bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0243681

Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico
Cited by: 11
Author(s): Enrique Jesús Delgado-Suárez, Tania Palós-Guitérrez, Francisco Alejandro Ruíz-López, Cindy Fabiola Hernández Pérez, Nayarit Emérita Ballesteros-Nova, Orbelín Soberanis-Ramos, Rubén Danilo Méndez-Medina, Marc W. Allard, María Salud Rubio Lozano
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0238190

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria
Cited by: 26
Author(s): Abdurrahman Hassan Jibril, Iruka N. Okeke, Anders Dalsgaard, Eglė Kudirkienė, Olabisi C. Akinlabi, Muhammad Bashir Bello
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0019650

A Variable Region within the Genome of Streptococcus pneumoniae Contributes to Strain-Strain Variation in Virulence
Cited by: 48
Author(s): Richard M. Harvey, Uwe H. Stroeher, Abiodun D. Ogunniyi, Heidi Smith‐Vaughan, Amanda J. Leach, James C. Paton
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0241942

Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences
Cited by: 6
Author(s): Abdoulie Kanteh, Jarra Manneh, Sona Jabang, Mariama A Kujabi, Bakary Sanyang, Mary Aigbiremo Oboh, Abdoulie Bojang, Haruna S. Jallow, Davis Nwakanma, Ousman Secka, Anna Roca, Alfred Amambua-Ngwa, Martín Antonio, Ignatius Baldeh, Karen Forrest, Ahmadou Lamin Samateh, Umberto D’Alessandro, Abdul Karim Sesay
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0165543

Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method
Cited by: 4
Author(s): Lei Zhang, Linlin Wang, Pu Tian, Suyan Tian
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0228463

Induction of systemic immunity through nasal-associated lymphoid tissue (NALT) of mice intranasally immunized with Brucella abortus malate dehydrogenase-loaded chitosan nanoparticles
Cited by: 12
Author(s): Soojin Shim, Sang Hee Soh, Young Jae Im, Cheol‐Hee Ahn, Hong-Tae Park, Woo Bin Park, Suji Kim, Han Sang Yoo
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0237242

Transcriptome analysis of the eggs of the silkworm pale red egg (rep-1) mutant at 36 hours after oviposition
Cited by: 1
Author(s): Meina Wu, Pingyang Wang, Mengjie Gao, Dongxu Shen, Qiaoling Zhao
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0256181

Identification and functional modelling of plausibly causative cis-regulatory variants in a highly-selected cohort with X-linked intellectual disability
Cited by: 1
Author(s): Hemant Bengani, Detelina Grozeva, Lambert Moyon, Shipra Bhatia, Susana R. Louros, Jilly Hope, Adam D. Jackson, James Prendergast, Liusaidh J Owen, Magali Naville, Jacqueline K. Rainger, Graeme R. Grimes, Mihail Halachev, Laura C. Murphy, Olivera Spasić-Bošković, Veronica van Heyningen, P. Kind, Catherine M. Abbott, Emily K. Osterweil, F. Lucy Raymond, Hugues Roest Crollius, David R. FitzPatrick
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0255410

Prevalence and risk factors for antimicrobial resistance among newborns with gram-negative sepsis
Cited by: 16
Author(s): Semaria Solomon, Oluwasefunmi Akeju, Oludare A. Odumade, Rozina Ambachew, Zenebe Gebreyohannes, Kimiko Van Wickle, Mahlet Abayneh, Gesit Metaferia, Maria J. Carvalho, Kathryn Thomson, Kirsty Sands, Timothy R. Walsh, Rebecca Milton, Frederick G. B. Goddard, Delayehu Bekele, Grace J Chan
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0256979

Longitudinal detection of somatic mutations in saliva and plasma for the surveillance of oral squamous cell carcinomas
Cited by: 13
Author(s): Ying Cui, Hae-Suk Kim, Eunae Sandra Cho, Dawool Han, Jung A Park, Ju Yeong Park, Woong Nam, Hyung Jun Kim, In‐Ho Cha, Yong Hoon
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0241098

Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala – characterization and phylogenetic analysis
Cited by: 7
Author(s): Prateek Dey, Sanjeev Kumar Sharma, Indrani Sarkar, Swapna Devi Ray, Padmanabhan Pramod, Venkata Hanumat Sastry Kochiganti, Goldin Quadros, Saurabh Singh Rathore, Vikram Singh, Ram Pratap Singh
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0166520

Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii
Cited by: 38
Author(s): Shahid Manzoor, Erik Bongcam‐Rudloff, Anna Schnürer, Bettina Müller
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0034158

Coexpression of Nuclear Receptors and Histone Methylation Modifying Genes in the Testis: Implications for Endocrine Disruptor Modes of Action
Cited by: 18
Author(s): Alison Anderson, Kim W. Carter, Denise Anderson, Michael J. Wise
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0059459

Global Gene Expression Profiling Reveals SPINK1 as a Potential Hepatocellular Carcinoma Marker
Cited by: 60
Author(s): Aileen Marshall, Margus Lukk, Claudia Kutter, Susan Davies, Graeme Alexander, Duncan T. Odom
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0229797

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome
Cited by: 2
Author(s): Michelle Coleman, Canaan Whitfield-Cargile, Noah D. Cohen, Jennifer S. Goldsby, Laurie A. Davidson, Ana M. Chamoun‐Emanuelli, Ivan Ivanov, Susan C. Eades, Nancy H. Ing, Robert S. Chapkin
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0074712

A Degenerative Retinal Process in HIV-Associated Non-Infectious Retinopathy
Cited by: 25
Author(s): Igor Kozák, Roman Šášik, William R. Freeman, Leslee Sprague, María Laura Gomez, Lingyun Cheng, Sharif El-Emam, Francesca Mojana, Dirk-Uwe Bartsch, Jenny Bosten, Radha Ayyagari, Gary Hardiman
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0116309

Gene Expression Dosage Regulation in an Allopolyploid Fish
Cited by: 14
Author(s): Isa Matos, Miguel P. Machado, Manfred Schartl, M. M. Coelho
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0246603

Establishment of the TALE-code reveals aberrantly activated homeobox gene PBX1 in Hodgkin lymphoma
Cited by: 13
Author(s): Stefan Nagel, Claudia Pommerenke, Corinna Meyer, Roderick A.F. MacLeod, Hans Drexler
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0012339

Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution
Cited by: 63
Author(s): Pawandeep Dhami, Peter Saffrey, Alexander W. Bruce, Shane C. Dillon, Kelly Chiang, Nicolas Bonhoure, Christof Koch, Jackie Bye, Keith James, Nicola Foad, Peter Ellis, Nicholas A. Watkins, Willem H. Ouwehand, Cordelia Langford, Robert Andrews, Ian Dunham, David Vetrie
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0248405

Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection
Cited by: 5
Author(s): Hadeer M. Aboshady, Nathalie Mandonnet, Anna M. Johansson, Elisabeth Jonas, Jean-Christophe Bambou
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0039469

Deregulation of Rab and Rab Effector Genes in Bladder Cancer
Cited by: 94
Author(s): Joël Rainui Ho, Élodie Chapeaublanc, Lisa A. Kirkwood, Rémy Nicolle, Simone Benhamou, Thierry Lebrét, Yves Allory, Jennifer Southgate, François Radvanyi, Bruno Goud
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0051693

StRAP: An Integrated Resource for Profiling High-Throughput Cancer Genomic Data from Stress Response Studies
Cited by: 0
Author(s): Seth Johnson, Biju Issac, Shuping Zhao, Mohit Bisht, Orieta Celiku, Philip J. Tofilon, Kevin Camphausen, Uma Shankavaram
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0066513

Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks – Evidence of a Tail Biting Resistant Phenotype
Cited by: 27
Author(s): Emma Brunberg, Per Jensen, Anders Isaksson, Linda J. Keeling
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0224927

Integrating long noncoding RNAs and mRNAs expression profiles of response to Plasmodiophora brassicae infection in Pakchoi (Brassica campestris ssp. chinensis Makino)
Cited by: 5
Author(s): Huifen Zhu, Xiaofeng Li, Dandan Xi, Wentao Zhai, Zhaohui Zhang
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0004128

Using Pathway Signatures as Means of Identifying Similarities among Microarray Experiments
Cited by: 26
Author(s): Luca Beltrame, Lisa Rizzetto, Raffaele Paola, Philippe Rocca-Serra, Luca Gambineri, Cristina Battaglia, Duccio Cavalieri
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pone.0229536

