bioconductor: made4 | Projects | Ecosyste.ms: Papers

10.1093/bib/bbv080

Public data and open source tools for multi-assay genomic investigation of disease
Cited by: 47
Author(s): Lavanya Kannan, Marcel Ramos, Angela Re, Nehmé El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez-Cabrero, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe‐Kains, Levi Waldron
Software Mentions: 15
Published: about 9 years ago

10.1186/s12859-016-1455-1

MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration
Cited by: 20
Author(s): Carles Hernández-Ferrer, Carlos Ruiz‐Arenas, Alba Beltran-Gomila, Juan R. González
Software Mentions: 14
Published: almost 8 years ago

10.1038/srep42130

Dissecting the brown adipogenic regulatory network using integrative genomics
Cited by: 20
Author(s): Rachana Pradhan, Johannes Bues, Vincent Gardeux, Petra Schwalie, Daniel Alpern, Wanze Chen, Julie Russeil, Sunil K. Raghav, Bart Deplancke
Software Mentions: 13
Published: almost 8 years ago

10.1038/s41416-019-0519-1

Stroma-normalised vessel density predicts benefit from adjuvant fluorouracil-based chemotherapy in patients with stage II/III colon cancer
Cited by: 5
Author(s): Artur Mezheyeuski, Ina Hrynchyk, Mercedes Herrera, Mia Karlberg, Erik Osterman, Peter Ragnhammar, David Edler, Anna Portyanko, Fredrik Pontén, Tobias Sjöblom, Bengt Glimelius, Arne Östman
Software Mentions: 12
Published: over 5 years ago

10.1186/1756-0500-5-282

Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results
Cited by: 9
Author(s): Yilin Dai, Ling Guo, Meng Li, Yibu Chen
Software Mentions: 11
Published: over 12 years ago

10.1186/s13073-016-0285-0

Long noncoding RNAs expressed in human hepatic stellate cells form networks with extracellular matrix proteins
Cited by: 55
Author(s): Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung, Alan C. Mullen
Software Mentions: 11
Published: over 8 years ago

10.1016/j.molcel.2018.08.004

Methylation of Structured RNA by the m6A Writer METTL16 Is Essential for Mouse Embryonic Development
Cited by: 226
Author(s): Mateusz Mendel, Kuan-Ming Chen, David Homolka, Pascal Gos, Radha Raman Pandey, A.A. McCarthy, Ramesh S. Pillai
Software Mentions: 9
Published: about 6 years ago

10.1038/s41598-020-65087-w

Expression of genes of the Pho regulon is altered in Streptomyces coelicolor
Cited by: 22
Author(s): Aarón Millán-Oropeza, Céline Henry, Clara Lejeune, Michelle David, Marie‐Joëlle Virolle
Software Mentions: 9
Published: over 4 years ago

10.3390/biom10081179

Dietary Supplementation with Sugar Beet Fructooligosaccharides and Garlic Residues Promotes Growth of Beneficial Bacteria and Increases Weight Gain in Neonatal Lambs
Cited by: 2
Author(s): Narciso M. Quijada, Raúl Bodas, José M. Lorenzo, Stephan Schmitz‐Esser, David Rodrı́guez-Làzaro, Marta Hernández
Software Mentions: 8
Published: over 4 years ago

10.3390/jof6040372

Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR
Cited by: 11
Author(s): S. Franco Ortega, Ilario Ferrocino, Ian Adams, Simone Silvestri, D. Spadaro, M. L. Gullino, Neil Boonham
Software Mentions: 8
Published: almost 4 years ago

10.15252/msb.20188503

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Cited by: 479
Author(s): Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn M. Hallström, Thomas A. Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Lihua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Fredrik Pontén, Mathias Uhlén, Julien Gagneur, Hannes Hahne, Bernhard Küster
Software Mentions: 8
Published: almost 6 years ago

10.1186/s40168-016-0213-y

Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort
Cited by: 361
Author(s): Colin Hill, Denise B. Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B. Jeffery, Carol Anne O’Shea, Claire Watkins, Eugene M. Dempsey, Fulvio Mattivi, Kieran Tuohy, R. Paul Ross, C. Anthony Ryan, Paul W. O’Toole, Catherine Stanton
Software Mentions: 8
Published: almost 8 years ago

