bioconductor: ArrayExpress | Projects

10.1371/journal.pone.0110840

Measuring the Effect of Inter-Study Variability on Estimating Prediction Error
Cited by: 19
Author(s): Shuyi Ma, Jaeyun Sung, Andrew T. Magis, Yuliang Wang, Donald Geman, Nathan D. Price
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0072591

Comparative Gene Expression Profiling Identifies Common Molecular Signatures of NF-κB Activation in Canine and Human Diffuse Large B Cell Lymphoma (DLBCL)
Cited by: 74
Author(s): Manikhandan Mudaliar, Ross Haggart, Gino Miele, Grant C. Sellar, Karen A. L. Tan, John Goodlad, Elspeth Milne, David M. Vail, Ilene D. Kurzman, Daniel Crowther, David Argyle
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0083762

The Effect of Gestational Age on Angiogenic Gene Expression in the Rat Placenta
Cited by: 13
Author(s): Kanchan Vaswani, Melissa Hum, Hsiu‐Wen Chan, Jennifer Ryan, Ryan J Wood-Bradley, Marloes Dekker Nitert, Murray D. Mitchell, James A. Armitage, Gregory E. Rice
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0009114

Functional Overlap between eIF4G Isoforms in Saccharomyces cerevisiae
Cited by: 51
Author(s): Bryan K. Clarkson, Wendy V. Gilbert, Jennifer A. Doudna
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0238923

Maternal supplementation with Bifidobacterium breve M-16V prevents their offspring from allergic airway inflammation accelerated by the prenatal exposure to an air pollutant aerosol
Cited by: 16
Author(s): Chiyoko Terada-Ikeda, Masahiro Kitabatake, Akari Hiraku, Koichi Kato, Satsuki Yasui, Natsuko Imakita, Noriko Ouji-Sageshima, Noriyuki Iwabuchi, Kaoru Hamada, Toshihiro Ito
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0242297

Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
Cited by: 0
Author(s): Swarnali Louha, Richard J. Meinersmann, Travis C. Glenn
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0243065

Differential plasma exosomal long non-coding RNAs expression profiles and their emerging role in E-cigarette users, cigarette, waterpipe, and dual smokers
Cited by: 16
Author(s): Gagandeep Kaur, K. R. P. Singh, Krishna Prahlad Maremanda, Dongmei Li, Hitendra S. Chand, Irfan Rahman
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0232972

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet
Cited by: 17
Author(s): Lei Chen, Liangyu Zhang, Wendong Wang, Wei Qiu, Lei Liu, Anhong Ning, Jing Cao, Min Huang, Ming-Chao Zhong
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0244056

Viruses in unexplained encephalitis cases in American black bears (Ursus americanus)
Cited by: 10
Author(s): Charles E. Alex, Elizabeth Fahsbender, Eda Altan, Robert J. Bildfell, Peregrine L. Wolff, Ling Jin, Wendy Black, K. A. Jackson, Leslie W. Woods, Brandon Munk, Tiffany Tse, Eric Delwart, Patricia A. Pesavento
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0237245

Increasing temperature can modify the effect of straw mulching on soil C fractions, soil respiration, and microbial community composition
Cited by: 10
Author(s): Xin Fu, Jun Wang, Meng-Yi Xie, Fazhu Zhao, Russell Doughty
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0121042

Host Glycan Sugar-Specific Pathways in Streptococcus pneumonia: Galactose as a Key Sugar in Colonisation and Infection
Cited by: 67
Author(s): Laura Paixão, J.Santos Oliveira, André Veríssimo, Susana Vinga, Eva C. Lourenço, M. Rita Ventura, Morten Kjos, Jan‐Willem Veening, Vitor E. Fernandes, Peter W. Andrew, Hasan Yeşilkaya, Ana Rute Neves
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0237463

Bio-activating ultrafine grain titanium: RNA sequencing reveals enhanced mechano-activation of osteoconduction on nanostructured substrates
Cited by: 4
Author(s): Rebecca A. Reiss, Terry C. Lowe, Johnny A. Sena, Oleg Makhnin, Melanie C. Connick, Patrick Erik Illescas, Casey F. Davis
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0148957

