bioconductor: ArrayExpress | Projects

10.1186/s13223-021-00584-9

Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells
Cited by: 1
Author(s): Jan Krzysztof Nowak, Marzena Dworacka, Nazgul Gubaj, Arystan Dossimov, Zhumabek Dossimov, Jarosław Walkowiak
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0244556

Pathways of calcium regulation, electron transport, and mitochondrial protein translation are molecular signatures of susceptibility to recurrent exertional rhabdomyolysis in Thoroughbred racehorses
Cited by: 6
Author(s): Kennedy Aldrich, Deborah Velez‐Irizarry, Clara Fenger, Melissa Schott, Stephanie J. Valberg
Software Mentions: 4
Published: over 5 years ago

10.1186/s13040-015-0052-6

DNA microarray integromics analysis platform
Cited by: 11
Author(s): Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, Wiktor Jurkowski
Software Mentions: 4
Published: over 11 years ago

10.1093/bib/bbv049

Empirical comparison of structure-based pathway methods
Cited by: 24
Author(s): Maria K. Jaakkola, Laura L. Elo
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-019-5850-7

Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks
Cited by: 6
Author(s): Kevin B. Walters, Radmir Sarsenov, Wen Siong Too, Roseanna K. Hare, Ian C. Paterson, D Lambert, Stephen Brown, James R. Bradford
Software Mentions: 4
Published: over 7 years ago

10.1093/bib/bbx080

‘Multi-omic’ data analysis using O-miner
Cited by: 13
Author(s): Ajanthah Sangaralingam, Abu Z. Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, A. Nagano, Helen Ross-Adams, Jun Wang, Nick R. Lemoine, Claude Chelala
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0015147

Analysis of Ultra Low Genome Conservation in Clostridium difficile
Cited by: 58
Author(s): Joy Scaria, Lalit Ponnala, Tavan Janvilisri, Weiwei Yan, Lukas A. Mueller, Yung-Fu Chang
Software Mentions: 4
Published: almost 16 years ago

10.1093/bioinformatics/btx143

The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Cited by: 26
Author(s): Robert Petryszak, Nuno A. Fonseca, Anja Füllgrabe, Laura Huerta, Maria Keays, Y. Amy Tang, Alvis Brāzma
Software Mentions: 4
Published: over 9 years ago

10.1186/s12864-017-4086-7

The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
Cited by: 59
Author(s): Victoria A. Ingham, Patricia Pignatelli, Jonathan D. Moore, Simon C. Wagstaff, Hilary Ranson
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pgen.1007961

A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Cited by: 17
Author(s): Michael Hecker, Nina Boxberger, Nicole Illner, Brit Fitzner, I Schröder, Alexander Winkelmann, Aleš Dudešek, Stefanie Meister, Dirk Koczan, Peter Lorenz, Hans‐Jürgen Thiesen, Uwe K. Zettl
Software Mentions: 4
Published: over 7 years ago

10.18632/oncotarget.22689

Systematic assessment of cervical cancer initiation and progression uncovers genetic panels for deep learning-based early diagnosis and proposes novel diagnostic and prognostic biomarkers
Cited by: 32
Author(s): Nguyen Phuoc Long, Kyung Hee Jung, Sang Jun Yoon, Nguyễn Hoàng Anh, Tran Diem Nghi, Yun Pyo Kang, Pengcheng Zhang, Jung Eun Min, Sung Kyung Hong, Sung Won Kwon
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2105-10-S12-S7

XML-based approaches for the integration of heterogeneous bio-molecular data
Cited by: 26
Author(s): Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga, Paolo Perlasca, Giorgio Valentini, David Manset
Software Mentions: 4
Published: about 17 years ago

10.1016/j.ccell.2019.08.003

Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis
Cited by: 230
Author(s): René Jackstadt, Sander R. van Hooff, Joshua D.G. Leach, Xabier Cortés-Lavaud, Jeroen Lohuis, Rachel A. Ridgway, Valérie M. Wouters, Jatin Roper, Timothy J. Kendall, Campbell S.D. Roxburgh, Paul G. Horgan, Colin Nixon, Craig Nourse, Matthias Gunzer, William Clark, Ann Hedley, Ömer H. Yılmaz, Mamunur Rashid, Peter J. Bailey, Andrew V. Biankin, Andrew D. Campbell, David J. Adams, Simon T. Barry, Colin W. Steele, Jan Paul Medema, Owen J. Sansom
Software Mentions: 4
Published: about 7 years ago

