bioconductor: ArrayExpress | Projects

10.1186/s12885-017-3103-1

Meta-analysis of gene expression in relapsed childhood B-acute lymphoblastic leukemia
Cited by: 21
Author(s): Yock-Ping Chow, Hamidah Alias, Rahman Jamal
Software Mentions: 5
Published: about 9 years ago

10.1186/1752-0509-7-12

Identification of ovarian cancer associated genes using an integrated approach in a Boolean framework
Cited by: 12
Author(s): Gaurav Kumar, Edmond J. Breen, Shoba Ranganathan
Software Mentions: 5
Published: about 13 years ago

10.1186/s12859-020-03633-z

PDXGEM: patient-derived tumor xenograft-based gene expression model for predicting clinical response to anticancer therapy in cancer patients
Cited by: 10
Author(s): Young‐Chul Kim, Daewon Kim, Biwei Cao, Rodrigo Carvajal, Minjung Kim
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pone.0225805

Food from faeces: Evaluating the efficacy of scat DNA metabarcoding in dietary analyses
Cited by: 25
Author(s): David Thuo, Elise M. Furlan, Femke Broekhuis, Joseph Kamau, Kyle Macdonald, Dianne Gleeson
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-020-0989-y

IDO1+ Paneth cells promote immune escape of colorectal cancer
Cited by: 22
Author(s): Sandra Pflügler, Jasmin Svinka, Irene Scharf, Ilija Crnčec, Martin Filipits, Pornpimol Charoentong, Markus Tschurtschenthaler, Lukas Kenner, Monira Awad, Judith Stift, Marina Schernthanner, Romana Bischl, Dietmar Herndler‐Brandstetter, Elisabeth Glitzner, Herwig P. Moll, Emilio Casanova, Gerald Timelthaler, Maria Sibilia, Michael Gnant, Sigurd Lax, Josef Thaler, Mathias Müller, Birgit Strobl, Thomas Mohr, Arthur Kaser, Zlatko Trajanoski, Gerwin Heller, Robert Eferl
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.dib.2019.103909

RNA-sequencing data highlighting the time-of-day-dependent transcriptome of the central circadian pacemaker in Sox2-deficient mice
Cited by: 4
Author(s): Arthur H. Cheng, Pascale Bouchard-Cannon, Rob W. Ness, Hai-Ying Mary Cheng
Software Mentions: 5
Published: almost 7 years ago

10.1186/1471-2229-8-99

Regulon organization of Arabidopsis
Cited by: 95
Author(s): Wieslawa I. Mentzen, Eve Syrkin Wurtele
Software Mentions: 5
Published: over 18 years ago

10.1186/1471-2105-14-75

virtualArray: a R/bioconductor package to merge raw data from different microarray platforms
Cited by: 51
Author(s): Andreas Heider, Rüdiger Alt
Software Mentions: 5
Published: about 13 years ago

10.1093/database/bau068

yStreX: yeast stress expression database
Cited by: 11
Author(s): Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranović
Software Mentions: 5
Published: over 12 years ago

10.1186/s13148-021-01083-9

Estimands in epigenome-wide association studies
Cited by: 9
Author(s): Jochen Kruppa, Miriam Sieg, Gregor Richter, Anne Pohrt
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13148-019-0608-2

Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes
Cited by: 34
Author(s): Louise F. Porter, Neil Saptarshi, Yongxiang Fang, Sonika Rathi, Anneke I. den Hollander, Eiko K. de Jong, Simon J. Clark, Paul Bishop, Timothy W. Olsen, Triantafillos Liloglou, Venkata R M Chavali, Luminita Paraoan
Software Mentions: 5
Published: about 7 years ago

10.1093/database/bau027

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences
Cited by: 11
Author(s): Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom
Software Mentions: 5
Published: over 12 years ago

10.1016/j.cels.2018.06.011

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
Cited by: 63
Author(s): Nils Eling, Alison F. Richard, Sylvia Richardson, John C. Marioni, Catalina A. Vallejos
Software Mentions: 5
Published: over 7 years ago

10.1038/s41422-018-0128-1

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis
Cited by: 46
Author(s): Marcos Morgan, Yuka Kabayama, Christian Much, Ivayla Ivanova, Monica Di Giacomo, Tatsiana Auchynnikava, Jack Monahan, Dimitrios Vitsios, Lina Vasiliauskaitė, Stefano Comazzetto, Juri Rappsilber, Robin C. Allshire, Bo T. Porse, Anton J. Enright, Dónal O’Carroll
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pbio.1001229