Identification of trypanosomatids and blood feeding preferences of phlebotomine sand fly species common in Sicily, Southern Italy
Cited by: 30
Author(s): Jessica Maria Abbate, Carla Maia, André Pereira, Francesca Arfuso, Gabriella Gaglio, Maria Rizzo, Giulia Caracappa, Gabriele Marino, Matthias Pollmeier, S. Giannetto, Emanuele Brianti
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0242874

Interaction of preimplantation factor with the global bovine endometrial transcriptome
Cited by: 3
Author(s): Ruth Wonfor, Christopher J. Creevey, Manuela Natoli, Matthew J. Hegarty, Deborah Nash, Michael T. Rose
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0235401

Antimalarial drug resistance molecular makers of Plasmodium falciparum isolates from Sudan during 2015–2017
Cited by: 13
Author(s): Maazza Hussien, Muzamil Mahdi Abdel Hamid, Elamin Abdelkarim Elamin, Abdalla O. Hassan, Arwa Elaagip, Abusofyan Hamattallah A. Salama, Mohammed H. Abdelraheem, Abdelrahim Mohamed
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0249432

PAH-pollution effects on sensitive and resistant embryos: Integrating structure and function with gene expression
Cited by: 4
Author(s): Goran Bozinovic, Damian Shea, Zuying Feng, David E. Hinton, Tim L. Sit, Marjorie F. Oleksiak
Software Mentions: 2
Published: over 5 years ago

10.3390/cells9122693

Targeting Acid Ceramidase to Improve the Radiosensitivity of Rectal Cancer
Cited by: 12
Author(s): Rachael Clifford, Naren Govindarajah, David Bowden, Paul Sutton, Mark A. Glenn, Mahnaz Darvish-Damavandi, Simon Buczacki, Ultan McDermott, Zdzisław M. Szulc, Besim Öğretmen, Jason L. Parsons, Dale Vimalachandran
Software Mentions: 2
Published: almost 6 years ago

10.1186/s13148-020-00884-8

meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes
Cited by: 19
Author(s): Diana‐Maria Ciuculete, Sarah Voisin, Lara Kular, Jan‐Ingvar Jönsson, Mathias Rask‐Andersen, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-018-0554-4

PRC2 targeting is a therapeutic strategy for EZ score defined high-risk multiple myeloma patients and overcome resistance to IMiDs
Cited by: 32
Author(s): Laurie Herviou, Alboukadel Kassambara, Stéphanie Boireau, Robert Naeije, Guilhem Requirand, Carsten Müller‐Tidow, Laure Vincent, Anja Seckinger, Hartmut Goldschmidt, Guillaume Cartron, Dirk Hose, Giacomo Cavalli, Jérôme Moreaux
Software Mentions: 2
Published: about 8 years ago

10.1186/s13148-019-0691-4

DNA methylation changes that precede onset of dysplasia in advanced sessile serrated adenomas
Cited by: 15
Author(s): Cheng Liu, Mark Bettington, Neal I. Walker, Joel Dwine, Barbara A. Leggett, Vicki Whitehall
Software Mentions: 2
Published: over 7 years ago

10.1186/s12014-017-9168-7

Proteomic profiling identifies markers for inflammation-related tumor–fibroblast interaction
Cited by: 16
Author(s): Daniel Drev, Andrea Bileck, Zeynep Erdem, Thomas Mohr, Gerald Timelthaler, Andrea Beer, Christopher Gerner, Brigitte Marian
Software Mentions: 2
Published: about 9 years ago

10.1038/s42003-021-02215-w

Actin cytoskeleton deregulation confers midostaurin resistance in FLT3-mutant acute myeloid leukemia
Cited by: 11
Author(s): Andoni Garitano‐Trojaola, Ana Sancho, Roland Götz, Patrick Eiring, Susanne Walz, Hardikkumar Jetani, Jesus Gil‐Pulido, Matteo Claudio Da Vià, Eva Teufel, Nadine Rhodes, Larissa Haertle, Estibaliz Arellano-Viera, Raoul Tibes, Andreas Rosenwald, Leo Rasche, Michael Hudecek, Markus Sauer, Jürgen Gröll, Hermann Einsele, Sabrina Kraus, Martin Kortüm
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-018-0215-3