10.18632/oncotarget.22423

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
Cited by: 2
Author(s): Shana Claeys, Geertrui Denecker, Robrecht Cannoodt, Candy Kumps, Kaat Durinck, Franki Speleman, Katleen De Preter
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2020.566734

Pituitary Tumor Transforming Gene 1 Orchestrates Gene Regulatory Variation in Mouse Ventral Midbrain During Aging
Cited by: 4
Author(s): Yujuan Gui, Mélanie Thomas, Pierre Garcia, Mona Karout, Rashi Halder, Alessandro Michelucci, Heike Kollmus, Cuiqi Zhou, Shlomo Melmed, Klaus Schughart, Rudi Balling, Michel Mittelbronn, Joseph H. Nadeau, Robert W. Williams, Thomas Sauter, Manuel Buttini, Lasse Sinkkonen
Software Mentions: 4
Published: about 6 years ago

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0243684

Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)
Cited by: 19
Author(s): Roger Brown, Lindsey Moore, Amir Mani, Sonal Patel, Irene Salinas
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0222921

Computational identification of key genes that may regulate gene expression reprogramming in Alzheimer’s patients
Cited by: 20
Author(s): Judith A. Potashkin, Virginie Bottero, José A. Santiago, James P. Quinn
Software Mentions: 3
Published: about 7 years ago

10.1007/s12551-018-0490-8

Mining data and metadata from the gene expression omnibus
Cited by: 64
Author(s): Zichen Wang, Alexander Lachmann, Avi Ma’ayan
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0253859

Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome
Cited by: 8
Author(s): Sujata Srikanth, Lavanya Jain, Cinthya J. Zepeda-Mendoza, Lauren Cascio, Kelly A. Jones, Rini Pauly, Barb DuPont, Curtis Rogers, Sara M. Sarasua, Katy Phelan, Cynthia C. Morton, Luigi Boccuto
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0154556

The Ontology for Biomedical Investigations
Cited by: 228
Author(s): Anita Bandrowski, Ryan R. Brinkman, Mathias Brochhausen, Matthew Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, F. Gibson, Alejandra González-Beltrán, Melissa Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez‐Boussard, Mark A. Jensen, Yuling Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa Soldatova, Christian J. Stoeckert, Chris Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel, Jie Zheng
Software Mentions: 3
Published: over 10 years ago

10.1042/BSR20210617

Integrated bioinformatics analysis reveals novel key biomarkers and potential candidate small molecule drugs in gestational diabetes mellitus
Cited by: 5
Author(s): Varun Alur, Varshita Raju, Basavaraj Vastrad, Anandkumar Tengli, Chanabasayya Vastrad, Shivakumar Kotturshetti
Software Mentions: 3
Published: over 5 years ago

10.3390/biom2010001

Exploring the Optimal Strategy to Predict Essential Genes in Microbes
Cited by: 4
Author(s): Jingyuan Deng, Lirong Tan, Xiaodong Lin, Yao Lu, Long Lu
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0226905

Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells
Cited by: 9
Author(s): Xiangqin Ji, Penglei Jiang, Juntao Luo, Mengjia Li, Yajing Bai, Junfang Zhang, Bingshe Han
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-12-610

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease
Cited by: 10
Author(s): Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B. Smit, Sabine Spijker, Robert W. Williams, Robert Geffers, Dunja Bruder, Klaus Schughart
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pone.0251565

The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum
Cited by: 7
Author(s): Kaylene R. Ballard, Anne Klein, R. Andrew Hayes, Tianfang Wang, Scott F. Cummins
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-462

Effects of functional feeds on the lipid composition, transcriptomic responses and pathology in heart of Atlantic salmon (Salmo salar L.) before and after experimental challenge with Piscine Myocarditis Virus (PMCV)
Cited by: 34
Author(s): Laura Martínez-Rubio, Øystein Evensen, Aleksei Krasnov, Sven Martin Jørgensen, Simón Wadsworth, Kari Ruohonen, Jose L. González Vecino, Douglas R. Tocher
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0179065

Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis
Cited by: 64
Author(s): Thomas Mohr, Verena Haudek-Prinz, Astrid Slany, Johannes Grillari, M. Micksche, Christopher Gerner
Software Mentions: 3
Published: over 9 years ago

10.1186/bcr3150

Relevance of PTEN loss in brain metastasis formation in breast cancer patients
Cited by: 87
Author(s): Harriet Wikman, Katrin Lamszus, Niclas Detels, Liubov Uslar, Michaela Wrage, Christian Benner, Ina Hohensee, Bauke Ylstra, Kathrin Eylmann, Marc Zapatka, Guido Sauter, Dirk Kemming, Markus Glatzel, Volkmar Müller, Manfred Westphal, Klaus Pantel
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0039205

Effect of Chemical Mutagens and Carcinogens on Gene Expression Profiles in Human TK6 Cells
Cited by: 15
Author(s): Lode Godderis, Reuben Thomas, Alan Hubbard, Ali Mustafa Tabish, Peter Hoet, Luoping Zhang, Martyn T. Smith, Hendrik Veulemans, Cliona M. McHale
Software Mentions: 3
Published: over 14 years ago

10.1523/ENEURO.0226-19.2019

Mega-Analysis of Gene Expression in Mouse Models of Alzheimer’s Disease
Cited by: 6
Author(s): Beryl Zhuang, B. Ogan Mancarci, Lilah Toker, Paul Pavlidis
Software Mentions: 3
Published: almost 7 years ago

10.1155/2020/5156304

Comprehensive Analyses of miRNA-mRNA Network and Potential Drugs in Idiopathic Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Chan Li, Zeyu Zhang, Qian Xu, Ruizheng Shi
Software Mentions: 3
Published: over 6 years ago

10.3390/nu13082521

A Convergent Functional Genomics Analysis to Identify Biological Regulators Mediating Effects of Creatine Supplementation
Cited by: 5
Author(s): Diego A. Bonilla, Yurany Moreno, Eric S. Rawson, Diego A. Forero, Jeffrey R. Stout, Chad M. Kerksick, Michael D. Roberts, Richard B. Kreider
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-11-455

Next generation tools for genomic data generation, distribution, and visualization
Cited by: 46
Author(s): David A. Nix, Tonya L Di Sera, Brian Dalley, Brett Milash, Robert M Cundick, Kevin S Quinn, Samir Courdy
Software Mentions: 3
Published: about 16 years ago

10.4172/jpb.1000370

Mining the Breast Cancer Proteome for Predictors of Drug Sensitivity
Cited by: 7
Author(s): Leslie C Timpe Dian Li, Ten Yang Yen Judi Wong
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2105-6-268

MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data
Cited by: 20
Author(s): Mahendra Navarange, Laurence Gamé, Derek Fowler, Vihar Wadekar, H. Stanley Banks, Nicola Cooley, Fatimah Rahman, Justin Hinshelwood, Peter Broderick, Helen C. Causton
Software Mentions: 3
Published: almost 21 years ago

10.1186/1471-2105-11-421

Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
Cited by: 35
Author(s): Wei‐Chung Cheng, Min-Lung Tsai, Cheng-Wei Chang, Ching-Lung Huang, Chaang-Ray Chen, Wun‐Yi Shu, Yun‐Shien Lee, Tzu‐Hao Wang, Ji-Hong Hong, Chia-Yang Li, Ian C. Hsu
Software Mentions: 3
Published: about 16 years ago

10.1155/2015/146250

An Association Rule Mining Approach to Discover lncRNAs Expression Patterns in Cancer Datasets
Cited by: 7
Author(s): Paolo Cremaschi, Roberta Carriero, Stefania Astrologo, Caterina Colì, Antonella Lisa, Silvia Parolo, Silvia Bione
Software Mentions: 3
Published: almost 12 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: almost 11 years ago