10.7554/eLife.41627

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming
Cited by: 38
Author(s): Mirko Francesconi, Bruno Di Stefano, Clara Berenguer, Luísa de Andrés-Aguayo, Marcos Plana-Carmona, María Méndez-Lago, Amy Guillaumet-Adkins, Gustavo Rodríguez-Esteban, Marta Gut, Holger Heyn, Ben Liu, Thomas Graf
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0015581

Therapeutic Implications of GIPC1 Silencing in Cancer
Cited by: 21
Author(s): Thomas Chittenden, Jane Pak, Renee Rubio, Hai‐Ling Margaret Cheng, Kristina M. Holton, Niall Prendergast, Vladimir Glinskii, Yi Cai, Aedín C. Culhane, Stefan Bentink, Mathew Schwede, Jessica C. Mar, Eleanor Howe, Martin J. Aryee, Răzvan Sultana, Anthony A. Lanahan, Jennifer Taylor, Chris Holmes, William C. Hahn, Jean J. Zhao, J. Dirk Iglehart, John Quackenbush
Software Mentions: 6
Published: almost 14 years ago

10.1186/s12920-015-0106-0

Integrated approaches to miRNAs target definition: time-series analysis in an osteosarcoma differentiative model
Cited by: 15
Author(s): Andrea Grilli, Marika Sciandra, Mario Terracciano, Piero Picci, Katia Scotlandi
Software Mentions: 6
Published: over 9 years ago

10.1371/journal.pone.0219807

Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm
Cited by: 12
Author(s): Korin Eckstrom, John W. Barlow
Software Mentions: 6
Published: about 5 years ago

10.1186/s12866-019-1540-5

Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa
Cited by: 13
Author(s): Stephanie L. Schnorr, Courtney A. Hofman, Shandukani R. Netshifhefhe, Frances D. Duncan, Tanvi P. Honap, Julie J. Lesnik, Cecil M. Lewis
Software Mentions: 6
Published: over 5 years ago

10.1371/journal.pone.0004481

Age and Diet Affect Gene Expression Profile in Canine Skeletal Muscle
Cited by: 17
Author(s): Ingmar S. Middelbos, Brittany M. Vester, Lisa K. Karr-Lilienthal, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 5
Published: almost 16 years ago

10.1038/s42003-021-02204-z

Random errors in protein synthesis activate an age-dependent program of muscle atrophy in mice
Cited by: 5
Author(s): James M. Moore, Rashid Akbergenov, Martina Nigri, Patricia Isnard-Petit, Amandine Grimm, Petra Seebeck, Lisa Michelle Restelli, Stephan Frank, Anne Eckert, Kader Thiam, David P Wolfer, Dimitri Shcherbakov, Erik C. Böttger
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-020-61192-y

Diet influences the functions of the human intestinal microbiome
Cited by: 104
Author(s): Maria De Angelis, Ilario Ferrocino, Francesco Maria Calabrese, Francesca De Filippis, Noemi Cavallo, Sonya Siragusa, Simone Rampelli, Raffaella Di Cagno, Kalliopi Rantsiou, Lucia Vannini, Nicoletta Pellegrini, Camilla Lazzi, Silvia Turroni, Nicola Lorusso, Mario Ventura, Marcello Chieppa, Erasmo Neviani, Patrizia Brigidi, Paul W. O’Toole, Marco Gobbetti, Luca Simone Cocolin
Software Mentions: 5
Published: over 4 years ago

10.1111/1751-7915.13485

Faecal microbiota and functional capacity associated with weaning weight in meat rabbits
Cited by: 19
Author(s): Shouguo Fang, Xuan Chen, Liwen Zhou, Chongchong Wang, Qiaohui Chen, Ruiyi Lin, Tianfang Xiao, Qianfu Gan
Software Mentions: 5
Published: about 5 years ago

10.1186/s40168-016-0164-3

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants
Cited by: 52
Author(s): Colin Hill, Jillian R. Brown, Denise B. Lynch, Ian B. Jeffery, C. Anthony Ryan, R. Paul Ross, Catherine Stanton, Paul W. O’Toole
Software Mentions: 5
Published: over 8 years ago

