bioconductor: ArrayExpress | Projects

10.3389/fphys.2017.00253

Identification, Classification, and Expression Analysis of GRAS Gene Family in Malus domestica
Cited by: 41
Author(s): Shiliang Fan, Dong Zhang, Giampiero Cai, Ming Zhao, Haiqin Wu, Youmei Li, Yongming Shen, Mingyu Han
Software Mentions: 2
Published: over 7 years ago

10.3389/fphys.2017.00753

Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference
Cited by: 9
Author(s): Tingting Zheng, Yueqiong Ni, Jun Li, Billy K. C. Chow, Gianni Panagiotou
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2015.01124

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress
Cited by: 16
Author(s): Anne-Antonella Serra, Ivan Couée, David Heijnen, Sophie Michon-Coudouel, Cécile Sulmon, Gwenola Gouesbet
Software Mentions: 2
Published: almost 9 years ago

10.3389/fpls.2021.604810

Toward Systematic Understanding of Flower Bud Induction in Apple: A Multi-Omics Approach
Cited by: 10
Author(s): Anton Milyaev, Julian Kofler, Iris Klaiber, Stefan Czemmel, Jens Pfannstiel, Henryk Flachowsky, D. Stefanelli, Magda‐Viola Hanke, J. Wünsche
Software Mentions: 2
Published: over 3 years ago

10.3389/fpls.2017.01640

RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response
Cited by: 23
Author(s): Arjun Krishnan, Chirag Gupta, Madana M.R. Ambavaram, Andy Pereira
Software Mentions: 2
Published: about 7 years ago

10.1534/g3.111.000836

Genome-wide Fitness Profiles Reveal a Requirement for Autophagy During Yeast Fermentation
Cited by: 24
Author(s): Nina Piggott, Michael A. Cook, Mike Tyers, Vivien Measday
Software Mentions: 2
Published: about 13 years ago

10.1534/g3.117.1133

The Effect of Common Inversion Polymorphisms In(2L)t and In(3R)Mo on Patterns of Transcriptional Variation in Drosophila melanogaster
Cited by: 35
Author(s): Erik Lavington, Andrew D. Kern
Software Mentions: 2
Published: about 7 years ago

10.1534/g3.117.1112

Genome-Wide Characterization of DNA Methylation in an Invasive Lepidopteran Pest, the Cotton Bollworm Helicoverpa armigera
Cited by: 21
Author(s): Christopher M. Jones, Koeng Su Lim, Jason W. Chapman, Chris Bass
Software Mentions: 2
Published: over 6 years ago

10.1111/jcmm.15429

Bioinformatics analysis of the biological changes involved in the osteogenic differentiation of human mesenchymal stem cells
Cited by: 16
Author(s): Tao Fan, Rongmei Qu, Qinghe Yu, Bing Sun, Xin Jiang, Yuchao Yang, Xiaolan Huang, Zhaoxi Zhou, Jun Ouyang, Shizhen Zhang, Jingxing Dai
Software Mentions: 2
Published: over 4 years ago

10.1242/jcs.226969

An essential role for dNTP homeostasis following CDK-induced replication stress
Cited by: 15
Author(s): Chen Chun Pai, Kuo–Feng Hsu, Samuel C. Durley, Andrea Keszthelyi, Stephen Kearsey, Charalampos Rallis, Lisa K. Folkes, Rachel S. Deegan, Sarah E. Wilkins, Sophia X. Pfister, Nagore de León, Christopher J. Schofield, Jürg Bähler, Antony Carr, Timothy C. Humphrey
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.0010045

Bordetella pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchiseptica
Cited by: 238
Author(s): Dimitri A. Diavatopoulos, Craig Cummings, Leo M. Schouls, Mary M. Brinig, David A. Relman, Frits R. Mooi
Software Mentions: 2
Published: almost 19 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 16 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: over 13 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: over 13 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: almost 10 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: over 5 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: about 9 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: over 4 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: about 15 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 9 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: about 5 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 12 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: over 10 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: almost 7 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 6 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: about 4 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: almost 4 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 9 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: almost 9 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: almost 9 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 8 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: almost 8 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: over 7 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: over 7 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 7 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 7 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: almost 7 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: almost 7 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: over 5 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: almost 5 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: almost 5 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: over 4 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: about 4 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: about 4 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: about 4 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: almost 4 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: about 3 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: almost 8 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: almost 8 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: about 7 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: almost 7 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: almost 5 years ago