10.1186/s13062-016-0152-3

Weighted-SAMGSR: combining significance analysis of microarray-gene set reduction algorithm with pathway topology-based weights to select relevant genes
Cited by: 14
Author(s): Suyan Tian, Howard H. Chang, Chi Wang
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-12-373

Spontaneous and evolutionary changes in the antibiotic resistance of Burkholderia cenocepacia observed by global gene expression analysis
Cited by: 64
Author(s): Andrea Saß, Angela Marchbank, Elizabeth Tullis, John J. LiPuma, Eshwar Mahenthiralingam
Software Mentions: 3
Published: about 15 years ago

10.1186/1471-2164-8-9

Ashbya Genome Database 3.0: a cross-species genome and transcriptome browser for yeast biologists
Cited by: 48
Author(s): Alexandre Gattiker, Riccarda Rischatsch, Philippe Demougin, Sylvia Voegeli, Fred S. Dietrich, Peter Philippsen, Michael Primig
Software Mentions: 3
Published: almost 20 years ago

10.1155/2020/5943014

Bioinformatic Identification of Neuroblastoma Microenvironment-Associated Biomarkers with Prognostic Value
Cited by: 4
Author(s): Yi Wang, Huan Luo, Jing Cao, Chi Ma
Software Mentions: 3
Published: about 6 years ago

10.1016/j.isci.2021.102848

Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana
Cited by: 10
Author(s): Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, C.-L. Jen, William Duddy, Γεράσιμος Δάρας, Polydefkis Hatzopoulos, David Westhead, Ioannis Michalopoulos
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0240269

Using association rule mining to jointly detect clinical features and differentially expressed genes related to chronic inflammatory diseases
Cited by: 6
Author(s): Rosana Veroneze, Sâmia Cruz Tfaile Corbi, Bárbara Roque da Silva, Cristiane S. Rocha, Cláudia Vianna Maurer-Morelli, Silvana Regina Perez Orrico, Joni Augusto Cirelli, Fernando J. Von Zuben, Raquel Mantuaneli Scarel‐Caminaga
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0238809

MicroRNA expression profiles in molecular subtypes of clear-cell renal cell carcinoma are associated with clinical outcome and repression of specific mRNA targets
Cited by: 3
Author(s): Annelies Verbiest, Vincent van Hoef, Cristina Rodríguez‐Antona, Jesús García-Donás, Osvaldo Graña‐Castro, Maarten Albersen, Marcella Baldewijns, Annouschka Laenen, Eduard Roussel, Patrick Schöffski, Agnieszka Woźniak, Stefano Caruso, Gabrielle Couchy, Jessica Zucman–Rossi, Benoît Beuselinck
Software Mentions: 3
Published: about 6 years ago

10.18632/oncotarget.7248

MicroRNA-34a promotes genomic instability by a broad suppression of genome maintenance mechanisms downstream of the oncogene KSHV-vGPCR
Cited by: 14
Author(s): Claudia J. Krause, Oliver Popp, Nanthakumar Thirunarayanan, Gunnar Dittmar, Martin Lipp, Gerd Müller
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0037287

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms
Cited by: 45
Author(s): Philipp Schulz, Jenny Neukermans, Katrien Van Der Kelen, Per Mühlenbock, Frank Van Breusegem, Graham Noctor, Markus Teige, Michael Metzlaff, Matthew A. Hannah
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-016-1210-7

Tilting the lasso by knowledge-based post-processing
Cited by: 9
Author(s): Kukatharmini Tharmaratnam, Matthew Sperrin, Thomas Jaki, Sjur Reppe, Arnoldo Frigessi
Software Mentions: 3
Published: about 10 years ago

10.1038/s41598-019-49410-8

Spodoptera frugiperda transcriptional response to infestation by Steinernema carpocapsae
Cited by: 13
Author(s): Louise Huot, Simon C. George, Pierre-Alain Girard, Dany Séverac, Nicolas Nègre, Bernard Duvic
Software Mentions: 3
Published: about 7 years ago

10.1186/s13040-016-0122-4

Elevated transcriptional levels of aldolase A (ALDOA) associates with cell cycle-related genes in patients with NSCLC and several solid tumors
Cited by: 25
Author(s): Fan Zhang, Jiediao Lin, Xiaoyu Zuo, Yingping Zhuang, Chao‐Qun Hong, Guojun Zhang, Xiaojiang Cui, Yukun Cui
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms21082818