10.3390/microorganisms8081134

Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome
Cited by: 10
Author(s): Elena Biagi, Carlo Mengucci, Monica Barone, Gianfranco Picone, Alex Lucchi, Pietro Celi, Gilberto Litta, Marco Candela, Gerardo Manfreda, Patrizia Brigidi, Francesco Capozzi, Alessandra De Cesare
Software Mentions: 5
Published: over 4 years ago

10.3390/ijms20225594

Lipid Related Genes Altered in NASH Connect Inflammation in Liver Pathogenesis Progression to HCC: A Canonical Pathway
Cited by: 19
Author(s): Christophe Desterke, Franck Chiappini
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0225001

Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status
Cited by: 38
Author(s): Tucker Andrews, Deborah A. Neher, Thomas R. Weicht, John W. Barlow
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0044736

Brain Transcriptional and Epigenetic Associations with Autism
Cited by: 131
Author(s): Matthew R. Ginsberg, Robert A. Rubin, Tatiana Falcone, Angela H. Ting, Marvin R. Natowicz
Software Mentions: 5
Published: about 12 years ago

10.1242/bio.040683

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Cited by: 4
Author(s): Isabel Reuter, Jana Jäckels, Susanne Kneitz, Jochen Kuper, Klaus–Peter Lesch, Christina Lillesaar
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0178151

Analysis of early mesothelial cell responses to Staphylococcus epidermidis isolated from patients with peritoneal dialysis-associated peritonitis
Cited by: 5
Author(s): Amanda L. McGuire, Kieran T. Mulroney, Christine Carson, Ram Ramesh, Grant Morahan, Aron Chakera
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-32361-x

Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model
Cited by: 12
Author(s): Stefan Rupf, Cédric Christian Laczny, Valentina Galata, Christina Backes, Andreas Keller, Natalia Umanskaya, Arzu Erol, Sascha Tierling, Christina Lo Porto, Jörn Walter, Jasmin Kirsch, Matthias Hannig, Christian Hannig
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-92027-z

Changes in gut microbiota in the acute phase after spinal cord injury correlate with severity of the lesion
Cited by: 29
Author(s): Gabriele Bazzocchi, Silvia Turroni, Maria Chiara Bulzamini, Federica D’Amico, Angelica Bava, Massimo Castiglioni, Valentina Cagnetta, Ernesto Losavio, Maurizio Cazzaniga, Laura Terenghi, Luisa De Palma, Giampiero Frasca, Beatrice Aiachini, Sonia Cremascoli, Antonino Massone, Claudia Oggerino, Maria Pia Onesta, Laura Rapisarda, Maria Cristina Pagliacci, Sauro Biscotto, Michele Scarazzato, Tiziana Giovannini, Mimosa Balloni, Marco Candela, Patrizia Brigidi, Carlotte Kiekens
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0224644

Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA- PCG pairs involved in intermediary metabolism
Cited by: 5
Author(s): Angela Zhang, Cindy Yanfei Li, Edward J. Kelly, Lianne Sheppard, Julia Yue Cui
Software Mentions: 4
Published: over 4 years ago

10.1128/mSystems.00484-19

Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia
Cited by: 21
Author(s): Feargal J. Ryan, Damian Paul Drew, Chloe A. Douglas, Lex E. X. Leong, Max Moldovan, Miriam A. Lynn, Naomi Fink, Anastasia Sribnaia, Irmeli A. Penttila, Andrew J McPhee, Carmel T Collins, Maria Makrides, Robert Gibson, Geraint B. Rogers, David J. Lynn
Software Mentions: 4
Published: about 5 years ago

10.1186/s13071-015-0974-3

Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210
Cited by: 58
Author(s): Benjamin Frank, Ana Marcu, Antônio Luis de Oliveira Almeida Petersen, Heike Weber, Christian Stigloher, Jeremy C. Mottram, Claus‐Jürgen Scholz, Uta Schurigt
Software Mentions: 4
Published: over 9 years ago

10.1186/s12885-015-1539-8

Identifying novel hypoxia-associated markers of chemoresistance in ovarian cancer
Cited by: 34
Author(s): Lynda McEvoy, Sharon O’Toole, Cathy Spillane, C Martín, Michael Gallagher, Britta K. Stordal, Gordon Blackshields, Orla Sheils, John O’Leary
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0151335

Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo
Cited by: 59
Author(s): Corinna Rosenbaum, Martin Alexander Schick, Jakob Wollborn, Andreas Heider, Claus‐Jürgen Scholz, Alexander Cecil, Beate Niesler, Johannes Hirrlinger, Heike Walles, Marco Metzger
Software Mentions: 4
Published: over 8 years ago

10.3389/fimmu.2020.01390

Alterations in Circulating Fatty Acid Are Associated With Gut Microbiota Dysbiosis and Inflammation in Multiple Sclerosis
Cited by: 94
Author(s): Marina Saresella, Ivana Marventano, Monica Barone, Francesca La Rosa, Federica Piancone, Laura Mendozzi, Alessia d’Arma, Valentina Rossi, Luigi Pugnetti, Gabriella Roda, Eleonora Casagni, Michele Dei, Rita Paroni, Patrizia Brigidi, Silvia Turroni, Mario Clerici
Software Mentions: 4
Published: over 4 years ago

10.1016/j.isci.2021.102816

The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs
Cited by: 7
Author(s): Simone Rampelli, Silvia Turroni, Florencia Debandi, Antton Alberdi, Stephanie L. Schnorr, Courtney A. Hofman, Alberto Taddia, Riccardo Helg, Elena Biagi, Patrizia Brigidi, Federica D’Amico, Maurizio Cattani, Marco Candela
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-8-90

Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data
Cited by: 10
Author(s): Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier, Pascal Roy
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2334-10-176

Tracking the transcriptional host response from the acute to the regenerative phase of experimental pneumococcal meningitis
Cited by: 16
Author(s): Matthias Wittwer, Denis Grandgirard, Janine Rohrbach, Stephen L. Leib
Software Mentions: 3
Published: over 14 years ago

10.1186/s12920-017-0252-7

Computational analysis of the mesenchymal signature landscape in gliomas
Cited by: 3
Author(s): Orieta Celiku, Anita Tandle, Joon‐Yong Chung, Stephen M. Hewitt, Kevin Camphausen, Uma Shankavaram
Software Mentions: 3
Published: over 7 years ago

10.1186/s12920-019-0494-7

Early gut microbiota signature of aGvHD in children given allogeneic hematopoietic cell transplantation for hematological disorders
Cited by: 48
Author(s): Elena Biagi, Daniele Zama, Simone Rampelli, Silvia Turroni, Patrizia Brigidi, Clarissa Consolandi, Marco Severgnini, Eleonora Picotti, Pietro Gasperini, Pietro Merli, Nunzia Decembrino, Marco Zecca, Simone Cesaro, Maura Faraci, Arcangelo Prete, Franco Locatelli, Andrea Pession, Marco Candela, Riccardo Masetti
Software Mentions: 3
Published: over 5 years ago

10.1186/1752-0509-8-S2-S4

Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data
Cited by: 12
Author(s): Oana Tomescu, Diethard Mattanovich, Gerhard Thallinger
Software Mentions: 3
Published: over 10 years ago

10.1186/s40168-016-0202-1

Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns
Cited by: 98
Author(s): Francesca De Filippis, Nicoletta Pellegrini, Luca Laghi, Marco Gobbetti
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0031490

The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis
Cited by: 44
Author(s): Franck Thuny, Julien Textoris, Amira Ben Amara, Adil El Filali, Christian Capo, Gilbert Habib, Didier Raoult, Jean‐Louis Mège
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0050985

Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke
Cited by: 50
Author(s): Ana-Maria Buga, Claus‐Jürgen Scholz, Krishan Kumar, James G. Herndon, Dragoş Ovidiu Alexandru, Gabriel Radu Cojocaru, Thomas Dandekar, Aurel Popa‐Wagner
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0082638

Evaluation of Current and New Biomarkers in Severe Preeclampsia: A Microarray Approach Reveals the VSIG4 Gene as a Potential Blood Biomarker
Cited by: 33
Author(s): Julien Textoris, Delphine Ivorra, Amira Ben Amara, Florence Sabatier, Jean-Pierre Ménard, H. Heckenroth, Florence Bretelle, Jean‐Louis Mège
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0220619

