bioconductor: ArrayExpress | Projects

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: about 15 years ago

10.1371/journal.ppat.1004609

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

10.1371/journal.ppat.1007729

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

10.1098/rsos.150402

Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts
Cited by: 21
Author(s): Brett Trost, Catherine A. Moir, Zoe E. Gillespie, Anthony Kusalik, Jennifer A. Mitchell, Christopher H. Eskiw
Software Mentions: 2
Published: almost 11 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 6 years ago

10.1186/1477-7827-7-94

A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
Cited by: 20
Author(s): Hang Zhao, Qishan Wang, Chen Bai, Kan He, Yuchun Pan
Software Mentions: 2
Published: almost 17 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: about 11 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: almost 7 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: about 14 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: about 12 years ago

10.1038/sdata.2018.13

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

10.1038/sdata.2018.158

The REMBRANDT study, a large collection of genomic data from brain cancer patients
Cited by: 101
Author(s): Yuriy Gusev, Krithika Bhuvaneshwar, Lei Song, Jean-Claude Zenklusen, Howard A. Fine, Subha Madhavan
Software Mentions: 2
Published: about 8 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: almost 6 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: over 5 years ago

10.1038/srep13113

Human cell dedifferentiation in mesenchymal condensates through controlled autophagy
Cited by: 34
Author(s): Rebecca Rose Pennock, Elen Bray, Paul R. Pryor, Sally James, Paul J. McKeegan, Roger G. Sturmey, Paul G. Genever
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep17470

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

10.1038/srep19729

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

10.1038/srep31209

Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation
Cited by: 69
Author(s): Marpe Bam, Xiaoming Yang, Elizabeth E. Zumbrun, Zhimin Yin, Juhua Zhou, J. P. Ginsberg, Quinne Leyden, Jiajia Zhang, Prakash Nagarkatti, Mitzi Nagarkatti
Software Mentions: 2
Published: about 10 years ago

10.1038/srep37988

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

10.1038/s41598-017-01141-4

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

10.1038/s41598-017-03986-1

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

10.1038/s41598-017-05451-5

Loss of Usp9x disrupts cell adhesion, and components of the Wnt and Notch signaling pathways in neural progenitors
Cited by: 26
Author(s): Susitha Premarathne, Mariyam Murtaza, Nicholas Matigian, Lachlan A. Jolly, Stephen A. Wood
Software Mentions: 2
Published: about 9 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: almost 9 years ago

10.1038/s41598-017-18043-0

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

10.1038/s41598-018-19357-3

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

10.1038/s41598-019-44235-x

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

10.1038/s41598-019-57076-5

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

10.1038/s41598-020-59514-1

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

10.1038/s41598-020-60235-8

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

10.1038/s41598-020-74417-x

Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)
Cited by: 9
Author(s): Ying Li, Qilu Song, Yamin Zhang, Zheng Li, Jialin Guo, Xinhong Chen, Gaisheng Zhang
Software Mentions: 2
Published: almost 6 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: almost 6 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: almost 6 years ago

10.3390/ijms21239332

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

10.3390/ijms221910785

Integrating Statistical and Machine-Learning Approach for Meta-Analysis of Bisphenol A-Exposure Datasets Reveals Effects on Mouse Gene Expression within Pathways of Apoptosis and Cell Survival
Cited by: 3
Author(s): Nina Lukashina, Michael J. Williams, Elena Kartysheva, Elizaveta Virko, Błażej Kudłak, Robert Fredriksson, Ola Spjuth, Helgi B. Schiöth
Software Mentions: 2
Published: almost 5 years ago

10.18632/oncotarget.14253

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

10.18632/oncotarget.14784

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

10.18632/oncotarget.22131

CD24, CD27, CD36 and CD302 gene expression for outcome prediction in patients with multiple myeloma
Cited by: 20
Author(s): Elina Alaterre, Sébastien Raimbault, Hartmut Goldschmidt, Salahedine Bouhya, Guilhem Requirand, Robert Naeije, Stéphanie Boireau, Anja Seckinger, Dirk Hose, Bernard Klein, Jérôme Moreaux
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.23973

