression of common Pekin, Muscovy, mule and hinny ducks fed ad libitum or overfed
Cited by: 8
Author(s): Frédéric Herault, Magalie Houée-Bigot, Élisabeth Baéza, Olivier Bouchez, Diane Esquerré, Christophe Klopp, Christian Diot
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2021.661437

Expression of Human Endogenous Retroviruses in Systemic Lupus Erythematosus: Multiomic Integration With Gene Expression
Cited by: 11
Author(s): Nathaniel Stearrett, Tyson Dawson, Ali Rahnavard, Prathyusha Bachali, Matthew L. Bendall, Chen Zeng, Roberto Caricchio, Marcos Pérez‐Losada, Amrie C. Grammer, Peter E. Lipsky, Keith A. Crandall
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-13171-z

The neonicotinoid insecticide Clothianidin adversely affects immune signaling in a human cell line
Cited by: 22
Author(s): Gennaro Di Prisco, Marco Iannaccone, Flora Ianniello, Renata Ferrara, Emilio Caprio, Francesco Pennacchio, Rosanna Capparelli
Software Mentions: 2
Published: about 7 years ago

10.1093/gbe/evy230

The transcriptional response of Aedes aegypti with variable extrinsic incubation periods for dengue virus
Cited by: 10
Author(s): Cassandra Koh, Scott L. Allen, Rosemarie I. Herbert, Elizabeth A. McGraw, Stephen F. Chenoweth
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0185511

Sunflower oil supplementation affects the expression of miR-20a-5p and miR-142-5p in the lactating bovine mammary gland
Cited by: 21
Author(s): Lenha Mobuchon, Sandrine Le Guillou, Sylvain Marthey, Johann Laubier, Dénis Laloë, Sébastien Bes, Fabienne Le Provost, Christine Leroux
Software Mentions: 1
Published: almost 7 years ago

Ecosyste.ms: Papers

Projects: bioconductor: HTSFilter

Papers Mentioning HTSFilter 35