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution
Cited by: 91
Author(s): Robert K. Bradley, Jason J. Merkin, Nicole Lambert, Christopher B. Burge
Software Mentions: 5
Published: over 14 years ago

10.1371/journal.pbio.3001166

Neural stem cells traffic functional mitochondria via extracellular vesicles
Cited by: 79
Author(s): Luca Peruzzotti-Jametti, Joshua D. Bernstock, Cory M. Willis, Giulia Manferrari, Rebecca Rogall, Erika Fernández-Vizarra, James C Williamson, Alice Braga, Aletta van den Bosch, Tommaso Leonardi, Grzegorz Krzak, Ágnes Kittel, Cristiane Benincá, Nunzio Vicario, Sisareuth Tan, Carlos Bastos, Iacopo Bicci, Nunzio Iraci, JA Smith, Ben Peacock, Karin H. Müller, Paul J. Lehner, Edit I. Buzás, Nuno Faria, Massimo Zeviani, Christian Frezza, Alain Brisson, Nicholas J Matheson, Carlo Viscomi, Stefano Pluchino
Software Mentions: 5
Published: about 5 years ago

10.1186/1471-2229-10-150

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms
Cited by: 129
Author(s): Dennis Janz, Katja Behnke, Jörg‐Peter Schnitzler, Basem Kanawati, Philippe Schmitt‐Kopplin, Andrea Polle
Software Mentions: 5
Published: over 15 years ago

10.1186/1471-2105-9-558

SPRINT: A new parallel framework for R
Cited by: 33
Author(s): Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence Sloan, Florian Scharinger, Arthur Trew, Peter Ghazal
Software Mentions: 5
Published: over 17 years ago

10.1371/journal.pone.0081167

Cytokeratin 15 Marks Basal Epithelia in Developing Ureters and Is Upregulated in a Subset of Urothelial Cell Carcinomas
Cited by: 21
Author(s): Guihua Tai, Parisa Ranjzad, Fiona Marriage, Samrina Rehman, Helen Denley, Jill Dixon, Karen S. Mitchell, Philip J. Day, Adrian S. Woolf
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0226616

Insights into fungal diversity of a shallow-water hydrothermal vent field at Kueishan Island, Taiwan by culture-based and metabarcoding analyses
Cited by: 25
Author(s): Ka−Lai Pang, Sheng−Yu Guo, I-An Chen, Gaëtan Burgaud, Zengwei Luo, Hans-Uwe Dahms, Jiang‐Shiou Hwang, Yi-Li Lin, Jian-Shun Huang, Tsz-Wai Ho, Ling Ming Tsang, Michael Chiang, Hyojung Cha
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0161504

Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis
Cited by: 58
Author(s): Obed Brew, Mark Sullivan, Anthony C. Woodman
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0244724

Geography as non-genetic modulation factor of chicken cecal microbiota
Cited by: 8
Author(s): Natalia Daniela Pin Viso, Enzo A. Redondo, Juan María Díaz Carrasco, Leandro M. Redondo, Javier García, Mariano E. Fernández‐Miyakawa, Marisa Diana Farber
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-10-63

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes
Cited by: 16
Author(s): Steven P. Wilder, Pamela J. Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 5
Published: about 17 years ago

10.1186/s12864-016-3288-8

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
Cited by: 24
Author(s): Giovanna Ambrosini, René Dreos, Sunil Kumar, Philipp Bücher
Software Mentions: 5
Published: over 9 years ago

10.1371/journal.pone.0102579

Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action
Cited by: 60
Author(s): Daniel Gusenleitner, Scott S. Auerbach, Tisha Melia, Harold F. Gómez, David H. Sherr, Stefano Monti
Software Mentions: 5
Published: over 11 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: over 7 years ago

10.7554/eLife.58716

Does the human placenta express the canonical cell entry mediators for SARS-CoV-2?
Cited by: 210
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Francesca Luca, Yi Xu, Adnan Alazizi, Yaozhu Leng, Chaur Dong Hsu, Nardhy Gomez-López
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0075578

Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach
Cited by: 7
Author(s): Lucía Spangenberg, Alejandro Correa, Bruno Dallagiovanna, Hugo Naya
Software Mentions: 5
Published: over 12 years ago