10.1186/s12967-020-02630-3

A machine learning-based clinical tool for diagnosing myopathy using multi-cohort microarray expression profiles
Cited by: 6
Author(s): Andrew Tran, Chris J. Walsh, Jane Batt, Claudia C. dos Santos, Pingzhao Hu
Software Mentions: 2
Published: almost 4 years ago

10.1186/1479-5876-10-186

Circulating miR-200c as a diagnostic and prognostic biomarker for gastric cancer
Cited by: 137
Author(s): Manuel Valladares‐Ayerbes, Margarita Reboredo, V. Medina-Villaamil, Pilar Iglesias-Díaz, María J. Lorenzo-Patiño, Mar Haz, Isabel Santamarina, Miguel Blanco, Juan Fernández‐Tajes, María Quindós, Alberto Carral, Angélica Figueroa, Luis Antón-Aparicio, Lourdes Calvo
Software Mentions: 2
Published: about 12 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: about 3 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: over 4 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: about 10 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: over 3 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: almost 4 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: almost 6 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: almost 4 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: over 4 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: over 4 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: about 3 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: over 9 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: over 4 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 15 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 3 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: about 10 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: about 12 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 12 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: about 13 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: almost 11 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 4 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 4 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 12 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: about 4 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 15 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 15 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 3 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: over 5 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: over 4 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 3 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: over 4 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: about 4 years ago

10.3390/genes8100243

Genetic Association between Amyotrophic Lateral Sclerosis and Cancer
Cited by: 20
Author(s): Y-h. Taguchi, Hsiuying Wang
Software Mentions: 2
Published: about 7 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 5 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 5 years ago

10.3390/genes10100797

Biological Network Approaches and Applications in Rare Disease Studies
Cited by: 22
Author(s): Peng Zhang, Yuval Itan
Software Mentions: 2
Published: about 5 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: about 5 years ago

10.3390/genes11091108

Transcriptomic Analysis Revealed an Emerging Role of Alternative Splicing in Embryonal Tumor with Multilayered Rosettes
Cited by: 1
Author(s): Dina Hesham, Shahenda El‐Naggar
Software Mentions: 2
Published: about 4 years ago

10.1016/j.gdata.2014.03.001

Transcriptomic profiling of cartilage ageing
Cited by: 11
Author(s): Mandy J. Peffers, Xuan Li, Peter Clegg
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2007-8-11-r249

MADS-complexes regulate transcriptome dynamics during pollen maturation
Cited by: 87
Author(s): Wim Verelst, David Twell, Stefan de Folter, Richard G. H. Immink, Heinz Saedler, Thomas Münster
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2007-8-7-r132

Evolutionary conservation of regulated longevity assurance mechanisms
Cited by: 190
Author(s): Joshua McElwee, Eugene F. Schuster, Eric Blanc, Matthew D. W. Piper, James H. Thomas, Dhaval Patel, Colin Selman, Dominic J. Withers, Janet M. Thornton, Linda Partridge, David Gems
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2007-8-7-r150

PHIDIAS: a pathogen-host interaction data integration and analysis system
Cited by: 60
Author(s): Zuoshuang Xiang, Yuan Tian, Yongqun He
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2009-10-1-r5

Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon
Cited by: 39
Author(s): Giselda Bucca, Emma Laing, Vassilis Mersinias, Nicholas E. E. Allenby, Douglas Hurd, Jolyon Holdstock, Volker Brenner, Marcus Harrison, Colin P. Smith
Software Mentions: 2
Published: almost 16 years ago

10.1186/gb-2009-10-9-r97

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function
Cited by: 49
Author(s): James C. Costello, Mehmet Dalkılıç, Scott Beason, Jeff R. Gehlhausen, Rupali P Patwardhan, Sumit Middha, Brian D. Eads, Justen Andrews
Software Mentions: 2
Published: almost 16 years ago

10.1186/gb-2010-11-12-r124

Large scale comparison of global gene expression patterns in human and mouse
Cited by: 110
Author(s): Xiangqun Zheng-Bradley, Johan Rung, Helen Parkinson, Alvis Brāzma
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-12-r125

Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
Cited by: 83
Author(s): Peter L. Chang, Brian P. Dilkes, Michelle M. McMahon, Luca Comai, Sergey V. Nuzhdin
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2012-13-8-r67

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Cited by: 197
Author(s): Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Software Mentions: 2
Published: almost 13 years ago

Projects: bioconductor: ArrayExpress

Papers Mentioning ArrayExpress 1,962