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

10.1098/rsob.190299

Molecular anatomy of the pre-primitive-streak chick embryo
Cited by: 17
Author(s): Hyung Chul Lee, Hui-Chun Lu, Mark Turmaine, Nidia M M Oliveira, Youwen Yang, Irene De Almeida, Claudio D. Stern
Software Mentions: 2
Published: over 6 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: over 5 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: almost 14 years ago

10.3390/nu11030639

Key Genes of Lipid Metabolism and WNT-Signaling Are Downregulated in Subcutaneous Adipose Tissue with Moderate Weight Loss
Cited by: 9
Author(s): Ruth Schübel, Disorn Sookthai, Judith Greimel, Theron Johnson, Mirja Grafetstätter, Romy Kirsten, Mario Kratz, Cornelia M. Ulrich, Rudolf Kaaks, Tilman Kühn
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0150982

A Human "eFP" Browser for Generating Gene Expression Anatograms
Cited by: 10
Author(s): Rohan Patel, Erin T. Hamanishi, Nicholas J. Provart
Software Mentions: 1
Published: over 10 years ago

10.1099/mic.0.000296

Developmental delay in a Streptomyces venezuelae glgE null mutant is associated with the accumulation of α-maltose 1-phosphate
Cited by: 11
Author(s): Farzana Miah, Maureen J. Bibb, J. Elaine Barclay, Kim Findlay, Stephen Bornemann
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0111168

The Porphyromonas gingivalis Ferric Uptake Regulator Orthologue Binds Hemin and Regulates Hemin-Responsive Biofilm Development
Cited by: 14
Author(s): Catherine A. Butler, Stuart G. Dashper, Lianyi Zhang, Christine A. Seers, Helen Mitchell, Deanne V. Catmull, Michelle D. Glew, Jacqueline E. Heath, Yan Tan, Hasnah Begum Said Ghulam Khan, Eric C. Reynolds
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0013069

Hfq Is a Global Regulator That Controls the Pathogenicity of Staphylococcus aureus
Cited by: 58
Author(s): Yu Liu, Na Wu, Jing Dong, Yaping Gao, Xin Zhang, Chunhua Mu, Ningsheng Shao, Guangxiao Yang
Software Mentions: 1
Published: almost 16 years ago

10.1099/mic.0.028282-0

The pneumococcal response to oxidative stress includes a role for Rgg
Cited by: 45
Author(s): Magda E. Bortoni, Vanessa S. Terra, Jason Hinds, Peter W. Andrew, Hasan Yeşilkaya
Software Mentions: 1
Published: over 16 years ago

10.1099/mic.0.000423

Identification of new members of the Escherichia coli K-12 MG1655 SlyA regulon
Cited by: 19
Author(s): Thomas D Curran, Fatima Abacha, Stephen P Hibberd, Matthew D. Rolfe, Melissa M. Lacey, Jeffrey Green
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0131335

Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage
Cited by: 64
Author(s): Lauren Endres, Ulrike Begley, Ryan R. Clark, Cheng Gu, Agnieszka Dziergowska, Andrzej Małkiewicz, J. Andrés Melendez, Peter C. Dedon, Thomas J. Begley
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0036776

MGEx-Udb: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer
Cited by: 9
Author(s): Akhilesh Kumar Bajpai, Sravanthi Davuluri, Darshan S. Chandrashekar, Ilakya Selvarajan, Mahalakshmi Dinakaran, Kshitish K. Acharya
Software Mentions: 1
Published: over 14 years ago

10.1186/ar3069

Gene expression profiling in circulating endothelial cells from systemic sclerosis patients shows an altered control of apoptosis and angiogenesis that is modified by iloprost infusion
Cited by: 19
Author(s): Elisa Tinazzi, Marzia Dolcino, Antonio Puccetti, Antonella Rigo, Ruggero Beri, Maria Teresa Valenti, Roberto Corrocher, Claudio Lunardi
Software Mentions: 1
Published: over 16 years ago

10.1186/1475-2859-6-4

A perspective on microarrays: current applications, pitfalls, and potential uses
Cited by: 90
Author(s): Pratik Jaluria, Κωνσταντίνος Κωνσταντόπουλος, Michael J. Betenbaugh, Joseph Shiloach
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0005198

Host Iron Binding Proteins Acting as Niche Indicators for Neisseria meningitidis
Cited by: 32
Author(s): Philip W. Jordan, N. Saunders
Software Mentions: 1
Published: over 17 years ago