10.3390/ijms20143543

Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice
Cited by: 9
Author(s): Francisco Alén, Isabel Gómez-Redondo, Patricia Rivera, Juan Suárez, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Serafín Pérez‐Cerezales, Keiko Horiuchi, Laura Orío, Fernando Rodríguez de Fonseca, Alfonso Gutiérrez‐Adán
Software Mentions: 5
Published: over 6 years ago

10.7554/eLife.53948

Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling
Cited by: 14
Author(s): Y. Claire, John C. Marioni, Gillian M. Griffiths, Alison F. Richard
Software Mentions: 5
Published: almost 6 years ago

10.3390/microarrays3040212

The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Cited by: 1
Author(s): Andrew R. Dalby, Ian Bailey
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pone.0241861

Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections
Cited by: 5
Author(s): Raquel Morais de Paiva Daibert, Carlos Alberto Oliveira de Biagi, Felipe de Oliveira Vieira, Marcos Vinícius Gualberto Barbosa da Silva, Eugênio D. Hottz, Mariana Brandi Mendonça Pinheiro, Daniele Ribeiro de Lima Reis Faza, Hyago Passe Pereira, Marta Fonseca Martins, Humberto M. Brandão, M. A. Machado, Wanessa A. Carvalho
Software Mentions: 5
Published: over 5 years ago

10.12688/f1000research.18276.2

Using equivalence class counts for fast and accurate testing of differential transcript usage
Cited by: 9
Author(s): Marek Cmero, N. Davidson, Alicia Oshlack
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pone.0050253

Analysis of Gene Expression Data from Non-Small Cell Lung Carcinoma Cell Lines Reveals Distinct Sub-Classes from Those Identified at the Phenotype Level
Cited by: 2
Author(s): Andrew R. Dalby, Ibrahim Emam, Raimo Franke
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pone.0236796

Comparative study of neighboring Holm oak and olive trees-belowground microbial communities subjected to different soil management
Cited by: 9
Author(s): Antonio J. Fernández‐González, Nuria M. Wentzien, Pablo J. Villadas, Antonio Valverde-Corredor, Ana V. Lasa, Carmen Gómez-Lama Cabanás, Jesús Mercado‐Blanco, Manuel Fernández‐López
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0254556

Simple mapping-based quantification of a mock microbial community using total RNA-seq data
Cited by: 4
Author(s): Shigeharu Moriya
Software Mentions: 5
Published: over 4 years ago

10.7554/eLife.03346

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network
Cited by: 82
Author(s): Carine Gubelmann, Petra Schwalie, Sunil K. Raghav, Eva Röder, Tenagne Delessa, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudofsky, Didier Trono, Christian Wolfrum, Bart Deplancke
Software Mentions: 5
Published: over 11 years ago

10.1038/s41598-019-48589-0

Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells
Cited by: 7
Author(s): Juan Bautista Menendez-Gonzalez, Samantha Sinnadurai, Alex Gibbs, Leigh-anne Thomas, Maria Konstantinou, Alfonso Garcia-Valverde, Magali Boyer, Zhengke Wang, Ashleigh S. Boyd, Allison Blair, Rhys G. Morgan, Neil P. Rodrigues
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-77777-6

Comparative analysis of transcriptomic profile, histology, and IDH mutation for classification of gliomas
Cited by: 6
Author(s): Paul Tran, Lynn Tran, John Nechtman, Bruno dos Santos, Sharad Purohit, Khaled Bin Satter, Boying Dun, Ravindra Kolhe, Suash Sharma, Roni J. Bollag, Jin Xiong She
Software Mentions: 5
Published: over 5 years ago

10.1371/journal.pone.0227303

Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection
Cited by: 8
Author(s): Yuanxiu Wang, Guihong Xiong, Zhe He, Mingfeng Yan, M. Q. Zou, Junxi Jiang
Software Mentions: 5
Published: over 6 years ago

10.3389/fgene.2019.00855

Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments
Cited by: 0
Author(s): Adele Ribeiro, Júlia Maria Pavan Soler, Roberto Hirata
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-47343-w

A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line
Cited by: 9
Author(s): Nikolaï Genov, Alireza Basti, Marconi Abreu, Rosario Astaburuaga, Angela Relógio
Software Mentions: 5
Published: over 6 years ago

10.3389/fimmu.2021.657162

Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness
Cited by: 3
Author(s): Eléna Gonçalves, Yolanda Guillén, Javier R. Lama, Jorge Sánchez, Christian Berthou, Roger Paredes, Béhazine Combadière
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pone.0226253