Low Concordance between Gene Expression Signatures in ER Positive HER2 Negative Breast Carcinoma Could Impair Their Clinical Application
Cited by: 9
Author(s): Enora Laas, Peter Mallon, François P. Duhoux, Amina Hamidouche, Roman Rouzier, Fabien Reyal
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0240025

PLA2R antibody, PLA2R rs4664308 polymorphism and PLA2R mRNA levels in Tunisian patients with primary membranous nephritis
Cited by: 2
Author(s): Tarak Dhaouadi, Jihen Abdellatif, R. Trabelsi, H. Gaied, Sameh Chamkhi, Imen Sfar, R. Goucha, Fethi Ben Hamida, T. Ben Abdallah, Yousr Gorgi
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0058992

Spatio-Temporal Expression Patterns of Arabidopsis thaliana and Medicago truncatula Defensin-Like Genes
Cited by: 55
Author(s): Mesfin Tesfaye, Kevin A.T. Silverstein, Sumitha Nallu, Lin Wang, Christopher Botanga, S. Karen Gomez, Liliana M. Costa, Maria J. Harrison, Deborah A. Samac, Jane Glazebrook, Fumiaki Katagiri, José Gutierrez-Marcos, Kathryn A. VandenBosch
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0249757

Genome-wide identification and expression analysis of late embryogenesis abundant protein-encoding genes in rye (Secale cereale L.)
Cited by: 7
Author(s): Mengyue Ding, Lijian Wang, Weimin Zhan, Guanghua Sun, Xiaolin Jia, Shizhan Chen, Wusi Ding, Jianping Yang
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0253866

Have maternal or paternal ages any impact on the prenatal incidence of genomic copy number variants associated with fetal structural anomalies?
Cited by: 4
Author(s): Marta Larroya, Marta Tortajada, Eduard Mensión, Montse Pauta, Laia Rodríguez‐Revenga, Antoni Borrell
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0004818

PTCH1+/− Dermal Fibroblasts Isolated from Healthy Skin of Gorlin Syndrome Patients Exhibit Features of Carcinoma Associated Fibroblasts
Cited by: 27
Author(s): Alexandre Valin, Stéphanie Barnay‐Verdier, Robert Thomas, Hugues Ripoche, Florence Brellier, Odile Chevallier-Lagente, Marie-Françoise Avril, Thierry Magnaldo
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0229415

Identification of two novel adenoviruses in smooth-billed ani and tropical screech owl
Cited by: 10
Author(s): Ana Paula Jejesky de Oliveira, Maria Cristina Valdetaro Rangel, Márton Z. Vidovszky, João Luiz Rossi, Fernando Vicentini, Balázs Harrach, Győző L. Kaján
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0166991

dCITE: Measuring Necessary Cladistic Information Can Help You Reduce Polytomy Artefacts in Trees
Cited by: 2
Author(s): Michael J. Wise
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0019651

Platelets Alter Gene Expression Profile in Human Brain Endothelial Cells in an In Vitro Model of Cerebral Malaria
Cited by: 35
Author(s): Mathieu Barbier, Dorothée Faille, Béatrice Loriod, Julien Textoris, Claire Camus, Denis Puthier, Laurence Flori, Samuel C. Wassmer, Geneviève Victoréro, Marie‐Christine Alessi, Thierry Fusaı̈, Catherine Nguyen, Georges E. Grau, Pascal Rihet
Software Mentions: 2
Published: almost 15 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: over 5 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: almost 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: over 7 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: almost 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: over 8 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: almost 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: over 7 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: over 10 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: about 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: about 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: over 5 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: over 6 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: over 11 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: over 11 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: over 6 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: over 9 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: about 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: over 6 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: almost 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: about 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: over 8 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: about 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: over 10 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: over 7 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: over 10 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: over 11 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: over 8 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: over 8 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: over 7 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: almost 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: about 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: almost 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: about 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: over 8 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: almost 7 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: almost 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: over 7 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: over 20 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: over 17 years ago