Sox9 regulates cell state and activity of embryonic mouse mammary progenitor cells
Cited by: 11
Author(s): Naoko Kogata, Philip Bland, Mandy Tsang, Erik Oliemuller, Anne Lowe, Beatrice A. Howard
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.csbj.2015.10.005

Blood transcriptomics and metabolomics for personalized medicine
Cited by: 66
Author(s): Shuzhao Li, Andrei Todor, Ruiyan Luo
Software Mentions: 2
Published: almost 11 years ago

10.1016/j.dib.2017.11.031

Data on novel DNA methylation changes induced by valproic acid in human hepatocytes
Cited by: 3
Author(s): Jarno E J Wolters, SimoneGJ van Breda, Sandra Claessen, T.D. Kok, J.C.S. Kleinjans
Software Mentions: 2
Published: over 8 years ago

10.1016/j.dib.2019.105053

Data describing the experimental design and quality control of RNA-Seq of human adipose-derived stem cells undergoing early adipogenesis and osteogenesis
Cited by: 5
Author(s): Bruna Hilzendeger Marcon, Lucía Spangenberg, Bernardo Bonilauri, Anny Waloski Robert, Addeli Bez Batti Angulski, Guillermo Cabrera Cabo, Axel R. Cofré, Paulo Sergio Loiacono Bettes, Bruno Dallagiovanna, Patrícia Shigunov
Software Mentions: 2
Published: over 6 years ago

10.1093/database/baab043

The Progenetix oncogenomic resource in 2021
Cited by: 8
Author(s): Qingyao Huang, Paula Carrio-Cordo, Bo Gao, Rahel Paloots, Michael Baudis
Software Mentions: 2
Published: almost 6 years ago

10.1093/database/baaa002

GXD’s RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest
Cited by: 2
Author(s): Cyndi M. Smith, James A. Kadin, Richard M. Baldarelli, Jonathan S Beal, Olin Blodgett, Sharon C Giannatto, Joel E. Richardson, Martin Ringwald
Software Mentions: 2
Published: almost 7 years ago

10.1093/database/bav019

BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis
Cited by: 75
Author(s): Qing Wan, Hayley Dingerdissen, Fan Yu, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Yan Cheng, Haichen Zhang, Raja Mazumder
Software Mentions: 2
Published: almost 12 years ago

10.1093/database/bav099

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases
Cited by: 7
Author(s): Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, A Namasivayam, Matthew J. Page, Martin Hofmann‐Apitius, Philipp Senger
Software Mentions: 2
Published: almost 12 years ago

10.1093/database/baaa111

MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle
Cited by: 2
Author(s): Olof Asplund, Johan Rung, Leif Groop, Rashmi B. Prasad, Ola Hansson
Software Mentions: 2
Published: almost 7 years ago

10.1093/database/bax069

IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes
Cited by: 0
Author(s): I-Man Ng, Jia-Hsin Huang, Shang-Chi Tsai, Huai-Kuang Tsai
Software Mentions: 2
Published: almost 10 years ago

10.1093/database/bau030

'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences
Cited by: 18
Author(s): Julio C. Bolívar, Fabian Machens, Yuri Brill, Artyom Romanov, Lorenz Bülow, Reinhard Hehl
Software Mentions: 2
Published: over 12 years ago

10.1093/database/baz149

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans
Cited by: 34
Author(s): L. Basten Snoek, M.G. Sterken, Margi Hartanto, Albert-Jan van Zuilichem, J.E. Kammenga, Dick de Ridder, Harm Nijveen
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.ydbio.2011.03.003

A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation
Cited by: 3
Author(s): Christopher Sugden, Scott R. Ross, Sarah J. Annesley, Christian Callebaut, Gareth Bloomfield, Alasdair Ivens, Jason Skelton, Paul R. Fisher, Geoffrey J. Barton, Jeffrey Williams
Software Mentions: 2
Published: over 15 years ago

10.1016/j.devcel.2016.12.023

Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline
Cited by: 72
Author(s): Mahesh N. Sangrithi, Hélène Royo, Shantha K. Mahadevaiah, Obah A. Ojarikre, Leena Bhaw, Abdul Karim Sesay, Antoine H.F.M. Peters, Michael Stadler, James M. A. Turner
Software Mentions: 2
Published: over 9 years ago