DNA metabarcoding-based diet survey for the Eurasian otter (Lutra lutra): Development of a Eurasian otter-specific blocking oligonucleotide for 12S rRNA gene sequencing for vertebrates
Cited by: 16
Author(s): Priyanka Kumari, Ke Dong, Kyung-Yeon Eo, Woo-Shin Lee, Junko Kimura, Naomichi Yamamoto
Software Mentions: 5
Published: over 6 years ago

10.1038/srep21911

Transcriptional profiling of human smooth muscle cells infected with gingipain and fimbriae mutants of Porphyromonas gingivalis
Cited by: 6
Author(s): Boxi Zhang, Allan Sirsjö, Hazem Khalaf, Torbjörn Bengtsson
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0106524

Discovering Study-Specific Gene Regulatory Networks
Cited by: 8
Author(s): V. Dal Bò, Tanya Y. Curtis, Artem Lysenko, Mansoor Saqi, Stephen Swift, Allan Tucker
Software Mentions: 5
Published: over 11 years ago

10.18632/oncotarget.23748

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of <i>COX7A1</i> in embryonic and cancer cells
Cited by: 27
Author(s): Michael West, Ivan Labat, Hal Sternberg, Dana Larocca, Igor O. Nasonkin, Karen Chapman, Ratnesh Singh, Eugene Makarev, Alex Aliper, Andrey Kazennov, Andrey Alekseenko, Nikolai Shuvalov, Evgenia Cheskidova, Aleksandr Alekseev, Artemov Av, Evgeny Putin, Polina Mamoshina, Nikita Pryanichnikov, Jacob Larocca, Karen A. F. Copeland, Evgeny Izumchenko, Mikhail Korzinkin, Alex Zhavoronkov
Software Mentions: 5
Published: over 8 years ago

10.1038/sdata.2018.136

A merged lung cancer transcriptome dataset for clinical predictive modeling
Cited by: 26
Author(s): Su Bin Lim, Swee Jin Tan, Wan-Teck Lim, Chwee Teck Lim
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-020-66721-3

Cardiac transcriptional and metabolic changes following thoracotomy
Cited by: 0
Author(s): Markus Heckmann, Ashraf Yusuf Rangrez, Daniel Finke, Andreas Jungmann, Julia S. Kreußer, Alexandra Rosskopf, Nesrin Schmiedel, Hugo A. Katus, Norbert Frey, Oliver Müller
Software Mentions: 5
Published: almost 6 years ago

10.3389/fnut.2021.675935

Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue
Cited by: 1
Author(s): Marianthi Kalafati, Michael Lenz, Gökhan Ertaylan, Ilja C. W. Arts, Chris T. Evelo, Marleen M.J. van Greevenbroek, Ellen E. Blaak, Michiel E. Adriaens, Martina Kutmon
Software Mentions: 5
Published: almost 5 years ago

10.3389/fimmu.2019.02999

Opioids Impair Intestinal Epithelial Repair in HIV-Infected Humanized Mice
Cited by: 37
Author(s): Jingjing Meng, Santanu Banerjee, Li Zhang, Gregory M. Sindberg, Shamsudheen Moidunny, Bin Li, David J. Robbins, Mohit Girotra, Bradley J. Segura, Sundaram Ramakrishnan, Sabita Roy
Software Mentions: 5
Published: about 6 years ago

10.3389/fonc.2014.00251

Hidden Treasures in â€œAncientâ€ Microarrays: Gene-Expression Portrays Biology and Potential Resistance Pathways of Major Lung Cancer Subtypes and Normal Tissue
Cited by: 14
Author(s): Konstantinos Kerkentzes, Vincenzo Lagani, Ioannis Tsamardinos, Mogens Vyberg, Oluf Dimitri Røe
Software Mentions: 5
Published: over 11 years ago