10.1371/journal.ppat.1002027

Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival
Cited by: 133
Author(s): Hebert Echenique-Rivera, Alessandro Muzzi, Elena Del Tordello, Kate L. Seib, Patrice François, Rino Rappuoli, Mariagrazia Pizza, Davide Serruto
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1002046

Transition of Plasmodium Sporozoites into Liver Stage-Like Forms Is Regulated by the RNA Binding Protein Pumilio
Cited by: 88
Author(s): Carina S. S. Gomes-Santos, Joanna A. M. Braks, Miguel Prudêncio, Céline Carret, Ana Gomes, Arnab Pain, Theresa Feltwell, Shahid M. Khan, Andrew P. Waters, Chris J. Janse, Gunnar R. Mair, Maria M. Mota
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.ppat.1004609

Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1
Cited by: 77
Author(s): Luis Apolonia, Reiner Schulz, Tomaž Curk, Paula Rocha, Chad M. Swanson, Torsten Schaller, Jernej Ule, Michael H. Malim
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.ppat.1007729

Niche-specific metabolic adaptation in biotrophic and necrotrophic oomycetes is manifested in differential use of nutrients, variation in gene content, and enzyme evolution
Cited by: 16
Author(s): Audrey M. V. Ah‐Fong, Meenakshi S. Kagda, Melania Abrahamian, Howard S. Judelson
Software Mentions: 2
Published: almost 7 years ago

10.1098/rsos.150402

Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts
Cited by: 21
Author(s): Brett Trost, Catherine A. Moir, Zoe E. Gillespie, Anthony Kusalik, Jennifer A. Mitchell, Christopher H. Eskiw
Software Mentions: 2
Published: over 10 years ago

10.1016/j.redox.2020.101450

Mitochondrial complex I derived ROS regulate stress adaptation in Drosophila melanogaster
Cited by: 37
Author(s): Filippo Scialò, Ashwin Sriram, Rhoda Stefanatos, Ruth V. Spriggs, Samantha H. Y. Loh, L. Miguel Martins, Alberto Sanz
Software Mentions: 2
Published: almost 6 years ago

10.1186/1477-7827-7-94

A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
Cited by: 20
Author(s): Hang Zhao, Qishan Wang, Chen Bai, Kan He, Yuchun Pan
Software Mentions: 2
Published: over 16 years ago

10.1186/s12958-015-0088-y

The rat placental renin-angiotensin system - a gestational gene expression study
Cited by: 14
Author(s): Kanchan Vaswani, Hsiu‐Wen Chan, Pali Verma, Marloes Dekker Nitert, Hassendrini N. Peiris, Ryan J Wood-Bradley, James A. Armitage, Gregory E. Rice, Murray D. Mitchell
Software Mentions: 2
Published: over 10 years ago

10.1093/rheumatology/kez358

Interleukin-36 family dysregulation drives joint inflammation and therapy response in psoriatic arthritis
Cited by: 29
Author(s): Marie-Astrid Boutet, Alessandra Nerviani, Gloria Lliso-Ribera, Davide Lucchesi, Edoardo Prediletto, Giulia Maria Ghirardi, Katriona Goldmann, Myles Lewis, Costantino Pitzalis
Software Mentions: 2
Published: over 6 years ago

10.1186/1939-8433-5-17

The Rice Oligonucleotide Array Database: an atlas of rice gene expression
Cited by: 156
Author(s): Peijian Cao, Ki‐Hong Jung, Daeseok Choi, Daehee Hwang, Jun Zhu, Pamela C. Ronald
Software Mentions: 2
Published: over 13 years ago