10.1242/dev.157081

Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network
Cited by: 38
Author(s): Simon Scofield, Alex Murison, Angharad Jones, John A. Fozard, Mitsuhiro Aida, Leah R. Band, Malcolm J. Bennett, James A. H. Murray
Software Mentions: 2
Published: almost 9 years ago

10.1007/s00125-020-05107-6

Metabolic alterations in immune cells associate with progression to type 1 diabetes
Cited by: 37
Author(s): Partho Sen, Alex M. Dickens, M.A. López-Bascón, Tuomas Lindeman, Esko Kemppainen, Santosh Lamichhane, Tuukka Rönkkö, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Heikki Hyöty, Tuulia Hyötyläinen, Mikael Knip, Matej Orešič
Software Mentions: 2
Published: over 6 years ago

10.1155/2016/2619828

Pathway Analysis Based on Attractor and Cross Talk in Colon Cancer
Cited by: 6
Author(s): Yanxia Liu, Lin Wang, Bingping Wang, Meng Yue, Yufeng Cheng
Software Mentions: 2
Published: almost 11 years ago

10.15252/embr.201846222

Budding yeast Rif1 binds to replication origins and protects <scp>DNA</scp> at blocked replication forks
Cited by: 30
Author(s): Shin‐ichiro Hiraga, Chandre Monerawela, Yuki Katou, Sophie Shaw, Kate Rosalind Mary Clark, Katsuhiko Shirahige, Anne Donaldson
Software Mentions: 2
Published: about 8 years ago

10.15252/embr.201540476

Abo1, a conserved bromodomain <scp>AAA</scp> ‐ <scp>ATP</scp> ase, maintains global nucleosome occupancy and organisation
Cited by: 20
Author(s): Csenge Gal, Heather E. Murton, Lakxmi Subramanian, Alex J. Whale, Karen Moore, Konrad Paszkiewicz, Sandra Codlin, Jürg Bähler, Kevin M. Creamer, Janet F. Partridge, Robin C. Allshire, Nicholas A. Kent, Simon K. Whitehall
Software Mentions: 2
Published: almost 11 years ago

10.1530/ERC-14-0454

HES5 silencing is an early and recurrent change in prostate tumourigenesis
Cited by: 10
Author(s): Charles E. Massie, Inmaculada Spiteri, Helen Ross-Adams, Hayley J. Luxton, Jonathan Kay, Hayley C. Whitaker, Mark J. Dunning, Alastair Lamb, Antonio Ramos-Montoya, Daniel Brewer, Christopher S. Cooper, Rosalind Eeles, _ _, Anne Y. Warren, Simon Tavaré, David E. Neal, Andy G. Lynch
Software Mentions: 2
Published: almost 12 years ago

10.1111/1462-2920.13930

Transcriptome and proteome dynamics in chemostat culture reveal howCampylobacter jejunimodulates metabolism, stress responses and virulence factors upon changes in oxygen availability
Cited by: 28
Author(s): Edward Guccione, John J. Kendall, Andrew Hitchcock, Nitanshu Garg, Michael A. White, Francis Mulholland, Robert K. Poole, David J. Kelly
Software Mentions: 2
Published: about 9 years ago

10.1007/s11356-017-0515-z

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments
Cited by: 7
Author(s): Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13072-018-0232-y

Non-canonical Drosophila X chromosome dosage compensation and repressive topologically associated domains
Cited by: 7
Author(s): Hangnoh Lee, Brian Oliver
Software Mentions: 2
Published: almost 8 years ago

10.1186/s40001-018-0328-7

Membrane-bound estrogen receptor alpha initiated signaling is dynamin dependent in breast cancer cells
Cited by: 9
Author(s): István Marczell, Petra Balogh, G Nyírő, Anna L. Kiss, Balázs Kovács, Gábor Békési, Kàroly Rácz, Attila Patócs
Software Mentions: 2
Published: over 8 years ago

10.12688/f1000research.28449.1

Recommendations for the FAIRification of genomic track metadata
Cited by: 7
Author(s): Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José Marı́a Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel R. Zerbino, Eivind Hovig
Software Mentions: 2
Published: over 5 years ago