10.3390/microarrays4040454

Genomic-Wide Analysis with Microarrays in Human Oncology
Cited by: 10
Author(s): Kenichi Inaoka, Yoshikuni Inokawa, Shuji Nomoto
Software Mentions: 1
Published: almost 11 years ago

10.3390/microarrays3040322

Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data
Cited by: 10
Author(s): Mario Fasold, Hans Binder
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0052875

Transcriptional Profiling of Human Dendritic Cell Populations and Models - Unique Profiles of In Vitro Dendritic Cells and Implications on Functionality and Applicability
Cited by: 88
Author(s): Kristina Lundberg, Ann-Sofie Albrekt, Inge Nelissen, Saskia J. Santegoets, Tanja D. de Gruijl, S. Gibbs, Malin Lindstedt
Software Mentions: 1
Published: over 13 years ago

10.3390/metabo2040983

Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore
Cited by: 3
Author(s): Andreas Hoppe, Iryna Ilkavets, Steven Dooley, Hermann−Georg Holzhütter
Software Mentions: 1
Published: over 13 years ago

10.1097/MD.0000000000004085

Expression profile of SIX family members correlates with clinic-pathological features and prognosis of breast cancer
Cited by: 32
Author(s): Xu Han, Kong Ju Wu, Yi Jun Tian, Qian Liu, Na Han, Xue Lian He, Xun Yuan, Gen Sheng Wu, Kai Wu
Software Mentions: 1
Published: about 10 years ago

10.1155/2010/784343

Leptin Administration Downregulates the Increased Expression Levels of Genes Related to Oxidative Stress and Inflammation in the Skeletal Muscle ofob/obMice
Cited by: 32
Author(s): Neira Sáinz, Amaia Rodríguez, Victoria Catalán, Sara Becerril, Beatriz Ramírez, Javier Gómez-Ambrosi, Gema Frühbeck
Software Mentions: 1
Published: over 16 years ago

10.3390/md17100576

Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
Cited by: 21
Author(s): Luca Ambrosino, Michael Tangherlini, Chiara Colantuono, Alfonso Esposito, Mara Sangiovanni, Marco Miralto, Clementina Sansone, Maria Luisa Chiusano
Software Mentions: 1
Published: almost 7 years ago

10.26508/lsa.201900371

Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS
Cited by: 9
Author(s): Shaked Afik, Gabriel Raulet, Nir Yosef
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0031577

Gis1 and Rph1 Regulate Glycerol and Acetate Metabolism in Glucose Depleted Yeast Cells
Cited by: 34
Author(s): Jakub Orzechowski Westholm, Susanna Tronnersjö, Niklas Nordberg, Ida Olsson, Jan Komorowski, Hans Ronne
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.ppat.1000066

The Uptake of Apoptotic Cells Drives Coxiella burnetii Replication and Macrophage Polarization: A Model for Q Fever Endocarditis
Cited by: 49
Author(s): Marie Benoit, Éric Ghigo, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: over 18 years ago

10.26508/lsa.201900494

The CCR4–NOT complex maintains liver homeostasis through mRNA deadenylation
Cited by: 15
Author(s): Akinori Takahashi, Toru Suzuki, Shou Soeda, Shohei Takaoka, Shungo Kobori, Tomokazu Yamaguchi, Haytham Mohamed Aly Mohamed, Akiko Yanagiya, Takaya Abe, Mayo Shigeta, Yasuhide Furuta, Keiji Kuba, Tadashi Yamamoto
Software Mentions: 1
Published: over 6 years ago

10.3390/ijms22126505

Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods
Cited by: 2
Author(s): Jishizhan Chen, Jia Hua, Wenhui Song
Software Mentions: 1
Published: about 5 years ago

10.3390/life6040042

Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects
Cited by: 60
Author(s): Lamya Al‐Haj, Yuen Tin Lui, Raeid M. M. Abed, Mohamed Gomaa, Saul Purton
Software Mentions: 1
Published: over 9 years ago