10.1038/sdata.2014.11

Genomes and phenomes of a population of outbred rats and its progenitors
Cited by: 28
Author(s): Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Amelie Baud, Victor Guryev, Oliver Hummel, Martina Johannesson, Roel Hermsen, Pernilla Stridh, Delyth Graham, Martin W. McBride, Tatiana Foroud, Sophie Caldérari, Margarita Diez, Johan Öckinger, Amennai Daniel Beyeen, Alan Gillett, Nada Abdelmagid, André Ortlieb Guerreiro-Cacais, Maja Jagodic, Jonatan Tuncel, Ulrika Norin, Elisabeth Beattie, Ngan Huynh, William H. Miller, Daniel L. Koller, Imranul Alam, Samreen Falak, Mary Osborne-Pellegrin, Esther Martínez-Membrives, Toni Cañete, Gloria Blázquez, Elia Vicens-Costa, Carme Mont-Cardona, Sira Díaz-Morán, Adolf Tobeña, Diana Zélénika, Kathrin Saar, Giannino Patone, Anja Bauerfeind, Marie-Thérèse Bihoreau, Matthias Heinig, Youngae Lee, Carola Rintisch, Herbert Schulz, David A. Wheeler, Kim C. Worley, Donna M. Muzny, Richard A. Gibbs, Mark Lathrop, Nico Lansu, Pim W. Toonen, Frans Paul Ruzius, Ewart de Bruijn, Heidi Hauser, David J. Adams, Thomas Keane, Santosh S. Atanur, Tim Aitman, Paul Flicek, Tomas Malinauskas, Elizabeth Jones, Diana Ekman, Regina López-Aumatell, Anna F. Dominiczak, Rikard Holmdahl, Tomas Olsson, Dominique Guyader, Norbert Hübner, Alberto Fernández-Teruel, Edwin Cuppen, Richard Mott, Jonathan Flint, Jonathan Flint
Software Mentions: 2
Published: almost 12 years ago

10.1038/sdata.2018.13

Single cell RNA sequencing of stem cell-derived retinal ganglion cells
Cited by: 41
Author(s): Maciej Daniszewski, Anne Senabouth, Quan Nguyen, Duncan E. Crombie, Samuel W. Lukowski, Tejal Kulkarni, Valentin M. Sluch, Jafar S. Jabbari, Xitiz Chamling, Donald J. Zack, Alice Pébay, Joseph E. Powell, Alex W. Hewitt
Software Mentions: 2
Published: about 8 years ago

10.1038/sdata.2018.158

The REMBRANDT study, a large collection of genomic data from brain cancer patients
Cited by: 101
Author(s): Yuriy Gusev, Krithika Bhuvaneshwar, Lei Song, Jean-Claude Zenklusen, Howard A. Fine, Subha Madhavan
Software Mentions: 2
Published: over 7 years ago

10.1038/s41597-020-00636-6

Cross-sectional study of human coding- and non-coding RNAs in progressive stages of Helicobacter pylori infection
Cited by: 1
Author(s): Sergio Lario, María José Ramírez‐Lázaro, Aintzane González-Lahera, José L. Lavín, María Vila-Casadesús, María Elisa Quílez, Anna Brunet-Vega, Juan José Lozano, Ana M. Aransay, Xavier Calvet
Software Mentions: 2
Published: over 5 years ago

10.1038/s41597-021-00808-y

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials
Cited by: 17
Author(s): Laura Aliisa Saarimäki, Antonio Federico, Iseult Lynch, Anastasios G. Papadiamantis, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis, Angela Serra, Dario Greco
Software Mentions: 2
Published: about 5 years ago

10.1038/srep13113

Human cell dedifferentiation in mesenchymal condensates through controlled autophagy
Cited by: 34
Author(s): Rebecca Rose Pennock, Elen Bray, Paul R. Pryor, Sally James, Paul J. McKeegan, Roger G. Sturmey, Paul G. Genever
Software Mentions: 2
Published: over 10 years ago

10.1038/srep17470

Fine-tuned SRF activity controls asymmetrical neuronal outgrowth: implications for cortical migration, neural tissue lamination and circuit assembly
Cited by: 14
Author(s): Marilyn Scandaglia, Eva Benito, Cruz Morenilla‐Palao, Anna Fiorenza, Beatriz del Blanco, Yaiza Coca, Eloı́sa Herrera, Ángel Barco
Software Mentions: 2
Published: over 10 years ago

10.1038/srep19729

Nucleosome architecture throughout the cell cycle
Cited by: 27
Author(s): Özgen Deniz, Oscar Flores, Martí Aldea, Montserrat Soler-López, Modesto Orozco
Software Mentions: 2
Published: about 10 years ago