10.3389/fimmu.2018.01661

Integrated Systems Biology Approach Identifies Novel Maternal and Placental Pathways of Preeclampsia
Cited by: 128
Author(s): Nándor Gábor Than, Roberto Romero, Adi L. Tarca, Katalin A. Kékesi, Yi Xu, Zhonghui Xu, Kata Juhász, Gaurav Bhatti, Ron Leavitt, Zsolt Gelencser, János Pálhalmi, Tzu Hung Chung, Balázs Győrffy, László Orosz, Attila Demeter, Anett Szecsi, Éva Hunyadi‐Gulyás, Zsuzsanna Darula, Attila Simor, Katalin Éder, S. Szabó, Vanessa Topping, Haidy Elazzamy, Christopher LaJeunesse, Andrea Balogh, Gábor Szalai, Susan Land, Olga Török, Zhong Dong, Ilona Kovalszky, András Falus, Hamutal Meiri, Sorin Drăghici, Sonia S. Hassan, Tinnakorn Chaiworapongsa, M Krispin, Martin Knöfler, Offer Erez, Graham J. Burton, Chong Jai Kim, Gábor Juhász, Zoltán Papp
Software Mentions: 5
Published: over 7 years ago

10.1016/j.joca.2018.12.015

Identification of long non-coding RNAs expressed in knee and hip osteoarthritic cartilage
Cited by: 30
Author(s): Bola Ajekigbe, Kathleen Cheung, Yaobo Xu, Andrew Skelton, Andreas Panagiotopoulos, Jamie Soul, Timothy E. Hardingham, David J. Deehan, M.J. Barter, David A. Young
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.ppat.1002567

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
Cited by: 197
Author(s): Adam J. Reid, Sarah J. Vermont, James A. Cotton, David J. Harris, Grant A. Hill-Cawthorne, Stephanie Könen‐Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam, Amandeep Sohal, James D. Wasmuth, Brian P. Brunk, Michael E. Grigg, Jonathan C. Howard, John Parkinson, David S. Roos, A. J. Trees, Matthew Berriman, Arnab Pain, Jonathan M. Wastling
Software Mentions: 5
Published: about 14 years ago

10.3389/fgene.2019.00159

A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures
Cited by: 22
Author(s): Adib Shafi, Tin Nguyen, Azam Peyvandipour, Hung Son Nguyen, Sorin Drăghici
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2020.566734

Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging
Cited by: 4
Author(s): Yujuan Gui, Mélanie Thomas, Pierre Garcia, Mona Karout, Rashi Halder, Alessandro Michelucci, Heike Kollmus, Cuiqi Zhou, Shlomo Melmed, Klaus Schughart, Rudi Balling, Michel Mittelbronn, Joseph H. Nadeau, Robert W. Williams, Thomas Sauter, Manuel Buttini, Lasse Sinkkonen
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0236348

Unraveling the molecular pathobiology of vocal fold systemic dehydration using an in vivo rabbit model
Cited by: 8
Author(s): Naíla Cannes do Nascimento, Andrea Pires dos Santos, M. Preeti Sivasankar, Abigail Cox
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.ppat.1009768

Trichuris muris infection drives cell-intrinsic IL4R alpha independent colonic RELMα+ macrophages
Cited by: 6
Author(s): Ruth Forman, Larisa Logunova, Hannah Smith, Kelly Wemyss, Iris Mair, Louis Boon, Judith E. Allen, Werner Müller, Joanne L. Pennock, Kathryn J. Else
Software Mentions: 4
Published: over 4 years ago

10.1093/jxb/eru094

Identification of predominant genes involved in regulation and execution of senescence-associated nitrogen remobilization in flag leaves of field grown barley
Cited by: 63
Author(s): Julien Hollmann, Per L. Gregersen, Karin Krupinska
Software Mentions: 4
Published: about 12 years ago

10.3389/fimmu.2017.01199

Plasmodium berghei NK65 in Combination with IFN-γ Induces Endothelial Glucocorticoid Resistance via Sustained Activation of p38 and JNK
Cited by: 9
Author(s): Karolina Zielińska, Lode De Cauwer, Sofie Knoops, Kristof Van der Molen, Alexander Sneyers, Jonathan Thommis, J. Brian de Souza, Ghislain Opdenakker, Karolien De Bosscher, Philippe E. Van den Steen
Software Mentions: 4
Published: over 8 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: almost 7 years ago

10.3389/fimmu.2018.02902

Maturing Human CD127+ CCR7+ PDL1+ Dendritic Cells Express AIRE in the Absence of Tissue Restricted Antigens
Cited by: 35
Author(s): Joannah R. Fergusson, Michael D. Morgan, Mélanie Bruchard, Leonie F. A. Huitema, Balthasar A. Heesters, Vincent van Unen, Jan Piet van Hamburg, Nicole N. van der Wel, Daisy I. Picavet, Frits Koning, Sander W. Tas, Mark S. Anderson, John C. Marioni, Georg A. Holländer, Hergen Spits
Software Mentions: 4
Published: about 7 years ago