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context
Cited by: 55
Author(s): Monica Barone, Silvia Turroni, Simone Rampelli, Matteo Soverini, Federica D’Amico, Elena Biagi, Patrizia Brigidi, Emidio Troiani, Marco Candela
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0208171

Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype
Cited by: 75
Author(s): Pamela Vernocchi, Federica Del Chierico, Alessandra Russo, Fabio Majo, Martina Rossitto, Mariacristina Valerio, Luca Casadei, Antonietta La Storia, Francesca De Filippis, Cristiano Rizzo, Cesare Manetti, Paola Paci, Federico Marini, Ersilia Fiscarelli, Bruno Dallapiccola, Vincenzina Lucidi, Alfredo Miccheli, Lorenza Putignani
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0089110

Otx2 ChIP-seq Reveals Unique and Redundant Functions in the Mature Mouse Retina
Cited by: 53
Author(s): Alexander Samuel, Michael Housset, Bruno Fant, Thomas Lamonerie
Software Mentions: 3
Published: almost 11 years ago

10.3390/cancers12020520

Intratumoral Heterogeneity and Longitudinal Changes in Gene Expression Predict Differential Drug Sensitivity in Newly Diagnosed and Recurrent Glioblastoma
Cited by: 35
Author(s): Ella L. Kim, Maxim Sorokin, Sven R. Kantelhardt, Darius Kalasauskas, Bettina Sprang, Julian Fauß, Florian Ringel, Andrew Garazha, Eugene Albert, Нуршат Гайфуллин, Christian Hartmann, Nicole Naumann, Sven-Ernö Bikar, Alf Giese, Anton Buzdin
Software Mentions: 3
Published: over 4 years ago

10.3389/fnagi.2014.00044

Transcriptomics of Post-Stroke Angiogenesis in the Aged Brain
Cited by: 84
Author(s): Ana-Maria Buga, Claudiu Mărgăritescu, Claus‐Jürgen Scholz, Eugen Radu, Christine Zelenak, Aurel Popa‐Wagner
Software Mentions: 3
Published: over 10 years ago

10.3389/fnins.2020.00732

Electric Stimulation of Neurogenesis Improves Behavioral Recovery After Focal Ischemia in Aged Rats
Cited by: 14
Author(s): Adrian Tudor Bălșeanu, Monica Grigore, Leonard-Radu Pinosanu, Mark Slevin, Dirk M. Hermann, Daniela Glăvan, Aurel Popa‐Wagner
Software Mentions: 3
Published: over 4 years ago

10.3389/fpls.2020.00700

Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Microbial Ecology and Chemical-Physical Grape Characteristics at Harvest
Cited by: 32
Author(s): Kalliopi Rantsiou, Simone Giacosa, Massimo Pugliese, Vasileios Englezos, Ilario Ferrocino, M. Monchiero, Ivana Gribaudo, Giorgio Gambino, M. L. Gullino
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-014-0526-8

Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier
Cited by: 92
Author(s): Filipe Correia Martins, Inês de Santiago, Anne Trinh, Xian Jian, Anne Guo, Karen Sayal, Mercedes Jimenez-Liñan, Suha Deen, Kristy Driver, Marie Mack, Jennifer Aslop, Paul D.P. Pharoah, Florian Markowetz, James D. Brenton
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep32826

Fecal metabolome of the Hadza hunter-gatherers: a host-microbiome integrative view
Cited by: 64
Author(s): Silvia Turroni, Jessica Fiori, Simone Rampelli, Stephanie L. Schnorr, Clarissa Consolandi, Monica Barone, Elena Biagi, Flaminia Fanelli, Marco Mezzullo, Alyssa N. Crittenden, Amanda G. Henry, Patrizia Brigidi, Marco Candela
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-30735-9

Changes in the gut microbiota composition during pregnancy in patients with gestational diabetes mellitus (GDM)
Cited by: 137
Author(s): Ilario Ferrocino, Valentina Ponzo, Roberto Gambino, Adriana Zarovska, Filomena Leone, C Monzeglio, Ilaria Goitre, Rosalba Rosato, Angelo Romano, Giorgio Grassi, Fabio Broglio, Maurizio Cassader, Luca Simone Cocolin, Simona Bo
Software Mentions: 3
Published: over 6 years ago