Identification of the Key Molecular Drivers of Phosphorus Utilization Based on Host miRNA-mRNA and Gut Microbiome Interactions
Cited by: 14
Author(s): Siriluck Ponsuksili, Henry Reyer, Frieder Hadlich, Frank Weber, Nares Trakooljul, Michael Oster, Puntita Siengdee, Eduard Muráni, M. Rodehutscord, Amélia Camarinha‐Silva, Jörn Bennewitz, Klaus Wimmers
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0253864

The KrasG12D;Trp53fl/fl murine model of undifferentiated pleomorphic sarcoma is macrophage dense, lymphocyte poor, and resistant to immune checkpoint blockade
Cited by: 3
Author(s): Karys Hildebrand, Arvind K. Singla, Reid McNeil, Kayla L. Marritt, Kurt Hildebrand, Franz J. Zemp, Jahanara Rajwani, Doha Itani, Pinaki Bose, Douglas J. Mahoney, Frank R. Jirik, Michael J. Monument
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-35868-5

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
Cited by: 11
Author(s): Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Franki Speleman, Katleen De Preter
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-015-2051-x

Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Cited by: 23
Author(s): Michael Petridis, Andrej Benjak, Gregory M. Cook
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0239450

Integrative analysis of long non-coding RNA and mRNA in broilers with valgus-varus deformity
Cited by: 10
Author(s): Hehe Tang, Yaping Guo, Zhenzhen Zhang, Zhuanjian Li, Yanhua Zhang, Yuanfang Li, Xiangtao Kang, Ruili Han
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0253340

Placental DNA methylation changes and the early prediction of autism in full-term newborns
Cited by: 11
Author(s): Ray O. Bahado‐Singh, Sangeetha Vishweswaraiah, Buket Aydas, Uppala Radhakrishna
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-43862-8

CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 and target genes
Cited by: 53
Author(s): Alex K. Datsomor, Nikola Zic, Keshuai Li, Rolf Erik Olsen, Yang Jin, Jon Olav Vik, Rolf B. Edvardsen, Fabian Grammes, Anna Wargelius, Per Winge
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-22284-y

Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis
Cited by: 19
Author(s): Li Jin, Peng Yu
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-17730-2

Constitutively elevated levels of SOCS1 suppress innate responses in DF-1 immortalised chicken fibroblast cells
Cited by: 28
Author(s): Efstathios S. Giotis, CS Ross, RC Robey, Axel Nohturfft, Stephen Goodbourn, Michael A. Skinner
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-018-25085-5

RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells
Cited by: 67
Author(s): Anda R. Gliga, Sebastiano Di Bucchianico, Jessica M. Lindvall, Bengt Fadeel, Hanna Karlsson
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0226707

High expression of olfactomedin-4 is correlated with chemoresistance and poor prognosis in pancreatic cancer
Cited by: 15
Author(s): Ryotaro Ohkuma, Erica Yada, Shumpei Ishikawa, Daisuke Komura, Hidenobu Ishizaki, Koji Tamada, Yutaro Kubota, Kazuyuki Hamada, Hiroo Ishida, Yuya Hirasawa, Hirotsugu Ariizumi, Etsuko Satoh, Midori Shida, Makoto Watanabe, Rie Onoue, Kiyohiro Ando, Junji Tsurutani, Kiyoshi Yoshimura, Takehiko Yokobori, Tetsuro Sasada, Takeshi Aoki, Masahiko Murakami, Tomoko Norose, Nobuyuki Ohike, Masafumi Takimoto, Masahiko Izumizaki, Shinichi Kobayashi, Takuya Tsunoda, Satoshi Wada
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-9-390

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays
Cited by: 100
Author(s): Alexandra B. Graf, Brigitte Gasser, Martin Dragosits, Michael Sauer, Germán Leparc, Thomas Tüchler, David P. Kreil, Diethard Mattanovich
Software Mentions: 3
Published: about 18 years ago

