bioconductor: ArrayExpress | Projects

10.7554/eLife.58659

A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
Cited by: 22
Author(s): Bjoern Gaertner, Sebastiaan van Heesch, Valentin Schneider-Lunitz, Jana Felicitas Schulz, Franziska Witte, Susanne Blachut, Steven Nguyen, Richard L. Wong, Ileana Matta, Norbert Hübner
Software Mentions: 5
Published: over 4 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 5 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 5 years ago

10.1038/s41598-021-84270-1

Serial transplantation unmasks galectin-9 contribution to tumor immune escape in the MB49 murine model
Cited by: 4
Author(s): Valentin Baloche, Julie Rivière, Thi Bao Tram Tran, Aurore Gelin, Olivia Bawa, Nicolas Signolle, Mouhamadou Diop, Philippe Dessen, Stéphanie Beq, Muriel D. David, P. Busson
Software Mentions: 5
Published: over 3 years ago

10.1186/s13068-021-01915-z

Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species
Cited by: 10
Author(s): Jose J De Vega, Abel Teshome, Manfred Klaas, Jim Grant, John Finnan, Susanne Barth
Software Mentions: 5
Published: over 3 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: about 4 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: over 8 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: over 10 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: over 4 years ago

10.1186/s12864-018-5396-0

s·nr: a visual analytics framework for contextual analyses of private and public RNA-seq data
Cited by: 0
Author(s): Paul Klemm, Peter Frommolt, Jan-Wilhelm Kornfeld
Software Mentions: 5
Published: almost 6 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 4 years ago

10.1155/2020/6034670

Bioinformatics Analysis to Screen the Key Prognostic Genes in Tumor Microenvironment of Bladder Cancer
Cited by: 6
Author(s): Zhao Zhang, Dongshan Chen, Zeyan Li, Zhao Liu, Lei Yan, Zhonghua Xu
Software Mentions: 5
Published: almost 5 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: over 12 years ago

10.1186/s13062-015-0051-z

Test on existence of histology subtype-specific prognostic signatures among early stage lung adenocarcinoma and squamous cell carcinoma patients using a Cox-model based filter
Cited by: 25
Author(s): Suyan Tian, Chi Wang, Ming-Wen An
Software Mentions: 5
Published: over 9 years ago

10.1007/s11306-015-0879-3

Data standards can boost metabolomics research, and if there is a will, there is a way
Cited by: 89
Author(s): Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Elon Correa, Saravanan Dayalan, Alejandra González-Beltrán, Timothy M. D. Ebbels, Royston Goodacre, Janna Hastings, Kenneth Haug, Albert Koulman, Macha Nikolski, Matej Orešič, Susanna-Assunta Sansone, Daniel Schober, James M. Smith, Christoph Steinbeck, Mark R. Viant, Steffen Neumann
Software Mentions: 5
Published: about 9 years ago

10.1186/1471-2105-14-174

PMTED: a plant microRNA target expression database
Cited by: 46
Author(s): Xiaofan Sun, Boquan Dong, Lingjie Yin, Rongzhi Zhang, Wei Du, Dongfeng Liu, Nan Shi, Aili Li, Yanchun Liang, Long Mao
Software Mentions: 5
Published: over 11 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: almost 4 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: about 10 years ago

10.1093/bioinformatics/btt016

Grape RNA-Seq analysis pipeline environment
Cited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12864-018-4746-2

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Cited by: 19
Author(s): Antonio Jordán-Pla, Simei Yu, Johan Waldholm, Thomas Källman, Ann‐Kristin Östlund Farrants, Neus Visa
Software Mentions: 5
Published: over 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: over 3 years ago

10.1186/s12918-015-0174-y

SEEK: a systems biology data and model management platform
Cited by: 79
Author(s): Katy Wolstencroft, Stuart Owen, Olga Krebs, Quyen Le Hoang Thuy To Nguyen, Natalie J. Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lin An, David Shockley, Jacky L. Snoep, Wolfgang Mueller, Carole Goble
Software Mentions: 5
Published: over 9 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: almost 5 years ago

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: almost 8 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: over 3 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 6 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: almost 12 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: almost 16 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: over 4 years ago

10.1371/journal.pone.0248485

16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya
Cited by: 21
Author(s): Edith M. Muwawa, Chinedu Christopher Obieze, Huxley Mae Makonde, Joyce Jefwa, James H. P. Kahindi, Damase Khasa
Software Mentions: 5
Published: over 3 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: about 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: almost 6 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: almost 17 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: over 11 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: over 5 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: about 8 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: over 3 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 14 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: almost 16 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: almost 13 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: almost 11 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: over 5 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 5 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: almost 11 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: over 4 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 4 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: about 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: over 4 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: about 6 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: almost 5 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: about 10 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: over 3 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: almost 5 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: about 10 years ago