10.1016/S2213-2600(19)30282-6

Concise whole blood transcriptional signatures for incipient tuberculosis: a systematic review and patient-level pooled meta-analysis
Cited by: 112
Author(s): Gupta Rk, Chris Turner, Cristina Venturini, Hanif Esmail, Molebogeng X Rangaka, Andrew Copas, Marc Lipman, Ibrahim Abubakar, Mahdad Noursadeghi
Software Mentions: 1
Published: over 6 years ago

10.1186/s41199-020-0047-y

Transcriptomics and Epigenomics in head and neck cancer: available repositories and molecular signatures
Cited by: 21
Author(s): Mara Serena Serafini, Laura Lopez-Perez, Giuseppe Fico, Lisa Licitra, Loris De Cecco, Carlo Resteghini
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.ppat.1000529

Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Cited by: 74
Author(s): Roy R. Chaudhuri, Sarah Peters, Stephen J. Pleasance, Helen Northen, Chrissie Willers, Gavin K. Paterson, Danielle B. Cone, Andrew G. Allen, Paul Owen, Gil Shalom, Dov J. Stekel, Ian G. Charles, Duncan J. Maskell
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.ppat.1000813

Innate Killing of Leishmania donovani by Macrophages of the Splenic Marginal Zone Requires IRF-7
Cited by: 60
Author(s): Rebecca A. Phillips, Mattias Svensson, Naveed Aziz, Asher Maroof, Najmeeyah Brown, Lynette Beattie, Nathalie Signoret, Paul M. Kaye
Software Mentions: 1
Published: over 16 years ago

10.1371/journal.pone.0036301

Cystatin A, a Potential Common Link for Mutant Myocilin Causative Glaucoma
Cited by: 20
Author(s): Kit Kennedy, S. A. AnithaChristy, LaKisha K. Buie, Teresa Borrás
Software Mentions: 1
Published: over 14 years ago

10.1002/cam4.34

Identification of multiple subclones in peripheral T ‐cell lymphoma, not otherwise specified with genomic aberrations
Cited by: 11
Author(s): Noriaki Yoshida, Akira Umino, Fang Liu, Kotaro Arita, Kennosuke Karube, Shinobu Tsuzuki, Koichi Ohshima, Masao Seto
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0184087

SEXCMD: Development and validation of sex marker sequences for whole-exome/genome and RNA sequencing
Cited by: 7
Author(s): Seongmun Jeong, Ji-Woong Kim, Won Park, Hongmin Jeon, Namshin Kim
Software Mentions: 1
Published: almost 9 years ago

10.1186/2051-5960-2-23

The prognostic role of intragenic copy number breakpoints and identification of novel fusion genes in paediatric high grade glioma
Cited by: 20
Author(s): Diana Carvalho, Alan Mackay, Lynn Bjerke, Richard G. Grundy, Célia Lopes, Rui Manuel Reis, Chris Jones
Software Mentions: 1
Published: over 12 years ago

10.1186/s12935-020-01465-8

Clinical value and potential mechanisms of COL8A1 upregulation in breast cancer: a comprehensive analysis
Cited by: 16
Author(s): Peng Wei, Jian‐Di Li, Jingjing Zeng, Xiaoping Zou, Deng Tang, Wei Tang, Minhua Rong, Ying Liu, Wei Dai, Zhong-Qing Tang, Zhaoyong Feng, Gang Chen
Software Mentions: 1
Published: about 6 years ago

10.1155/2019/1697913

Plasticity of Drug-Naïve and Vemurafenib- or Trametinib-Resistant Melanoma Cells in Execution of Differentiation/Pigmentation Program
Cited by: 24
Author(s): Małgorzata Czyż, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Marta Osrodek, Mariusz L. Hartman
Software Mentions: 1
Published: about 7 years ago

10.1093/bib/bbv013

Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures
Cited by: 9
Author(s): A. Modelska, Alessandro Quattrone, Angela Re
Software Mentions: 1
Published: over 11 years ago

10.1186/1472-6750-13-2

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Cited by: 67
Author(s): Dennis Thomas, Sharon Gaheen, Stacey L. Harper, M. J. Fritts, Fred Klaessig, Elizabeth Hahn-Dantona, David S. Paik, Sue Pan, Grace A. Stafford, Elaine T. Freund, Juli Klemm, Nathan A. Baker
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0127427