10.1038/srep31209

Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation
Cited by: 69
Author(s): Marpe Bam, Xiaoming Yang, Elizabeth E. Zumbrun, Zhimin Yin, Juhua Zhou, J. P. Ginsberg, Quinne Leyden, Jiajia Zhang, Prakash Nagarkatti, Mitzi Nagarkatti
Software Mentions: 2
Published: over 9 years ago

10.1038/srep37988

Global gene regulation during activation of immunoglobulin class switching in human B cells
Cited by: 22
Author(s): Youming Zhang, David Fear, Saffron A.G. Willis‐Owen, William Cookson, Miriam F. Moffatt
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-017-01141-4

The yeast osmostress response is carbon source dependent
Cited by: 52
Author(s): Roja Babazadeh, Petri‐Jaan Lahtvee, Caroline B. Adiels, Mattias Goksör, Jens Nielsen, Stefan Hohmann
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-03986-1

Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks
Cited by: 70
Author(s): Yun Xiao, Jingpu Zhang, Lei Deng
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-017-05451-5

Loss of Usp9x disrupts cell adhesion, and components of the Wnt and Notch signaling pathways in neural progenitors
Cited by: 26
Author(s): Susitha Premarathne, Mariyam Murtaza, Nicholas Matigian, Lachlan A. Jolly, Stephen A. Wood
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-09430-8

Cerium oxide nanoparticles inhibit differentiation of neural stem cells
Cited by: 59
Author(s): Anda R. Gliga, Karin Edoff, Fanny Caputo, Thomas Källman, Hans Blom, Hanna Karlsson, Lina Ghibelli, Enrico Traversa, Sandra Ceccatelli, Bengt Fadeel
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-18043-0

Aedes aegypti microRNA miR-2b regulates ubiquitin-related modifier to control chikungunya virus replication
Cited by: 21
Author(s): Sunil Kumar Dubey, Jatin Shrinet, Jaspreet Jain, Shakir Ali, Sujatha Sunil
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-19357-3

TPGLDA: Novel prediction of associations between lncRNAs and diseases via lncRNA-disease-gene tripartite graph
Cited by: 73
Author(s): Liang Ding, Minghui Wang, Dongdong Sun, Ao Li
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-019-44235-x

Cynomolgus macaque IL37 polymorphism and control of SIV infection
Cited by: 3
Author(s): Takashi Shiina, Shingo Suzuki, Nicolas Congy-Jolivet, Alice Aarnink, Henri‐Jean Garchon, Nathalie Dereuddre‐Bosquet, Bruno Vaslin, Nicolas Tchitchek, Delphine Desjardins, Brigitte Autran, Olivier Lambotte, Ioannis Théodorou, Roger Le Grand, Antoine Blancher
Software Mentions: 2
Published: almost 7 years ago

10.1038/s41598-019-57076-5

The ETS transcription factor ETV5 is a target of activated ALK in neuroblastoma contributing to increased tumour aggressiveness
Cited by: 19
Author(s): Liselot Mus, Irina Lambertz, Shana Claeys, Candy Kumps, Wouter Van Loocke, Christophe Van Neste, Ganesh Umapathy, Marica Vaapil, Christoph Bartenhagen, Geneviève Laureys, Olivier De Wever, Daniel Bexell, Matthias Fischer, Bengt Hållberg, Johannes H. Schulte, Bram De Wilde, Kaat Durinck, Geertrui Denecker, Katleen De Preter, Frank Speleman
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-020-59514-1

Combined HER3-EGFR score in triple-negative breast cancer provides prognostic and predictive significance superior to individual biomarkers
Cited by: 24
Author(s): Angela Ogden, Shristi Bhattarai, Bikram Sahoo, Nigel P. Mongan, Mansour Alsaleem, Andrew Green, Mohammed A. Aleskandarany, Ian O. Ellis, Sonal Pattni, Xiaoxian Bill Li, Carlos S. Moreno, Uma Krishnamurti, Emiel A. M. Janssen, Kristín Jónsdóttir, Emad A. Rakha, Padmashree C.G. Rida, Ritu Aneja
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-60235-8

Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction
Cited by: 8
Author(s): Jessica Gliozzo, Paolo Perlasca, Marco Mesiti, Elena Casiraghi, Viviana Vallacchi, Elisabetta Vergani, Giuliano Grossi, Alessandro Petrini, Matteo Ré, Alberto Paccanaro, Giorgio Valentini
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-020-74417-x

Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)
Cited by: 9
Author(s): Ying Li, Qilu Song, Yamin Zhang, Zheng Li, Jialin Guo, Xinhong Chen, Gaisheng Zhang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-74288-2

Cell-free DNA in plasma as an essential immune system regulator
Cited by: 19
Author(s): Marie Korabečná, Alžběta Zinková, Iva Brynychova, Blanka Chylíková, Petr Přikryl, Lucie Šedová, Pavel Neužil, Ondřej Šeda
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21176220

Downregulation of TAP1 in Tumor-Free Tongue Contralateral to Squamous Cell Carcinoma of the Oral Tongue, an Indicator of Better Survival
Cited by: 9
Author(s): Nima Attaran, Xiaolian Gu, Philip J. Coates, Robin Fåhræus, Linda Boldrup, Torben Wilms, Lixiao Wang, Nicola Sgaramella, Katarína Zborayová, Karin Nylander
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21239332

Genomic Instability Is an Early Event in Aluminium-Induced Tumorigenesis
Cited by: 8
Author(s): Stefano J. Mandriota, Mirna Tenan, Adeline Nicolle, Julia Jankowska, Paolo Ferrari, Jean-Christophe Tille, Mary-Anne Durin, Catherine Green, Sébastien P. Tabruyn, Daniela Moralli, André‐Pascal Sappino
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms221910785

Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
Cited by: 3
Author(s): Nina Lukashina, Michael J. Williams, Elena Kartysheva, Elizaveta Virko, Błażej Kudłak, Robert Fredriksson, Ola Spjuth, Helgi B. Schiöth
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.14253

MiR-21 as prognostic biomarker in head and neck squamous cell carcinoma patients undergoing an organ preservation protocol
Cited by: 45
Author(s): Lídia Maria Rebolho Batista Arantes, Ana Carolina Laus, Matias Eliseo Melendez, Ana Carolina de Carvalho, Bruna Pereira Sorroche, Pedro Rafael Martins De Marchi, Adriane Feijó Evangelista, Cristovam Scapulatempo‐Neto, Luciano de Souza Viana, André Lopes Carvalho
Software Mentions: 2
Published: over 9 years ago

10.18632/oncotarget.14784

The homeoprotein Dlx5 drives murine T-cell lymphomagenesis by directly transactivating Notch and upregulating Akt signaling
Cited by: 9
Author(s): Yinfei Tan, Eleonora Sementino, Jiawen Xu, Jianming Pei, Zemin Liu, Timothy Ito, Kathy Q. Cai, Suraj Peri, Andres J. Klein‐Szanto, David L. Wiest, Joseph R. Testa
Software Mentions: 2
Published: about 9 years ago

10.18632/oncotarget.22131

CD24, CD27, CD36 and CD302 gene expression for outcome prediction in patients with multiple myeloma
Cited by: 20
Author(s): Elina Alaterre, Sébastien Raimbault, Hartmut Goldschmidt, Salahedine Bouhya, Guilhem Requirand, Robert Naeije, Stéphanie Boireau, Anja Seckinger, Dirk Hose, Bernard Klein, Jérôme Moreaux
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.23973

Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer
Cited by: 15
Author(s): Debashis Sahoo, Wei Wei, Heidi Auman, Antonio Hurtado-Coll, Peter R. Carroll, Ladan Fazli, Martin Gleave, Daniel W. Lin, Peter S. Nelson, Jeff Simko, Ian M. Thompson, Robin J. Leach, Dean A. Troyer, Lawrence D. True, Jesse K. McKenney, Ziding Feng, James D. Brooks
Software Mentions: 2
Published: over 8 years ago

10.1098/rsob.190299

Molecular anatomy of the pre-primitive-streak chick embryo
Cited by: 17
Author(s): Hyung Chul Lee, Hui-Chun Lu, Mark Turmaine, Nidia M M Oliveira, Youwen Yang, Irene De Almeida, Claudio D. Stern
Software Mentions: 2
Published: about 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962