10.1038/s41598-017-09490-w

The epigenetic modifier Fam208a is required to maintain epiblast cell fitness
Cited by: 6
Author(s): Shohag Bhargava, Brian Cox, Christiana Polydorou, Veronika Gresakova, Vladimír Kořínek, Hynek Strnad, Radislav Sedláček, Trevor Epp, Kallayanee Chawengsaksophak
Software Mentions: 3
Published: about 9 years ago

10.1186/s12918-017-0520-3

Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology
Cited by: 13
Author(s): Joanna H. Sier, Alfred E. Thumser, Nick Plant
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0078868

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets
Cited by: 4
Author(s): Wensheng Zhang, Andrea Edwards, Erik K. Flemington, Kun Zhang
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2105-15-S1-S2

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Cited by: 11
Author(s): Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0115911

The Transcriptomic and Proteomic Landscapes of Bone Marrow and Secondary Lymphoid Tissues
Cited by: 14
Author(s): Sandra Andersson, Kenneth Nilsson, Linn Fagerberg, Björn M. Hallström, Christer Sundström, Anna Danielsson, Karolina Edlund, Mathias Uhlén, Anna Asplund
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-017-12989-x

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells
Cited by: 62
Author(s): Simone Rizzetto, Auda A. Eltahla, Peijie Lin, Rowena A. Bull, Andrew R. Lloyd, Joshua W. K. Ho, Vanessa Venturi, Fabio Luciani
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-018-26170-5

Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions
Cited by: 6
Author(s): David Talavera, Christopher J. Kershaw, Joseph L. Costello, Lydia M. Castelli, William Rowe, Paul F. G. Sims, Mark P. Ashe, Chris M. Grant, Graham D. Pavitt, Simon J. Hubbard
Software Mentions: 3
Published: over 8 years ago

10.1038/s41597-019-0046-1

Navigating in vitro bioactivity data by investigating available resources using model compounds
Cited by: 1
Author(s): Sten Ilmjärv, Fiona Augsburger, Jerven Bolleman, Robin Liechti, Alan Bridge, Jenny Sandström, Vincent Jaquet, Ioannis Xenarios, Karl-Heinz Krause
Software Mentions: 3
Published: over 7 years ago

10.1038/sdata.2018.198

RNA-seq of macrophages of amoeboid or mesenchymal migratory phenotype due to specific structure of environment
Cited by: 13
Author(s): Vladimı́r Čermák, Aneta Gandalovičová, Ladislav Merta, Jitka Fučíková, Radek Špíšek, Daniel Rösel, Jan Brábek
Software Mentions: 3
Published: about 8 years ago

10.1038/s41597-019-0011-z

Targeted enrichment by solution-based hybrid capture to identify genetic sequence variants in barley
Cited by: 21
Author(s): Camilla Beate Hill, Debbie Wong, Josquin Tibbits, Kerrie Forrest, Matthew Hayden, Xiaoqi Zhang, Sharon Westcott, Tefera Tolera Angessa, Chengdao Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-015-1785-9

MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data
Cited by: 11
Author(s): Khadija El Amrani, Harald Stachelscheid, Fritz Lekschas, Armin Kurtz, Miguel A. Andrade‐Navarro
Software Mentions: 3
Published: about 11 years ago

10.1186/s12870-015-0643-x

Changes in Lolium perenne transcriptome during cold acclimation in two genotypes adapted to different climatic conditions
Cited by: 29
Author(s): Shamila Abeynayake, Stephen Byrne, Istvàn Nagy, Kristina Jonavičienė, Thomas Etzerodt, Birte Boelt, Torben Asp
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0234299

Yellow sea mediated segregation between North East Asian Dryophytes species
Cited by: 18
Author(s): Amaël Borzée, Kevin R. Messenger, Shinhyeok Chae, Desiree Andersen, Jordy Groffen, Ye Inn Kim, Junghwa An, Siti N. Othman, Kyongsin Ri, Tu Yong Nam, Yoonhyuk Bae, Jin Ren, Jia Tang Li, Ming‐Feng Chuang, Yoonjung Yi, Yucheol Shin, Taejoon Kwon, Yikweon Jang, Mi Sook Min
Software Mentions: 3
Published: over 6 years ago