MiRNA Profiles in Lymphoblastoid Cell Lines of Finnish Prostate Cancer Families
Cited by: 9
Author(s): Daniel Fischer, Tiina Wahlfors, Henna Mattila, Hannu Oja, Teuvo L.J. Tammela, Johanna Schleutker
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.ppat.1003083

A Strong Immune Response in Young Adult Honeybees Masks Their Increased Susceptibility to Infection Compared to Older Bees
Cited by: 70
Author(s): James C. Bull, Eugene V. Ryabov, Gill Prince, Andrew Mead, Cunjin Zhang, Laura Baxter, J. K. Pell, Juliet L. Osborne, Dave Chandler
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0042853

Cationic Amphiphilic Drugs Are Potent Inhibitors of Yeast Sporulation
Cited by: 8
Author(s): Ulrich Schlecht, Robert P. St.Onge, Thomas Walther, Jean François, Ronald W. Davis
Software Mentions: 1
Published: about 14 years ago

10.1186/ar2104

Cited by: 69
Author(s): Kelly S. Santangelo, Amanda L. Johnson, Amy S. Ruppert, Alicia L. Bertone
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pone.0152859

R-Spondins Are Expressed by the Intestinal Stroma and are Differentially Regulated during Citrobacter rodentium- and DSS-Induced Colitis in Mice
Cited by: 19
Author(s): Ellen S. Kang, Mitra Yousefi, Samantha Gruenheid
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.ppat.1005469

In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis
Cited by: 44
Author(s): Lucy Bell, Gabriele Pollara, Pascoe Mellissa, Gillian S. Tomlinson, Rannakoe Lehloenya, Jennifer Roe, Richard Meldau, R F Miller, Alan D. Ramsay, Benjamin M. Chain, Keertan Dheda, Mahdad Noursadeghi
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.ppat.1007315

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing
Cited by: 47
Author(s): Daniela Begolo, Isabel M. Vincent, Federica Giordani, Ina Pöhner, Michael Witty, T.G. Rowan, Zakaria Bengaly, Kirsten Gillingwater, Yvonne R. Freund, Rebecca C. Wade, Michael P. Barrett, Christine Clayton
Software Mentions: 1
Published: almost 8 years ago

10.1093/bib/bbv018

Adapting bioinformatics curricula for big data
Cited by: 38
Author(s): Anna C. Greene, Kristine A. Giffin, Casey S. Greene, Jason H. Moore
Software Mentions: 1
Published: over 11 years ago

10.1186/bcr2819

Prolactin-induced mouse mammary carcinomas model estrogen resistant luminal breast cancer
Cited by: 54
Author(s): Lisa M. Arendt, Debra E. Rugowski, Tara A Grafwallner-Huseth, Maria J. García-Barchino, Hallgeir Rui, Linda A. Schuler
Software Mentions: 1
Published: over 15 years ago

10.1186/s13058-014-0441-7

Subtype-specific overexpression of the Rac-GEF P-REX1 in breast cancer is associated with promoter hypomethylation
Cited by: 32
Author(s): Laura Barrio-Real, Lorena Benedetti, Nora Engel, Yaping Tu, Soonweng Cho, Saraswati Sukumar, Marcelo G. Kazanietz
Software Mentions: 1
Published: almost 12 years ago

10.1007/s00204-012-0967-3

Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach
Cited by: 208
Author(s): Anne Krug, Raivo Kolde, John Antonydas Gaspar, Eugen Rempel, Nina V. Balmer, Kesavan Meganathan, Kinga Vojnits, Mathurin Baquié, Tanja Waldmann, Roberto Enseñat-Waser, Smita Jagtap, Richard Evans, Stéphanie Julien, Hedi Peterson, Dimitra Zagoura, Suzanne Kadereit, Daniel Gerhard, Isaia Sotiriadou, Michael Heke, Karthick Natarajan, Margit Henry, Johannes Winkler, Rosemarie Marchan, Luc Stoppini, Sieto Bosgra, Joost Westerhout, Miriam Verwei, Jaak Vilo, Andreas Kortenkamp, Jürgen Hescheler, Ludwig A. Hothorn, Susanne Bremer, Christoph van Thriel, Karl‐Heinz Krause, Jan G. Hengstler, Jörg Rahnenführer, Marcel Leist, Agapios Sachinidis
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0218950