10.7554/eLife.35788

A promoter interaction map for cardiovascular disease genetics
Cited by: 111
Author(s): Lindsey Montefiori, Débora R. Sobreira, Noboru Jo Sakabe, Ivy Aneas, Amelia C Joslin, Grace Hansen, Grazyna Bozek, Ivan P. Moskowitz, Elizabeth M. McNally, Marcelo A. Nóbrega
Software Mentions: 5
Published: over 6 years ago

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-9-548

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Cited by: 34
Author(s): Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J. Butte
Software Mentions: 4
Published: almost 16 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: almost 4 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: almost 12 years ago

10.1038/leu.2016.251

Hemopoietic-specific Sf3b1-K700E knock-in mice display the splicing defect seen in human MDS but develop anemia without ring sideroblasts
Cited by: 99
Author(s): Annalisa Mupo, Monika Seiler, Vijitha Sathiaseelan, Alena Pance, Yi Yang, Anant A. Agrawal, Francesco Iorio, Rubén Bautista, Suruchi Pacharne, Konstantinos Tzelepis, Nicla Manes, Penny Wright, Elli Papaemmanuil, David G. Kent, Peter Campbell, Silvia Buonamici, Niccolò Bolli, George S. Vassiliou
Software Mentions: 4
Published: about 8 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 4 years ago

10.1038/s41396-017-0043-3

Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12935-021-01834-x

High expression of CDCA7 predicts poor prognosis for clear cell renal cell carcinoma and explores its associations with immunity
Cited by: 12
Author(s): Shouyong Liu, Yi Wang, Chenkui Miao, Zengjun Wang
Software Mentions: 4
Published: over 3 years ago

10.1002/cam4.3367

Identification of small molecule drugs and development of a novel autophagy‐related prognostic signature for kidney renal clear cell carcinoma
Cited by: 9
Author(s): Qianwei Xing, Chengjian Ji, Bingye Zhu, Rong Cong
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0183679

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization
Cited by: 31
Author(s): Ewa Surdziel, Ieuan Clay, Florian Nigsch, Anke Thiemeyer, Cyril Allard, Gregory R. Hoffman, John S. Reece‐Hoyes, Tanushree Phadke, Romain Gambert, Caroline Gubser Keller, Marie-Gabrielle Ludwig, Birgit Baumgarten, Mathias Frederiksen, Dirk Schübeler, Klaus Seuwen, Tewis Bouwmeester, Barna D. Fodor
Software Mentions: 4
Published: about 7 years ago

10.1186/1748-7188-7-19

Getting DNA copy numbers without control samples
Cited by: 1
Author(s): María Ortiz-Estévez, Ander Aramburu, Ángel Rubio
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-017-4086-7

The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
Cited by: 59
Author(s): Victoria A. Ingham, Patricia Pignatelli, Jonathan D. Moore, Simon C. Wagstaff, Hilary Ranson
Software Mentions: 4
Published: about 7 years ago

10.1093/bib/bbx080

‘Multi-omic’ data analysis using O-miner
Cited by: 13
Author(s): Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, A. Nagano, Helen Ross-Adams, Jun Wang, Nick R. Lemoine, Claude Chelala
Software Mentions: 4
Published: over 7 years ago

10.7150/thno.36378

Exosome-dependent immune surveillance at the metastatic niche requires BAG6 and CBP/p300-dependent acetylation of p53
Cited by: 41
Author(s): Maximiliane Schuldner, Bastian Dörsam, Olga Shatnyeva, Katrin S. Reiners, Andriy V. Kubarenko, Hinrich P. Hansen, Florian Finkernagel, Katrin Roth, Sebastian Theurich, Andrea Nist, Thorsten Stiewe, Annette Paschen, Gero Knittel, Hans Christian Reinhardt, Rolf Müller, Michael Hallek, Elke Pogge von Strandmann
Software Mentions: 4
Published: almost 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: about 6 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pone.0086699

Meta-Analysis and Gene Set Analysis of Archived Microarrays Suggest Implication of the Spliceosome in Metastatic and Hypoxic Phenotypes
Cited by: 2
Author(s): Bertrand De Meulder, Fabrice Berger, Eric Bareke, Sophie Depiereux, Carine Michiels, Eric Depiereux
Software Mentions: 4
Published: almost 11 years ago

10.1128/mSystems.00187-19

Systems Analyses Reveal the Resilience of Escherichia coli Physiology during Accumulation and Export of the Nonnative Organic Acid Citramalate
Cited by: 10
Author(s): Joseph P. Webb, V S Springthorpe, Luca Rossoni, David-Paul Minde, Swen Langer, Heather Walker, Amias Alstrom-Moore, Tony R. Larson, Kathryn S. Lilley, Graham R. Eastham, Gill Stephens, Gavin H. Thomas, David J. Kelly, Jeffrey Green
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-92932-3