10.1186/s13063-020-04444-6

Modulation of gut microbiota through nutritional interventions in Behçet’s syndrome patients (the MAMBA study): study protocol for a randomized controlled trial
Cited by: 16
Author(s): Giuditta Pagliai, Monica Dinu, Claudia Fiorillo, Matteo Becatti, Silvia Turroni, Giacomo Emmi, Francesco Sofi
Software Mentions: 3
Published: over 4 years ago

10.3390/ijms21114057

Embryonic Program Activated during Blast Crisis of Chronic Myelogenous Leukemia (CML) Implicates a TCF7L2 and MYC Cooperative Chromatin Binding
Cited by: 3
Author(s): Christophe Desterke, Patricia Hugues, Jin Wook Hwang, Annelise Bennaceur-Griscelli, Ali G. Turhan
Software Mentions: 3
Published: over 4 years ago

10.1534/g3.119.400051

Expression Signatures of Cisplatin- and Trametinib-Treated Early-Stage Medaka Melanomas
Cited by: 5
Author(s): Barbara Klotz, Susanne Kneitz, Yuan Lu, William Boswell, John H. Postlethwait, Wesley C. Warren, Ronald B. Walter, Manfred Schartl
Software Mentions: 2
Published: over 5 years ago

10.1038/srep21871

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate
Cited by: 139
Author(s): Francesca De Filippis, Alessandro Genovese, Pasquale Ferranti, Jack A. Gilbert
Software Mentions: 2
Published: over 8 years ago

10.1038/srep32027

Prognostic significance of nuclear expression of UMP-CMP kinase in triple negative breast cancer patients
Cited by: 12
Author(s): Ning Qing Liu, Tommaso De Marchi, Annemieke M. Timmermans, Anita M A C Trapman-Jansen, Renée Foekens, Maxime P. Look, Marcel Smid, Carolien H.M. van Deurzen, Paul N. Span, Fred C.G.J. Sweep, Julie Benedicte Brask, Vera Timmermans-Wielenga, John A. Foekens, John W.M. Martens, Arzu Umar
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0012190

Sex-Related Differences in Gene Expression Following Coxiella burnetii Infection in Mice: Potential Role of Circadian Rhythm
Cited by: 36
Author(s): Julien Textoris, Leang Heng Ban, Christian Capo, Didier Raoult, Marc Léone, Jean‐Louis Mège
Software Mentions: 2
Published: over 14 years ago

10.1038/s41598-017-06743-6

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants
Cited by: 14
Author(s): Carola Parolin, Barbara Giordani, Rogers Alberto Ñahui Palomino, Elena Biagi, Marco Severgnini, Clarissa Consolandi, Giada Caredda, Stefano Storelli, L Strohmenger, Beatrice Vitali
Software Mentions: 2
Published: over 7 years ago

10.15252/emmm.201809571

Cobalt protoporphyrin <scp>IX</scp> increases endogenous G‐ <scp>CSF</scp> and mobilizes <scp>HSC</scp> and granulocytes to the blood
Cited by: 12
Author(s): Agata Szade, Krzysztof Szade, Witold Nowak, Karolina Bukowska-Strakovà, Lucie Muchová, Monika Gońka, Monika Żukowska, Maciej Cieśla, Neli Kachamakova‐Trojanowska, Marzena Rams-Baron, A. Ratuszna, Józef Dulak, Alicja Józkowicz
Software Mentions: 2
Published: about 5 years ago

10.1038/s42003-019-0626-9

Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis
Cited by: 32
Author(s): Dmitry Shcherbakov, Youjin Teo, Heithem Boukari, Adrian Cortes-Sanchon, Matilde Mantovani, Ivan Osinnii, James M. Moore, Reda Juskeviciene, Margarita Brilkova, Stefan Duscha, Harshitha Santhosh Kumar, Endre Laczkó, Hubert Rehrauer, Éric Westhof, Rashid Akbergenov, Erik C. Böttger
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0099420