10.12688/f1000research.15119.1

Norwegian e-Infrastructure for Life Sciences (NeLS)
Cited by: 10
Author(s): Kidane Tekle, Sveinung Gundersen, Kjetil Klepper, Lars Ailo Bongo, Inge Alexander Raknes, Xiaxi Li, Zhang Wei, Christian Andreetta, Teshome Dagne Mulugeta, Matúš Kalaš, Morten Rye, Erik Hjerde, Jeevan Karloss Antony Samy, Ghislain Fornous, Abdulrahman Azab, Dag Inge Våge, Eivind Hovig, Nils Peder Willassen, Finn Drabløs, Ståle Nygård, Kjell Petersen, Inge Jonassen
Software Mentions: 2
Published: over 8 years ago

10.1111/febs.15261

Data libraries – the missing element for modeling biological systems
Cited by: 3
Author(s): Anastasia Baryshnikova
Software Mentions: 2
Published: over 6 years ago

10.1002/2211-5463.12354

The clinical value of miR-193a-3p in non-small cell lung cancer and its potential molecular mechanism exploredin silicousing RNA-sequencing and microarray data
Cited by: 11
Author(s): Xiang Gao, Rongjiang Tang, Qiongni Xie, Jiaying Lin, Hong-lan Shi, Gang Chen, Zu‐Yun Li
Software Mentions: 2
Published: almost 9 years ago

10.3389/fbioe.2019.00106

Cyberbiosecurity Challenges of Pathogen Genome Databases
Cited by: 15
Author(s): Boris A. Vinatzer, Lenwood S. Heath, Hussain M. J. Almohri, Michael J. Stulberg, Christopher J. Lowe, Song Li
Software Mentions: 2
Published: over 7 years ago

10.3390/genes8100243

Genetic Association between Amyotrophic Lateral Sclerosis and Cancer
Cited by: 20
Author(s): Y-h. Taguchi, Hsiuying Wang
Software Mentions: 2
Published: about 9 years ago

10.3390/genes10070494

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi
Cited by: 16
Author(s): Maria Immacolata Ferrante, Laura Entrambasaguas, Mathias Johansson, Mats Töpel, Anke Kremp, Marina Montresor, Anna Godhe
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10080608

DNILMF-LDA: Prediction of lncRNA-Disease Associations by Dual-Network Integrated Logistic Matrix Factorization and Bayesian Optimization
Cited by: 16
Author(s): Yan Li, Junyi Li, Naizheng Bian
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10100797

Biological Network Approaches and Applications in Rare Disease Studies
Cited by: 22
Author(s): Peng Zhang, Yuval Itan
Software Mentions: 2
Published: about 7 years ago

10.3390/genes10110864

Meta-Analysis of Polymyositis and Dermatomyositis Microarray Data Reveals Novel Genetic Biomarkers
Cited by: 4
Author(s): Jaeseung Song, Daeun Kim, Juyeon Hong, Go Woon Kim, Junghyun Jung, Se Jin Park, Hee Jung Park, Jong Wha J. Joo, Wonhee Jang
Software Mentions: 2
Published: almost 7 years ago

10.3390/genes11091108

Transcriptomic Analysis Revealed an Emerging Role of Alternative Splicing in Embryonal Tumor with Multilayered Rosettes
Cited by: 1
Author(s): Dina Hesham, Shahenda El‐Naggar
Software Mentions: 2
Published: about 6 years ago

10.1016/j.gdata.2014.03.001

Transcriptomic profiling of cartilage ageing
Cited by: 11
Author(s): Mandy J. Peffers, Xuan Li, Peter Clegg
Software Mentions: 2
Published: almost 12 years ago

10.1186/gb-2007-8-11-r249

MADS-complexes regulate transcriptome dynamics during pollen maturation
Cited by: 87
Author(s): Wim Verelst, David Twell, Stefan de Folter, Richard G. H. Immink, Heinz Saedler, Thomas Münster
Software Mentions: 2
Published: almost 20 years ago

10.1186/gb-2007-8-7-r132

Evolutionary conservation of regulated longevity assurance mechanisms
Cited by: 190
Author(s): Joshua McElwee, Eugene F. Schuster, Eric Blanc, Matthew D. W. Piper, James H. Thomas, Dhaval Patel, Colin Selman, Dominic J. Withers, Janet M. Thornton, Linda Partridge, David Gems
Software Mentions: 2
Published: almost 20 years ago