Dietary phosphorus and calcium in feed affects miRNA profiles and their mRNA targets in jejunum of two strains of laying hens
Cited by: 6
Author(s): Muhammad Arsalan Iqbal, Asghar Ali, Frieder Hadlich, Michael Oster, Henry Reyer, Nares Trakooljul, Vera Sommerfeld, M. Rodehutscord, Klaus Wimmers, Siriluck Ponsuksili
Software Mentions: 4
Published: over 3 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: almost 5 years ago

10.1186/s13395-019-0196-z

Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field
Cited by: 8
Author(s): Apostolos Malatras, Stéphanie Duguez, William Duddy
Software Mentions: 4
Published: over 5 years ago

10.1128/AEM.00853-19

Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens
Cited by: 25
Author(s): Eugen Pfeifer, Slawomir Michniewski, Cornelia Gätgens, Eugenia Münch, Felix L. Müller, Tino Polen, Andrew Millard, Bastian Blombach, Julia Frunzke
Software Mentions: 4
Published: about 5 years ago

10.1016/j.ccell.2019.08.003

Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis
Cited by: 230
Author(s): René Jackstadt, Sander R. van Hooff, Joshua D.G. Leach, Xabier Cortés-Lavaud, Jeroen Lohuis, Rachel A. Ridgway, Valérie M. Wouters, Jatin Roper, Timothy J. Kendall, Campbell S.D. Roxburgh, Paul G. Horgan, Colin Nixon, Craig Nourse, Matthias Gunzer, William Clark, Ann Hedley, Ömer H. Yılmaz, Mamunur Rashid, Peter J. Bailey, Andrew V. Biankin, Andrew D. Campbell, David J. Adams, Simon T. Barry, Colin W. Steele, Jan Paul Medema, Owen J. Sansom
Software Mentions: 4
Published: about 5 years ago

10.4056/sigs.1423520

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10
Cited by: 8
Author(s): Elizabeth M. Glass, Patrick Meyer, Jack A. Gilbert, Dawn Field, Sarah Hunter, Renzo Kottmann, Nikos C. Kyrpides, Susanna Assunta Sansone, Lynn M. Schriml, Peter J. Sterk, Owen White, John Wooley
Software Mentions: 4
Published: almost 15 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: almost 5 years ago

10.1186/s12864-015-1308-8

A comprehensive evaluation of ensembl, RefSeq, and UCSC annotations in the context of RNA-seq read mapping and gene quantification
Cited by: 109
Author(s): Shanrong Zhao, Baohong Zhang
Software Mentions: 4
Published: almost 10 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: about 4 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: about 17 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: over 6 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 6 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: about 5 years ago

10.1371/journal.pone.0256353

Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes
Cited by: 6
Author(s): Claus M. Zacho, Martina Abenhus Bager, Ashot Margaryan, Peter Gravlund, Anders Galatius, Arne Redsted Rasmussen, Morten E. Allentoft
Software Mentions: 4
Published: about 3 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: about 6 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 8 years ago

10.1186/s12864-015-1689-8

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal
Cited by: 15
Author(s): Lars Eijssen, Varshna Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjić
Software Mentions: 4
Published: over 9 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: almost 7 years ago

10.1155/2013/983805

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases
Cited by: 10
Author(s): Alberto Anguita, Miguel García-Remesal, Diana de la Iglesia, Víctor Maojo
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12859-015-0485-4

NMF-mGPU: non-negative matrix factorization on multi-GPU systems
Cited by: 44
Author(s): Edgardo Mejía-Roa, Daniel Tabas-Madrid, Javier Setoaín, Carlos Garcı́a, Francisco Tirado, Alberto Pascual-Montano
Software Mentions: 4
Published: almost 10 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 3 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: over 10 years ago

10.1038/s41598-021-91864-2

Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML
Cited by: 2
Author(s): Parastoo Modarres, Farzaneh Mohamadi Farsani, Amir Abas Nekouie, Sadeq Vallian
Software Mentions: 4
Published: over 3 years ago

10.1530/REP-19-0293

Blastocyst transfer in mice alters the placental transcriptome and growth
Cited by: 4
Author(s): Katerina Menelaou, Malwina Prater, Simon James Tunster, Georgina E T Blake, Colleen Geary Joo, James C. Cross, Russell S. Hamilton, Erica D. Watson
Software Mentions: 4
Published: almost 5 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: about 5 years ago

10.1186/s12864-016-2695-1

Improving microRNA target prediction with gene expression profiles
Cited by: 22
Author(s): Cesaré Ovando-Vázquez, Daniel Lepe-Soltero, Cei Abreu‐Goodger
Software Mentions: 4
Published: over 8 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: almost 5 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962