Intracellular Bacteria Interfere with Dendritic Cell Functions: Role of the Type I Interferon Pathway
Cited by: 40
Author(s): Laurent Gorvel, Julien Textoris, Romain Banchereau, Amira Ben Amara, Wiwit Tantibhedhyangkul, Kristin von Bargen, Mignane Ka, Christian Capo, Éric Ghigo, Jean‐Pierre Gorvel, Jean‐Louis Mège
Software Mentions: 2
Published: over 10 years ago

10.1186/s11689-018-9237-x

Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex
Cited by: 43
Author(s): Matthew Schwede, Shailender Nagpal, Michael J. Gandal, Neelroop N. Parikshak, Károly Mirnics, Daniel H. Geschwind, Eric M. Morrow
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2017.02079

Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients
Cited by: 19
Author(s): Matteo Soverini, Silvia Turroni, Elena Biagi, Sara Quercia, Patrizia Brigidi, Marco Candela, Simone Rampelli
Software Mentions: 2
Published: about 7 years ago

10.3389/fmicb.2016.01058

Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome
Cited by: 15
Author(s): Matteo Soverini, Simone Rampelli, Silvia Turroni, Stephanie L. Schnorr, Sara Quercia, Andréa Castagnetti, Elena Biagi, Patrizia Brigidi, Marco Candela
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2020.01835

Effects of Gut Microbiome and Short-Chain Fatty Acids (SCFAs) on Finishing Weight of Meat Rabbits
Cited by: 25
Author(s): Shouguo Fang, Xuan Chen, Xiaoxing Ye, Liwen Zhou, Shuaishuai Xue, Qianfu Gan
Software Mentions: 2
Published: over 4 years ago

10.3389/fvets.2020.00146

Influence of Lactobacillus kefiri on Intestinal Microbiota and Fecal IgA Content of Healthy Dogs
Cited by: 11
Author(s): Alba Gaspardo, Augusta Zannoni, Silvia Turroni, Monica Barone, Maria Chiara Sabetti, Renato Giulio Zanoni, Monica Forni, Patrizia Brigidi, Marco Pietra
Software Mentions: 2
Published: over 4 years ago

10.3389/fcimb.2014.00179

Myeloid decidual dendritic cells and immunoregulation of pregnancy: defective responsiveness to Coxiella burnetii and Brucella abortus
Cited by: 16
Author(s): Laurent Gorvel, Amira Ben Amara, Mignane Ka, Julien Textoris, Jean‐Pierre Gorvel, Jean‐Louis Mège
Software Mentions: 2
Published: almost 10 years ago

10.1080/19490976.2020.1747335

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition
Cited by: 62
Author(s): Martín Beaumont, Charlotte Paës, Eloïse Mussard, Christelle Knudsen, Laurent Cauquil, Patrick Aymard, Céline Barilly, Béatrice Gabinaud, Olivier Zemb, Sandra Fourré, Roselyne Gautier, Corinne Lencina, Hélène Eutamene, Vassilia Théodorou, Cécile Canlet, Sylvie Combes
Software Mentions: 2
Published: over 4 years ago

10.1126/sciadv.aaz2015

Mapping of host-parasite-microbiome interactions reveals metabolic determinants of tropism and tolerance in Chagas disease
Cited by: 34
Author(s): Ekram Hossain, Shugufta Khanam, Danya A. Dean, Chao‐Yi Wu, Sharon Lostracco-Johnson, Diane Thomas, Shelley S. Kane, Adwaita R. Parab, Karina Flores, Mitchelle Katemauswa, Camil Gosmanov, Susana Hayes, Y. Zhang, D. Li, Christine Woelfel-Monsivais, Krithivasan Sankaranarayanan, Laura-Isobel McCall
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.59399

Drosophila serotonin 2A receptor signaling coordinates central metabolic processes to modulate aging in response to nutrient choice
Cited by: 18
Author(s): Yang Lyu, Kristina J Weaver, Humza A Shaukat, Marta L Plumoff, Maria Tjilos, Daniel Promislow, Scott D. Pletcher
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-018-32688-5

Comparative assessment of autochthonous bacterial and fungal communities and microbial biomarkers of polluted agricultural soils of the Terra dei Fuochi
Cited by: 45
Author(s): Valeria Ventorino, Alberto Pascale, Paola Adamo, Claudia Rocco, Nunzio Fiorentino, Mauro Mori, Vincenza Faraco, Olimpia Pepe, Massimo Fagnano
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-53183-5