10.1186/gb-2007-8-7-r150

PHIDIAS: a pathogen-host interaction data integration and analysis system
Cited by: 60
Author(s): Zuoshuang Xiang, Yuan Tian, Yongqun He
Software Mentions: 2
Published: almost 20 years ago

10.1186/gb-2009-10-1-r5

Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon
Cited by: 39
Author(s): Giselda Bucca, Emma Laing, Vassilis Mersinias, Nicholas E. E. Allenby, Douglas Hurd, Jolyon Holdstock, Volker Brenner, Marcus Harrison, Colin P. Smith
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2009-10-9-r97

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
Cited by: 49
Author(s): James C. Costello, Mehmet Dalkılıç, Scott Beason, Jeff R. Gehlhausen, Rupali P Patwardhan, Sumit Middha, Brian D. Eads, Justen Andrews
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2010-11-12-r124

Large scale comparison of global gene expression patterns in human and mouse
Cited by: 110
Author(s): Xiangqun Zheng-Bradley, Johan Rung, Helen Parkinson, Alvis Brāzma
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2010-11-12-r125

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
Cited by: 83
Author(s): Peter L. Chang, Brian P. Dilkes, Michelle M. McMahon, Luca Comai, Sergey V. Nuzhdin
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2012-13-8-r67

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Cited by: 197
Author(s): Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2014-15-1-r14

Dissecting the expression landscape of RNA-binding proteins in human cancers
Cited by: 195
Author(s): Bobak D. Kechavarzi, Sarath Chandra Janga
Software Mentions: 2
Published: almost 13 years ago

10.1186/gb-2013-14-12-r138

The physical map of wheat chromosome 1BS provides insights into its gene space organization and evolution
Cited by: 43
Author(s): Dina Raats, Zeev Frenkel, Tamar Krugman, Itay Dodek, Hanan Sela, Hana Šimková, Federica Magni, Federica Cattonaro, Sonia Vautrin, Hélène Bergès, Thomas Wicker, Beat Keller, Philippe Leroy, Romain Philippe, Etienne Paux, Jaroslav Doležel, Catherine Feuillet, Abraham B. Korol, Tzion Fahima
Software Mentions: 2
Published: almost 14 years ago

10.1186/gb-2014-15-4-r62

Arabidopsis replacement histone variant H3.3 occupies promoters of regulated genes
Cited by: 54
Author(s): Huan Shu, Miyuki Nakamura, Alexey Siretskiy, Loris Borghi, Izabel Cristina Freitas Moraes, Thomas Wildhaber, Wilhelm Gruissem, Lars Hennig
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13059-015-0719-9

Estrogen-induced chromatin decondensation and nuclear re-organization linked to regional epigenetic regulation in breast cancer
Cited by: 42
Author(s): Sehrish Rafique, Jeremy Thomas, Duncan Sproul, Wendy A. Bickmore
Software Mentions: 2
Published: about 11 years ago

10.1186/s13059-016-0957-5

Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation
Cited by: 62
Author(s): Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew N. J. McKenzie, Ruddy Montandon, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario Nicodemi, Sarah A. Teichmann
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-016-1070-5

Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression
Cited by: 1,710
Author(s): Étienne Becht, Nicolás A. Giraldo, Laetitia Lacroix, Bénédicte Buttard, Nabila Elarouci, Florent Petitprez, Janick Sèlves, Pierre Laurent‐Puig, Catheriné Sautès-Fridman, Wolf H. Fridman, Aurélien de Reyniès
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2004-5-9-r69

Cited by: 199
Author(s): Jingjing Wang, Laura Kean, Jingli Yang, Adrian K. Allan, Shireen A. Davies, Paweł Herzyk, Julian A. T. Dow
Software Mentions: 2
Published: almost 23 years ago

10.1186/s13059-017-1338-4

Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses
Cited by: 34
Author(s): Joseph L. Costello, Christopher J. Kershaw, Lydia M. Castelli, David Talavera, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Simon J. Hubbard, Graham D. Pavitt
Software Mentions: 2
Published: almost 9 years ago

10.1093/gbe/evz103

The Role of Chromatin Accessibility in cis-Regulatory Evolution
Cited by: 14
Author(s): Pei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P. Reddington, David Garfield, Eileen E. M. Furlong, Saurabh Sinha
Software Mentions: 2
Published: over 7 years ago

