bioconductor: ArrayExpress | Projects

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: about 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: almost 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: about 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: over 5 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: about 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: almost 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: almost 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: almost 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: almost 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: over 4 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: almost 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: almost 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: about 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: over 14 years ago

10.1371/journal.pone.0225873

Dual oxidase Duox and Toll-like receptor 3 TLR3 in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis in Hermetia illucens L.
Cited by: 17
Author(s): Yaqing Huang, Yongqiang Yu, Shuai Zhan, Jeffery K. Tomberlin, Dian Huang, Minmin Cai, Longyu Zheng, Yu Zhou, Jibin Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0106479

De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae
Cited by: 19
Author(s): Sisi Ma, Patrick Kemmeren, David Gresham, Alexander Statnikov
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0248233

R-locus for roaned coat is associated with a tandem duplication in an intronic region of USH2A in dogs and also contributes to Dalmatian spotting
Cited by: 3
Author(s): Takeshi Kawakami, Meghan K. Jensen, Andrea Slavney, Petra E. Deane, Ausra Milano, Vandana Raghavan, Brett Ford, Erin T. Chu, Aaron J. Sams, Adam R. Boyko
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0246144

Xylanase modulates the microbiota of ileal mucosa and digesta of pigs fed corn-based arabinoxylans likely through both a stimbiotic and prebiotic mechanism
Cited by: 14
Author(s): Amy L Petry, John F. Patience, Lucas R Koester, Nichole F. Huntley, M.R. Bedford, Stephan Schmitz‐Esser
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0211716

Sepsis induces long-lasting impairments in CD4+ T-cell responses despite rapid numerical recovery of T-lymphocyte populations
Cited by: 22
Author(s): Christoph Ammer‐Herrmenau, Upasana Kulkarni, Nico Andreas, Martin Ungelenk, Sarina Ravens, Christian G. Hübner, Angela Kather, Ingo Kurth, Michael Bauer, Thomas Kamradt
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0245160

Rapid detection of ERG11 polymorphism associated azole resistance in Candida tropicalis
Cited by: 6
Author(s): Saikat Paul, Rajneesh Dadwal, Shreya Singh, Dipika Shaw, Arunaloke Chakrabarti, Shivaprakash M Rudramurthy, Anup Ghosh
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0224643

Genome-wide transcriptomic analysis of the response of Botrytis cinerea to wuyiencin
Cited by: 5
Author(s): Liming Shi, Binghua Liu, Qiuhe Wei, Beibei Ge, Kecheng Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0230802

Detection of novel coronaviruses in bats in Myanmar
Cited by: 66
Author(s): Marc Valitutto, Ohnmar Aung, Kyaw Yan Naing Tun, Megan E. Vodzak, Dawn Zimmerman, Jennifer H. Yu, Ye Tun Win, Min Thein Maw, Wai Zin Thein, Htay Htay Win, Jasjeet K. Dhanota, Victoria Ontiveros, Brett Smith, Alexandre Tremeau-Brevard, Tracey Goldstein, Christine K. Johnson, Suzan Murray, Jonna A. K. Mazet
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0256588

Characterization of microRNA expression in B cells derived from Japanese black cattle naturally infected with bovine leukemia virus by deep sequencing
Cited by: 5
Author(s): Chihiro Ochiai, Sonoko Miyauchi, Yuta Kudo, Yuta Naruke, Syuji Yoneyama, Keisuke Tomita, Leng Dongze, Yusuke Chiba, To-ichi Hirata, Toshihiro Ichijo, Kazuya Nagai, Sota Kobayashi, Shinji Yamada, Hirokazu Hikono, Kenji Murakami
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0121846

Global Spectrum of Copy Number Variations Reveals Genome Organizational Plasticity and Proposes New Migration Routes
Cited by: 6
Author(s): Avinash M. Veerappa, Sangeetha Vishweswaraiah, Kusuma Lingaiah, Megha Murthy, Raviraj V. Suresh, Dinesh S. Manjegowda, Nallur B. Ramachandra
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0230822

Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases
Cited by: 7
Author(s): Chinho Lin, Kai Fang, Xing-Fan Dong, Ai-Ling Yang, Yuxuan Li, Hanbo Zhang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0006447

Mining Biological Pathways Using WikiPathways Web Services
Cited by: 107
Author(s): Thomas Kelder, Alexander R. Pico, Kristina Hanspers, Martijn P. van Iersel, Chris T. Evelo, Bruce R. Conklin
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0256158

Cohort profile: Epigenetics in Pregnancy (EPIPREG) – population-based sample of European and South Asian pregnant women with epigenome-wide DNA methylation (850k) in peripheral blood leukocytes
Cited by: 7
Author(s): Nicolás Fragoso-Bargas, Julia O Opsahl, Nadezhda Kiryushchenko, Yvonne Böttcher, Sindre Lee, Elisabeth Qvigstad, Kåre Rønn Richardsen, Christin W. Waage, Line Sletner, Anne Karen Jenum, Rashmi B. Prasad, Leif Groop, Gunn-Helen Moen, Kåre I. Birkeland, Christine Sommer
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0111668

A Network-Based Classification Model for Deriving Novel Drug-Disease Associations and Assessing Their Molecular Actions
Cited by: 42
Author(s): Min Kyu Oh, Jaegyoon Ahn, Yoon Yong-Jin
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0045527

Reconstruction of the Evolutionary History of Saccharomyces cerevisiae x S. kudriavzevii Hybrids Based on Multilocus Sequence Analysis
Cited by: 28
Author(s): David Peris, Christian A. Lopes, Armando Arias, Eladio Barrio
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0040521

Molecular Resistance Fingerprint of Pemetrexed and Platinum in a Long-Term Survivor of Mesothelioma
Cited by: 33
Author(s): Oluf Dimitri Røe, Adam Szulkin, Endre Anderssen, Arnar Flatberg, Helmut Sandeck, Tore Amundsen, Sten Even Erlandsen, Katalin Dobra, Stein Sundstrøm
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0026801

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44
Cited by: 104
Author(s): Alicia N. Massa, Kevin L. Childs, Haining Lin, Glenn J. Bryan, Giovanni Giuliano, C. Robin Buell
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0083772

Transcriptome Analysis of Nodes and Buds from High and Low Tillering Switchgrass Inbred Lines
Cited by: 9
Author(s): Wang Yixing, Xin Zeng, Lila Peal, Yuhong Tang, Yanqi Wu, Ramamurthy Mahalingam
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0236006

Isolation and diversity of sediment bacteria in the hypersaline aiding lake, China
Cited by: 18
Author(s): Tong-Wei Guan, Yijin Lin, Meng-Ying Ou, Ke-Bao Chen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0234803

Genetic analysis of body weight in wild populations of medaka fish from different latitudes
Cited by: 3
Author(s): Tamiris I. Yassumoto, Mana Nakatsukasa, Atsushi J. Nagano, Masaki Yasugi, Takashi Yoshimura, Ai Shinomiya
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0042161

Identification of Pluripotent and Adult Stem Cell Genes Unrelated to Cell Cycle and Associated with Poor Prognosis in Multiple Myeloma
Cited by: 18
Author(s): Alboukadel Kassambara, Dirk Hose, Jérôme Moreaux, Thierry Rème, Jennifer Torrent, Jean François Rossi, Hartmut Goldschmidt, Bernard Klein
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0241174

Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16
Cited by: 1
Author(s): Yuanliang Hu, Yang Zhen, Shenglan Wang, Danxiong Sun, Mi Zhong, Mudong Wen, Longding Liu, Yunhui Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0005657

Highly Active Microbial Phosphoantigen Induces Rapid yet Sustained MEK/Erk- and PI-3K/Akt-Mediated Signal Transduction in Anti-Tumor Human γδ T-Cells
Cited by: 47
Author(s): Daniel V. Correia, Francisco d’Orey, Bruno Cardoso, Telma Lança, Ana Rita Grosso, Ana deBarros, Leila R. Martins, João T. Barata, Bruno Silva‐Santos
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0005662