10.7150/jca.38741

Construction and validation of an eight-gene signature with great prognostic value in bladder cancer
Cited by: 13
Author(s): Xin Yan, Xun Fu, Zixin Guo, Xiaoping Li, Tong-Zu Liu, Sheng Li
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2229-13-14

Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem
Cited by: 34
Author(s): Hardy Hall, Brian E. Ellis
Software Mentions: 3
Published: almost 14 years ago

10.1186/s12859-019-2705-9

Network meta-analysis correlates with analysis of merged independent transcriptome expression data
Cited by: 11
Author(s): Christine Winter, Robin Kosch, Martin Ludlow, Albert D. M. E. Osterhaus, Klaus Jung
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-10-133

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes
Cited by: 4
Author(s): Hideya Kawaji, Yoshihide Hayashizaki, Carsten O. Daub
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2229-9-67

Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set
Cited by: 39
Author(s): Laura Pascual, José Blanca, Joaquı́n Cañizares, Fernado Nuez
Software Mentions: 3
Published: over 17 years ago

10.7150/jca.60647

FOXD3-induced miR-133a blocks progression and metastasis of colorectal cancer through regulating UBA2
Cited by: 4
Author(s): Yuanfang Cheng, Yajuan Wang, Yuanzun Cheng, Qingmei Yang, Lejing Zhang, Zhaoxi Li, Jiancheng Cheng
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12870-020-2305-x

Linking crop traits to transcriptome differences in a progeny population of tetraploid potato
Cited by: 7
Author(s): Erik Alexandersson, Sandeep Kushwaha, Aastha Subedi, Deborah Weighill, Sharlee Climer, Daniel Jacobson, Erik Andréasson
Software Mentions: 3
Published: over 6 years ago

10.1534/g3.119.401031

Loss of N-Glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines
Cited by: 13
Author(s): William F. Mueller, Petra Jakob, Han Sun, Sandra Clauder‐Münster, Sonja Ghidelli-Disse, Diana Paola Serralde Ordóñez, Markus Böesche, Marcus Bantscheff, Paul Collier, Bettina Haase, Vladimı́r Beneš, Malte Paulsen, Peter Sehr, Joe Lewis, Gerard Drewes, Lars M. Steinmetz
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-595

Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors
Cited by: 34
Author(s): Mark Kidd, Irvin M. Modlin, Ignat Drozdov
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pntd.0005559

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni
Cited by: 32
Author(s): Anna V. Protasio, Stijn van Dongen, Julie Collins, Leonor Quintais, Diogo M Ribeiro, Florian Sessler, Martin Hunt, Gabriel Rinaldi, James J. Collins, Anton J. Enright, Matthew Berriman
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2105-14-153

Iterative rank-order normalization of gene expression microarray data
Cited by: 106
Author(s): Eric A. Welsh, Steven Eschrich, Anders Berglund, David Fenstermacher
Software Mentions: 3
Published: over 13 years ago

10.3389/fphar.2019.00198

A Meta-Analysis of the Performance of a Blood-Based Exposure Response Gene Signature Across Clinical Studies on the Tobacco Heating System 2.2 (THS 2.2)
Cited by: 2
Author(s): Florian Martin, Marja Talikka, Nikolai V. Ivanov, Christelle Haziza, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: over 7 years ago

10.3389/fphys.2019.00433

Increasing Upstream Chromatin Long–Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells
Cited by: 16
Author(s): Angus Li, Yu Sun, Charles Drummer, Yifan Lu, Daohai Yu, Yan Zhou, Xinyuan Li, Simone J. Pearson, Candice Johnson, Catherine C. Yu, William Y. Yang, Kevin Mastascusa, Xiaohua Jiang, Jianxin Sun, Thomas J. Rogers, Wenhui Hu, Hong Wang, Xiaofeng Yang
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-12-218

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript
Cited by: 36
Author(s): Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson, Morris A. Swertz
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pntd.0008059