10.3389/fimmu.2018.03075

Pregnancy Epigenetic Signature in T Helper 17 and T Regulatory Cells in Multiple Sclerosis
Cited by: 22
Author(s): Andrea Iannello, Simona Rolla, Alessandro Maglione, Giulio Ferrero, Valentina Bardina, Ilenia Inaudi, Stefania De Mercanti, Francesco Novelli, Lucrezia D'Antuono, Simona Cardaropoli, Tullia Todros, Maria Vittoria Turrini, Cinzia Cordioli, Giorgia Puorro, Angela Marsili, Roberta Lanzillo, Vincenzo Brescia Morra, Francesca Cordero, Michele De Bortoli, Luca Durelli, Andrea Visconti, Santina Cutrupi, Marinella Clerico
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.636108

Impact of Tenascin-C on Radiotherapy in a Novel Syngeneic Oral Squamous Cell Carcinoma Model With Spontaneous Dissemination to the Lymph Nodes
Cited by: 5
Author(s): Caroline Spenlé, Thomas Loustau, Hélène Burckel, Gilles Riegel, Chérine Abou Faycal, Chengbei Li, Alev Yılmaz, Luciana Petti, Fanny Steinbach, Constance Ahowesso, Camille Jost, Nicodème Paul, Raphaël Carapito, Georges Noël, Fabienne Anjuère, Nathalie Salomé, Gertraud Orend
Software Mentions: 4
Published: almost 5 years ago

10.7150/jca.44413

Comprehensive Analysis of the Tumor Microenvironment in Cutaneous Melanoma associated with Immune Infiltration
Cited by: 17
Author(s): Pan Wang, Xinyu Zhang, Nan Sun, Zhihong Zhao, Jie He
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0238202

Immune and sex-biased gene expression in the threatened Mojave desert tortoise, Gopherus agassizii
Cited by: 2
Author(s): Cindy Xu, Greer A. Dolby, K. Kristina Drake, Todd C. Esque, Kenro Kusumi
Software Mentions: 4
Published: over 5 years ago

10.3390/genes6010001

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1
Cited by: 53
Author(s): Kristina B. V. Døssing, Tina Binderup, Bogumił Kaczkowski, Anders Jacobsen, Maria Rossing, Ole Winther, Birgitte Federspiel, Ulrich Knigge, Andreas Kjær, Lennart Friis‐Hansen
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2015.00718

A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones
Cited by: 20
Author(s): Itziar Frades, Kibrom B. Abreha, Estelle Proux‐Wéra, Åsa Lankinen, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2020.00495

Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator
Cited by: 7
Author(s): Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0056228

canEvolve: A Web Portal for Integrative Oncogenomics
Cited by: 39
Author(s): Mehmet K. Samur, Zhenyu Yan, Xujun Wang, Qingyi Cao, Nikhil C. Munshi, Li Cheng, Parantu K. Shah
Software Mentions: 4
Published: about 13 years ago

10.3389/fmicb.2016.01688

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways
Cited by: 19
Author(s): Sadegh Azimzadeh Jamalkandi, Sayed‐Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
Software Mentions: 4
Published: over 9 years ago

10.3389/fmolb.2021.719982

Identification of Mast Cell-Based Molecular Subtypes and a Predictive Signature in Clear Cell Renal Cell Carcinoma
Cited by: 5
Author(s): Hanxiang Liu, Yi Yang
Software Mentions: 4
Published: over 4 years ago

10.3389/fnmol.2018.00363

Assessing Transcriptome Quality in Patch-Seq Datasets
Cited by: 33
Author(s): Shreejoy J. Tripathy, Lilah Toker, Claire Bomkamp, B. Ogan Mancarci, Manuel Belmadani, Paul Pavlidis
Software Mentions: 4
Published: over 7 years ago

10.3389/fnmol.2021.699562

Spatial RNA Sequencing Identifies Robust Markers of Vulnerable and Resistant Human Midbrain Dopamine Neurons and Their Expression in Parkinson’s Disease
Cited by: 20
Author(s): Julio Águila, Shu Cheng, Nigel Kee, Mengshu Cao, Menghan Wang, Qiaolin Deng, Eva Hedlund
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0232436