10.1186/s13073-014-0097-z

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease
Cited by: 7
Author(s): Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi, Martin Hofmann‐Apitius
Software Mentions: 2
Published: almost 12 years ago

10.1136/gutjnl-2017-314817

DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
Cited by: 110
Author(s): Judith Kraiczy, Komal Nayak, Kate J. Howell, Alex Ross, Jessica L. Forbester, Camilla Salvestrini, Roxana C. Mustata, Sally Perkins, Amanda Andersson-Rolf, Esther Leenen, Anke Liebert, Ludovic Vallier, Philip Rosenstiel, Oliver Stegle, Gordon Dougan, Robert Heuschkel, Bon–Kyoung Koo, Matthias Zilbauer
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.jacbts.2020.09.010

Cardiorenal Tissues Express SARS-CoV-2 Entry Genes and Basigin (BSG/CD147) Increases With Age in Endothelial Cells
Cited by: 30
Author(s): Blerina Ahmetaj‐Shala, Ricky Vaja, Santosh S. Atanur, Peter M. George, Nicholas S. Kirkby, Jane A. Mitchell
Software Mentions: 2
Published: almost 6 years ago

10.1172/jci.insight.140785

Neonatal hyperoxia inhibits proliferation and survival of atrial cardiomyocytes by suppressing fatty acid synthesis
Cited by: 15
Author(s): Ethan D. Cohen, Min Yee, George A. Porter, Erin E Ritzer, Andrew McDavid, Paul S. Brookes, Gloria S. Pryhuber, Michael A. O’Reilly
Software Mentions: 2
Published: over 5 years ago

10.1074/jbc.RA118.006865

Translational regulation contributes to the secretory response of chondrocytic cells following exposure to interleukin-1β
Cited by: 10
Author(s): B.T. McDermott, Mandy J. Peffers, Brian McDonagh, Simon R. Tew
Software Mentions: 2
Published: about 7 years ago

10.1186/2041-1480-5-S1-S3

Semantic Web repositories for genomics data using the eXframe platform
Cited by: 7
Author(s): Emily Merrill, Stéphane Corlosquet, Paolo Ciccarese, Tim W. Clark, Sudeshna Das
Software Mentions: 2
Published: almost 13 years ago

10.1186/2041-1480-5-31

CSEO – the Cigarette Smoke Exposure Ontology
Cited by: 8
Author(s): Erfan Younesi, Sam Ansari, Michaela Guendel, Shiva Ahmadi, Chris R. E. Coggins, Julia Hoeng, Martin Hofmann‐Apitius, Manuel C. Peitsch
Software Mentions: 2
Published: over 12 years ago

10.1186/s13326-016-0055-3

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates
Cited by: 7
Author(s): Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
Software Mentions: 2
Published: over 10 years ago

10.1111/jcmm.15429

Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells
Cited by: 16
Author(s): Tao Fan, Rongmei Qu, Qinghe Yu, Bing Sun, Xin Jiang, Yuchao Yang, Xiaolan Huang, Zhaoxi Zhou, Jun Ouyang, Shizhen Zhang, Jingxing Dai
Software Mentions: 2
Published: over 6 years ago

10.1242/jcs.226969

An essential role for dNTP homeostasis following CDK-induced replication stress
Cited by: 15
Author(s): Chen Chun Pai, Kuo–Feng Hsu, Samuel C. Durley, Andrea Keszthelyi, Stephen Kearsey, Charalampos Rallis, Lisa K. Folkes, Rachel S. Deegan, Sarah E. Wilkins, Sophia X. Pfister, Nagore de León, Christopher J. Schofield, Jürg Bähler, Antony Carr, Timothy C. Humphrey
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.ppat.0010045

Bordetella pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchiseptica
Cited by: 238
Author(s): Dimitri A. Diavatopoulos, Craig Cummings, Leo M. Schouls, Mary M. Brinig, David A. Relman, Frits R. Mooi
Software Mentions: 2
Published: almost 21 years ago

10.1371/journal.ppat.1000105

Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides
Cited by: 215
Author(s): Nathalie Pujol, Olivier Zugasti, Daniel Wong, Carole Couillault, C. Léopold Kurz, Hinrich Schulenburg, Jonathan J. Ewbank
Software Mentions: 2
Published: about 18 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962