Exposure of Anopheles mosquitoes to trypanosomes reduces reproductive fitness and enhances susceptibility to Plasmodium
Cited by: 10
Author(s): Constentin Dieme, Natalia Marta Zmarlak, Emma Brito-Fravallo, Christelle Travaillé, Adrien Pain, Floriane Cherrier, Corinne Genève, Estefanía Calvo-Álvarez, Michelle M. Riehle, Kenneth D. Vernick, Brice Rotureau, Christian Mitri
Software Mentions: 3
Published: over 6 years ago

10.3389/fphys.2018.00618

Coactivation of TLR2 and TLR8 in Primary Human Monocytes Triggers a Distinct Inflammatory Signaling Response
Cited by: 14
Author(s): Korbinian Bösl, Miriam S. Giambelluca, Markus Haug, Marit Bugge, Terje Espevik, Richard K. Kandasamy, Bjarte Bergstrøm
Software Mentions: 3
Published: over 8 years ago

10.3389/fonc.2020.570281

A Three-Metabolic-Genes Risk Score Model Predicts Overall Survival in Clear Cell Renal Cell Carcinoma Patients
Cited by: 8
Author(s): Yiqiao Zhao, Zijia Tao, Xiaonan Chen
Software Mentions: 3
Published: almost 6 years ago

10.3389/fonc.2019.00190

OSlms: A Web Server to Evaluate the Prognostic Value of Genes in Leiomyosarcoma
Cited by: 24
Author(s): Qiang Wang, Longxiang Xie, Yifang Dang, Xiaoxiao Sun, Tiantian Xie, JJ Guo, Yali Han, Zhongyi Yan, Wan Zhu, Yunlong Wang, Wei Li, Xiangqian Guo
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-10-472

Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes
Cited by: 132
Author(s): Sylvain Forêt, Robert Kucharski, Yvonne Pittelkow, Gabrielle A. Lockett, Ryszard Maleszka
Software Mentions: 3
Published: about 17 years ago

10.1371/journal.pone.0240178

Occurrence of Brucella ceti in striped dolphins from Italian Seas
Cited by: 14
Author(s): Giuliano Garofolo, A. Petrella, Giuseppe Lucifora, Gabriella Di Francesco, Giovanni Di Guardo, Alessandra Pautasso, Barbara Iulini, Katia Varello, Federica Giorda, Maria Goria, Alessandro Dondo, Simona Zoppi, Cristina Esmeralda Di Francesco, Stefania Giglio, Furio Ferringo, Luigina Serrecchia, Mattia Anna Rita Ferrantino, Katiuscia Zilli, Anna Janowicz, Manuela Tittarelli, Walter Mignone, Cristina Casalone, Carla Grattarola
Software Mentions: 3
Published: about 6 years ago

10.1136/annrheumdis-2020-217204

Investigation of genetically regulated gene expression and response to treatment in rheumatoid arthritis highlights an association between <i>IL18RAP</i> expression and treatment response
Cited by: 10
Author(s): Svetlana Cherlin, Myles Lewis, Darren Plant, Nisha Nair, Katriona Goldmann, Evan Tzanis, Michael R. Barnes, Paul McKeigue, Jennifer H. Barrett, Costantino Pitzalis, Anne Barton, Heather J. Cordell
Software Mentions: 3
Published: about 6 years ago

10.1186/2043-9113-2-22

mCOPA: analysis of heterogeneous features in cancer expression data
Cited by: 18
Author(s): Chenwei Wang, Alperen Taciroglu, Stefan Maetschke, Colleen C. Nelson, Mark A. Ragan, Melissa J. Davis
Software Mentions: 3
Published: almost 15 years ago

10.1038/s41598-018-23514-z

Comparative transcriptomics gives insights into the evolution of parasitism in Strongyloides nematodes at the genus, subclade and species level
Cited by: 22
Author(s): Vicky L. Hunt, Akinori Hino, Akemi Yoshida, Taisei Kikuchi
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2180-8-109

Dictyostelium transcriptional responses to Pseudomonas aeruginosa: common and specific effects from PAO1 and PA14 strains
Cited by: 40
Author(s): Sergio Carilla-Latorre, Javier Calvo‐Garrido, Gareth Bloomfield, Jason Skelton, Robert R. Kay, Alasdair Ivens, José Luis Martínez, Ricardo Escalante
Software Mentions: 3
Published: over 18 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962