Screening of urine identifies PLA2G16 as a field defect methylation biomarker for prostate cancer detection
Cited by: 6
Author(s): William E. Jarrard, Adam Schultz, Tyler Etheridge, Shivashankar Damodaran, Glenn O. Allen, David F. Jarrard, Bing Yang
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0182455

Accounting for cell lineage and sex effects in the identification of cell-specific DNA methylation using a Bayesian model selection algorithm
Cited by: 6
Author(s): Nicole White, Miles C. Benton, Daniel W. Kennedy, Andrew Fox, Lyn R. Griffiths, Kerrie Mengersen
Software Mentions: 1
Published: almost 9 years ago

10.1186/1472-6750-7-24

Comparison of target labeling methods for use with Affymetrix GeneChips
Cited by: 3
Author(s): William Lonergan, Toni Whistler, Suzanne D. Vernon
Software Mentions: 1
Published: about 19 years ago

10.1073/pnas.1912109117

The circadian clock protein REVERBα inhibits pulmonary fibrosis development
Cited by: 50
Author(s): Peter Cunningham, P. J. J. De Meijer, Alicja Nazgiewicz, Simon Anderson, Lee A. Borthwick, James Bagnall, Gareth Kitchen, Monika Lodyga, Nicola Begley, Rajamiyer Venkateswaran, Rajesh Shah, Paul F. Mercer, Hannah J. Durrington, Neil C. Henderson, Karen Piper Hanley, Andrew J. Fisher, Rachel C. Chambers, David A. Bechtold, Julie Gibbs, A. S. I. Loudon, Martin K. Rutter, Boris Hinz, David Ray, John Blaikley
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0005349

The Genetic Requirements for Fast and Slow Growth in Mycobacteria
Cited by: 113
Author(s): Dany J. V. Beste, Mateu Espasa, Bhushan Bonde, Andrzej M. Kierzek, Graham R. Stewart, Johnjoe McFadden
Software Mentions: 1
Published: over 17 years ago

10.1186/s12915-019-0725-6

Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans
Cited by: 35
Author(s): Katharina Jovic, Jacopo Grilli, M.G. Sterken, L. Basten Snoek, J.A.G. Riksen, Stefano Allesina, J.E. Kammenga
Software Mentions: 1
Published: over 6 years ago

10.1186/bcr3576

A mammosphere formation RNAi screen reveals that ATG4A promotes a breast cancer stem-like phenotype
Cited by: 106
Author(s): Jonas Michel Wolf, Dyah Laksmi Dewi, Johannes Fredebohm, Karin Müller‐Decker, Christa Flechtenmacher, Jörg D. Hoheisel, Michael Boettcher
Software Mentions: 1
Published: almost 13 years ago

10.1186/bcr3048

Metastatic breast cancer cells inhibit osteoblast differentiation through the Runx2/CBFβ-dependent expression of the Wnt antagonist, sclerostin
Cited by: 89
Author(s): Daniel Mendoza-Villanueva, Leo Zeef, Paul Shore
Software Mentions: 1
Published: almost 15 years ago

10.1186/bcr3191

Preclinical and clinical studies of estrogen deprivation support the PDGF/Abl pathway as a novel therapeutic target for overcoming endocrine resistance in breast cancer
Cited by: 39
Author(s): Marion T. Weigel, Zara Ghazoui, Anita K. Dunbier, Sunil Pancholi, Mitch Dowsett, Lesley-Ann Martin
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0053545

Transcript Profile Analyses of Maize Silks Reveal Effective Activation of Genes Involved in Microtubule-Based Movement, Ubiquitin-Dependent Protein Degradation, and Transport in the Pollination Process
Cited by: 15
Author(s): Xiao Hui Xu, Fang Wang, Hao Chen, Wei Sun, Xian Sheng Zhang
Software Mentions: 1
Published: over 13 years ago

10.4161/rna.29196

Contributions of transcription and mRNA decay to gene expression dynamics of fission yeast in response to oxidative stress
Cited by: 23
Author(s): Samuel Marguerat, Katherine Lawler, Alvis Brāzma, Jürg Bähler
Software Mentions: 1
Published: about 12 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Papers Mentioning ArrayExpress 1,962