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed
Cited by: 9
Author(s): Christos Dadousis, Francesca Cecchi, Michela Ablondi, Maria Chiara Fabbri, Alessandra Stella, Rıccardo Bozzi
Software Mentions: 4
Published: about 5 years ago

10.3389/fphar.2019.00747

Bioinformatic Study of Transcriptome Changes in the Mice Lumbar Spinal Cord After the 30-Day Spaceflight and Subsequent 7-Day Readaptation on Earth: New Insights Into Molecular Mechanisms of the Hypogravity Motor Syndrome
Cited by: 8
Author(s): M. S. Kuznetsov, Artur Nicolaevich Lisukov, Albert A. Rizvanov, O. V. Tyapkina, Oleg Gusev, P. N. Rezvyakov, I. B. Kozlovskaya, E. E. Nikolskiy, Р. Р. Исламов
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0227076

All of gene expression (AOE): An integrated index for public gene expression databases
Cited by: 29
Author(s): Hidemasa Bono
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0001061

Cell Cycle Genes Are the Evolutionarily Conserved Targets of the E2F4 Transcription Factor
Cited by: 52
Author(s): Caitlin B. Conboy, Christiana Spyrou, Natalie Thorne, Elizabeth J. Wade, Nuno L. Barbosa‐Morais, Michael D. Wilson, Arindam Bhattacharjee, Richard A. Young, Simon Tavaré, Jacqueline A. Lees, Duncan T. Odom
Software Mentions: 4
Published: over 18 years ago

10.18632/oncotarget.24906

Glucose transporter 1 expression as a marker of prognosis in oesophageal adenocarcinoma
Cited by: 12
Author(s): Jaine K. Blayney, Lauren Cairns, Gerald Li, Niamh McCabe, Leanne Stevenson, Christopher J. Peters, N. Reid, Veronica J. Spence, Chintapuza Chisambo, Damian McManus, Jacqueline James, Stephen McQuaid, Stephanie G. Craig, Ken Arthur, Darragh G. McArt, Chin-Ann Johnny Ong, Pierre Lao–Sirieix, Peter Hamilton, Manuel Salto-Tellez, Martin Eatock, Helen Coleman, Rebecca C. Fitzgerald, Richard D. Kennedy, Richard Turkington, Oesophageal Cancer Clinical
Software Mentions: 4
Published: about 8 years ago

10.18632/oncotarget.23280

Validation of a hypoxia related gene signature in multiple soft tissue sarcoma cohorts
Cited by: 32
Author(s): Lingjian Yang, Laura Forker, Joely J. Irlam, Nischalan Pillay, Ananya Choudhury, Catharine M L West
Software Mentions: 4
Published: over 8 years ago

10.18632/oncotarget.22689

Systematic assessment of cervical cancer initiation and progression uncovers genetic panels for deep learning-based early diagnosis and proposes novel diagnostic and prognostic biomarkers
Cited by: 32
Author(s): Nguyen Phuoc Long, Kyung Hee Jung, Sang Jun Yoon, Nguyễn Hoàng Anh, Tran Diem Nghi, Yun Pyo Kang, Pengcheng Zhang, Jung Eun Min, Sung Kyung Hong, Sung Won Kwon
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0229606

Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves
Cited by: 13
Author(s): Benedikt Kirchner, Dominik Buschmann, Vijay Paul, Michael W. Pfaffl
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0228503

Lumenal calcification and microvasculopathy in fetuin-A-deficient mice lead to multiple organ morbidity
Cited by: 33
Author(s): Marietta Herrmann, Anne Babler, Irina Moshkova, Felix Gremse, Fabian Kießling, Ulrike Kusebauch, Valentin Nelea, Rafael Kramann, Robert L. Moritz, Marc D. McKee, Willi Jahnen‐Dechent
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-32972-4

Cytoplasmic location of NR4A1 in aggressive lymphomas is associated with a favourable cancer specific survival
Cited by: 4
Author(s): Karoline Fechter, Julia Feichtinger, Katharina Prochazka, Julia Judith Unterluggauer, Katrin Pansy, Elisabeth Steinbauer, Martin Pichler, Johannes Haybaeck, Andreas Prokesch, Hildegard Greinix, Christine Beham–Schmid, Peter Neumeister, Gerhard G. Thallinger, Alexander Deutsch
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.22423

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
Cited by: 2
Author(s): Shana Claeys, Geertrui Denecker, Robrecht Cannoodt, Candy Kumps, Kaat Durinck, Franki Speleman, Katleen De Preter
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-29077-3

Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks
Cited by: 58
Author(s): Franziska Liesecke, Dimitri Daudu, Rodolphe Dugé de Bernonville, Sébastien Besseau, Marc Clastre, Vincent Courdavault, Johan-Owen De Craene, Joël Crèche, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0181902

EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas
Cited by: 4
Author(s): Karol Nowicki-Osuch, Yaoyong Li, Mairi Challinor, Dave T. Gerrard, Neil A. Hanley, Andrew D. Sharrocks
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-018-25302-1

Egr2-independent, Klf1-mediated induction of PD-L1 in CD4+ T cells
Cited by: 8
Author(s): Shuzo Teruya, Tomohisa Okamura, Takashi Komai, Mariko Inoue, Yukiko Iwasaki, Shuji Sumitomo, Hirofumi Shoda, Kazuhiko Yamamoto, Keishi Fujio
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-017-16747-x

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models
Cited by: 193
Author(s): Peter W. Eide, Jarle Bruun, Ragnhild Lothe, Anita Sveen
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0205499

CaSTLe – Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments
Cited by: 84
Author(s): Yuval Lieberman, Lior Rokach, Tal Shay
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0231125

Analysis of circulating-microRNA expression in lactating Holstein cows under summer heat stress
Cited by: 14
Author(s): Jihwan Lee, Mi Kyung Lee, Jun-Kyu Son, Hyeonju Lim, Euntae Kim, Dong-Hyun Kim, Seungmin Ha, Tai-Young Hur, Seung Hwan Lee, Inchul Choi
Software Mentions: 4
Published: over 5 years ago

10.1038/srep29832

Identification of host transcriptional networks showing concentration-dependent regulation by HPV16 E6 and E7 proteins in basal cervical squamous epithelial cells
Cited by: 7
Author(s): Stephen Smith, Cinzia G. Scarpini, Ian J. Groves, Richard Odle, Nicholas Coleman
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms21114115

Minor Splicing Factors Zrsr1 and Zrsr2 Are Essential for Early Embryo Development and 2-Cell-Like Conversion
Cited by: 16
Author(s): Isabel Gómez-Redondo, Priscila Ramos‐Ibeas, Eva Pericuesta, Raúl Fernández‐González, Ricardo Laguna‐Barraza, Alfonso Gutiérrez‐Adán
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41597-019-0205-4

The Personal Genome Project-UK, an open access resource of human multi-omics data
Cited by: 18
Author(s): Olga Chervova, Lucía Conde, José Afonso Guerra-Assunção, Ismail Moghul, A. D. B. Webster, Alison Berner, Elizabeth Larose Cadieux, Yuan Tian, Vitaly Voloshin, Tiago S. Jesus, Rifat Hamoudi, Javier Herrero, Stephan Beck
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0227882

Comparison of the myometrial transcriptome from singleton and twin pregnancies by RNA-Seq
Cited by: 5
Author(s): Sarah Arrowsmith, Yongxiang Fang, Andrew Sharp
Software Mentions: 4
Published: about 6 years ago

10.3389/fcvm.2021.627873

Essential Genes and MiRNA–mRNA Network Contributing to the Pathogenesis of Idiopathic Pulmonary Arterial Hypertension
Cited by: 7
Author(s): Shengyu Hao, Pan Jiang, Liang Xie, Guiling Xiang, Zilong Liu, Weiping Hu, Qiao Wu, Liyan Jiang, Yi Xiao, Shanqun Li
Software Mentions: 4
Published: almost 5 years ago

10.3389/fcell.2019.00299

Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data
Cited by: 23
Author(s): Geng Chen, Jiwei Chen, Huanlong Liu, Shuangguan Chen, Yang Zhang, Peng Li, Danielle Thierry-Mieg, Jean Thierry‐Mieg, William B. Mattes, Baitang Ning, Tieliu Shi
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0206665

Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer
Cited by: 11
Author(s): Kanthida Kusonmano, Mari K. Halle, Elisabeth Wik, Erling A. Høivik, Camilla Krakstad, Karen Klepsland Mauland, Ingvild L. Tangen, Ansgar Berg, Henrica M.J. Werner, Jone Trovik, Anne Margrete Øyan, Karl‐Henning Kalland, Inge Jonassen, Helga B. Salvesen, Kjell Petersen
Software Mentions: 4
Published: over 7 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962