Human faecal collection methods demonstrate a bias in microbiome composition by cell wall structure
Cited by: 30
Author(s): Emma-Jane Watson, Jennifer Giles, Benjamin L. Scherer, Paul Blatchford
Software Mentions: 1
Published: about 5 years ago

10.3389/fmicb.2017.01465

Proteomic Response of Pseudomonas aeruginosa PAO1 Adhering to Solid Surfaces
Cited by: 23
Author(s): Morgan Guilbaud, Jérôme Bruzaud, Emeline Bouffartigues, Nicole Orange, Alain Guillot, Anne Aubert-Frambourg, Véronique Monnet, Jean‐Marie Herry, Sylvie Chevalier, Marie‐Nöelle Bellon‐Fontaine
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0200923

Aryl hydrocarbon receptor (AHR) is a novel druggable pathway controlling malignant progenitor proliferation in chronic myeloid leukemia (CML)
Cited by: 14
Author(s): Melanie Gentil, Patricia Hugues, Christophe Desterke, Gladys Telliam, Ivan Sloma, Lucas Eduardo Botelho de Souza, Seda Baykal, Jérôme Artus, Frank Griscelli, Agnès Guerci, Hyacinthe Johnson‐Ansah, Adlen Foudi, Annelise Bennaceur-Griscelli, Ali G. Turhan
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0029954

TWIST1 a New Determinant of Epithelial to Mesenchymal Transition in EGFR Mutated Lung Adenocarcinoma
Cited by: 58
Author(s): Karine Pallier, Anatole Cessot, Jean‐François Côté, Pierre‐Alexandre Just, Aurélie Cazes, Elizabeth Fabre, Claire Danel, Marc Riquet, Mojgan Devouassoux‐Shisheboran, Stéphane Ansieau, Alain Puisieux, Pierre Laurent‐Puig, Hélène Blons
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0052227

Characterization of Shear-Sensitive Genes in the Normal Rat Aorta Identifies Hand2 as a Major Flow-Responsive Transcription Factor
Cited by: 17
Author(s): Hanna M. Björck, Johan Renner, Shohreh Maleki, Stefan Nilsson, Johan Kihlberg, Lasse Folkersen, Matts Karlsson, Tino Ebbers, Per Eriksson, Toste Länne
Software Mentions: 1
Published: almost 12 years ago

10.1002/ece3.4045

Differential levels of gene expression and molecular mechanisms between red maple (<i>Acer rubrum</i> ) genotypes resistant and susceptible to nickel toxicity revealed by transcriptome analysis
Cited by: 8
Author(s): K. K. Nkongolo, Gabriel Theriault, M. Paul
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.00895-17

A Single Regulator Mediates Strategic Switching between Attachment/Spread and Growth/Virulence in the Plant Pathogen <i>Ralstonia solanacearum</i>
Cited by: 61
Author(s): Devanshi Khokhani, Tiffany M. Lowe‐Power, Tuan Minh Tran, Caitilyn Allen
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-10394-y

Small molecule-based lineage switch of human adipose-derived stem cells into neural stem cells and functional GABAergic neurons
Cited by: 26
Author(s): Jihye Park, Nayeon Lee, Jaekwang Lee, Eun Kyung Choe, Min Kyung Kim, Jeong-Hoon Lee, Min Soo Byun, Myong-Wuk Chon, Seong Who Kim, C. Justin Lee, Ju Han Kim, Jun Soo Kwon, Mi-Sook Chang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12885-016-2988-4

MALAT1 promoted invasiveness of gastric adenocarcinoma
Cited by: 52
Author(s): Na Keum Lee, Jung Hwa Lee, Cristina Ivan, Hui Ling, Xinna Zhang, Chan Hyuk Park, George A. Calin, Sang Kil Lee
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0153762

Comprehensive Transcriptome Analysis of Response to Nickel Stress in White Birch (Betula papyrifera)
Cited by: 26
Author(s): Gabriel Theriault, M. Paul, K. K. Nkongolo
Software Mentions: 1
Published: over 8 years ago

Projects: bioconductor: made4

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