Accumulating Progenitor Cells in the Luminal Epithelial Cell Layer Are Candidate Tumor Initiating Cells in a Pten Knockout Mouse Prostate Cancer Model
Cited by: 66
Author(s): Hanneke Korsten, Angelique Ziel-van der Made, Xiaoqian Ma, Theodorus H. van der Kwast, Jan Trapman
Software Mentions: 2
Published: over 16 years ago

10.3390/cancers13153755

Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma
Cited by: 6
Author(s): Laure Dutrieux, Yea-Lih Lin, Malik Lutzmann, Raphaël Rodriguez, Michel Cogné, Philippe Pasero, Jérôme Moreaux
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers13184577

The Stress-Inducible BCL2A1 Is Required for Ovarian Cancer Metastatic Progression in the Peritoneal Microenvironment
Cited by: 5
Author(s): Rui Liang, Mingo M. H. Yung, Fengjiao He, Peili Jiao, Ki Chan, Hextan Ys Ngan, David W. Chan
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers11040507

Integrative Analysis Reveals Subtype-Specific Regulatory Determinants in Triple Negative Breast Cancer
Cited by: 8
Author(s): Shujun Huang, Wayne Xu, Pingzhao Hu, Ted M. Lakowski
Software Mentions: 2
Published: almost 7 years ago

10.3390/cancers12051136

Increased Level of Long Non-Coding RNA MALAT1 Is a Common Feature of Amoeboid Invasion
Cited by: 4
Author(s): Ladislav Merta, Aneta Gandalovičová, Vladimı́r Čermák, Michal Dibus, Tony Gutschner, Sven Diederichs, Daniel Rösel, Jan Brábek
Software Mentions: 2
Published: almost 6 years ago

10.3390/cancers13133358

Comprehensive Profiling of Hypoxia-Related miRNAs Identifies miR-23a-3p Overexpression as a Marker of Platinum Resistance and Poor Prognosis in High-Grade Serous Ovarian Cancer
Cited by: 7
Author(s): Paola Todeschini, Elisa Salviato, Chiara Romani, Vittoria Raimondi, Francesco Ciccarese, Federico Ferrari, Germana Tognon, Sérgio Marchini, Maurizio D’Incalci, Laura Zanotti, Antonella Ravaggi, Franco Odicino, Enrico Sartori, Donna M. D’Agostino, Michele Samaja, Chiara Romualdi, Eliana Bignotti
Software Mentions: 2
Published: over 4 years ago

10.3390/cancers12030549

Sphere-Forming Culture for Expanding Genetically Distinct Patient-Derived Glioma Stem Cells by Cellular Growth Rate Screening
Cited by: 2
Author(s): Ki Soon Shin, Hong-Jae Shin, Hee Jin Cho, Hyunju Kang, Jin Ku Lee, Yun Jee Seo, Yong Jae Shin, Donggeon Kim, Harim Koo, Doo‐Sik Kong, Ho Jun Seol, Jung-Il Lee, Hye Won Lee, Do‐Hyun Nam
Software Mentions: 2
Published: almost 6 years ago

10.3390/cancers12102823

Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling
Cited by: 5
Author(s): Ian M. Overton, Andrew H. Sims, Jeremy A. Owen, Bret S.E. Heale, Matthew J. Ford, Alexander L R Lubbock, Erola Pairo-Castineira, Abdelkader Essafi
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: about 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: over 5 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: over 6 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: over 4 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: about 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: about 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: about 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: about 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: about 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: about 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: about 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: about 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: almost 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: about 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: about 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: about 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: about 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: about 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: about 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: over 7 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: almost 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 7 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: almost 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: about 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: over 6 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: over 8 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 6 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: over 6 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: over 6 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: over 6 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: over 5 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: about 11 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: about 19 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: about 19 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: about 19 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: about 17 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: about 17 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: about 16 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: about 16 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: about 14 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962