bioconductor: ArrayExpress | Projects

10.1111/mmi.12358

Induced ectopic expression of <scp>HigB</scp> toxin in <scp>M</scp>ycobacterium tuberculosis results in growth inhibition, reduced abundance of a subset of <scp>mRNAs</scp> and cleavage of <scp>tmRNA</scp>
Cited by: 46
Author(s): Dorothée L. Schuessler, Teresa Cortes, Amanda S. Fivian‐Hughes, Kathryn Lougheed, Evelyn Harvey, Roger S. Buxton, E. A. Davis, Douglas B. Young
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0181231

CSmiRTar: Condition-Specific microRNA targets database
Cited by: 20
Author(s): Wei Wu, Bor Wen Tu, Tsung Te Chen, Shang Wei Hou, Joseph T. Tseng
Software Mentions: 1
Published: almost 9 years ago

10.3390/genes5030726

Enterococcus faecalis Infection and Reactive Oxygen Species Down-Regulates the miR-17-92 Cluster in Gastric Adenocarcinoma Cell Culture
Cited by: 22
Author(s): Jesper A.B. Strickertsson, Lene Juel Rasmussen, Lennart Friis‐Hansen
Software Mentions: 1
Published: almost 12 years ago

10.1111/mmi.12381

Genome‐wide profiling of chromosome interactions in <scp>P</scp> lasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
Cited by: 47
Author(s): Jacob E. Lemieux, Sue Kyes, Thomas D. Otto, Avi Feller, Richard T. Eastman, Robert Pinches, Matthew Berriman, Xin‐zhuan Su, Chris Newbold
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0054717

Global Transcriptional Profiling of Longitudinal Clinical Isolates of Mycobacterium tuberculosis Exhibiting Rapid Accumulation of Drug Resistance
Cited by: 43
Author(s): Anirvan Chatterjee, Dhananjaya Saranath, Purva Bhatter, Nerges Mistry
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0089318

Global Meta-Analysis of Transcriptomics Studies
Cited by: 11
Author(s): José Caldas, Susana Vinga
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2407-13-184

Expressional alterations in functional ultra-conserved non-coding rnas in response to all-transretinoic acid - induced differentiation in neuroblastoma cells
Cited by: 34
Author(s): Karen M. Watters, Kenneth Bryan, Niamh H. Foley, Maria Meehan, Raymond L. Stallings
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0037646

Stromal Genes Add Prognostic Information to Proliferation and Histoclinical Markers: A Basis for the Next Generation of Breast Cancer Gene Signatures
Cited by: 17
Author(s): Dwain Mefford, Joel Mefford
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0084428

DACH1: Its Role as a Classifier of Long Term Good Prognosis in Luminal Breast Cancer
Cited by: 24
Author(s): Desmond G. Powe, Gopal Krishna Dhondalay, Christophe Lemetre, Tony Allen, Hany Onsy Habashy, Ian O. Ellis, Robert C. Rees, Graham Ball
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0067802

Insulin Receptor-Overexpressing β-Cells Ameliorate Hyperglycemia in Diabetic Rats through Wnt Signaling Activation
Cited by: 14
Author(s): Mi‐Hyun Kim, Seung-Hyun Hong, Moon‐Kyu Lee
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0006576

Genome-Scale Identification Method Applied to Find Cryptic Aminoglycoside Resistance Genes in Pseudomonas aeruginosa
Cited by: 17
Author(s): Julie M. Struble, Ryan T. Gill
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2407-14-871

Estrogen independent gene expression defines clinically relevant subgroups of estrogen receptor positive breast cancer
Cited by: 4
Author(s): Robin Hallett, John A. Hassell
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0006554

Genome-Wide Profile of Pleural Mesothelioma versus Parietal and Visceral Pleura: The Emerging Gene Portrait of the Mesothelioma Phenotype
Cited by: 63
Author(s): Oluf Dimitri Røe, Endre Anderssen, E. Helge, Caroline Hild Pettersen, Anja Olsen, Helmut Sandeck, Rune Haaverstad, Steinar Lundgren, Erik G. Larsson
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2407-10-176

Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells
Cited by: 12
Author(s): Michael St.Pierre, Benoît DeHertogh, Anthoula Gaigneaux, Bertrand DeMeulder, Fabrice Berger, Eric Bareke, Carine Michiels, Eric Depiereux
Software Mentions: 1
Published: about 16 years ago

10.1186/1471-2407-10-482

Differential detection of alternatively spliced variants of Ciz1 in normal and cancer cells using a custom exon-junction microarray
Cited by: 22
Author(s): Faisal Rahman, Naveed Aziz, Dawn Coverley
Software Mentions: 1
Published: almost 16 years ago

10.1111/jcmm.13023

Reduced angiogenic gene expression in morbillivirus‐triggered oncolysis in a translational model for histiocytic sarcoma
Cited by: 24
Author(s): Vanessa Maria Pfankuche, Ingo Spitzbarth, Stefanie Lapp, Reiner Ulrich, Ulrich Deschl, Arno Kalkuhl, Wolfgang Baumgärtner, Christina Puff
Software Mentions: 1
Published: over 9 years ago

10.1111/jcmm.13051

Acquired TET 2 mutation in one patient with familial platelet disorder with predisposition to AML led to the development of pre‐leukaemic clone resulting in T2‐ ALL and AML ‐M0
Cited by: 10
Author(s): Vladimir T. Manchev, Hind Bouzid, Iléana Antony-Debré, Betty Leite, Guillaume Meurice, Nathalie Droin, Thomas Prébet, Régis Costello, William Vainchenker, Isabelle Plo, M’Boyba Diop, Elizabeth Macintyre, Vahid Asnafi, Rémi Favier, Véronique Baccini, Hana Raslová
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms21218069

Intra-Individual Behavioural Variability: A Trait under Genetic Control
Cited by: 12
Author(s): Rie Henriksen, Andrey Höglund, Jesper Fogelholm, Robin N. Abbey-Lee, Martin Johnsson, Niels Jeroen Dingemanse, Dominic Wright
Software Mentions: 1
Published: over 5 years ago

10.1371/annotation/121b04a1-0cbb-4e24-8a63-fc9cdd31ec76

Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 24
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0218934

Ticagrelor induces paraoxonase-1 (PON1) and better protects hypercholesterolemic mice against atherosclerosis compared to clopidogrel
Cited by: 10
Author(s): Hasseri Halim, Decha Pinkaew, Preedakorn Chunhacha, Patuma Sinthujaroen, Perumal Thiagarajan, Kenichi Fujise
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0065034

Cholecalciferol (Vitamin D3) Improves Myelination and Recovery after Nerve Injury
Cited by: 102
Author(s): Jean-François Chabas, Delphine Stephan, Tanguy Marqueste, Stéphane García, Marie‐Noëlle Lavaut, Catherine Nguyen, R. Legré, Michel Khrestchatisky, Patrick Decherchi, François Féron
Software Mentions: 1
Published: about 13 years ago

10.1016/j.mcpro.2021.100071

Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future
Cited by: 21
Author(s): Nuno Bandeira, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, Juan Antonio Vizcaíno
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2407-12-608

Molecular pathways undergoing dramatic transcriptomic changes during tumor development in the human colon
Cited by: 16
Author(s): Rosalia Maglietta, Vania C. Liuzzi, Elisa Cattaneo, Endre Laczkó, Ada Piepoli, Anna Panza, Massimo Carella, Orazio Palumbo, Teresa Staiano, Federico Buffoli, Angelo Andriulli, Giancarlo Marra, Nicola Ancona
Software Mentions: 1
Published: over 13 years ago

10.1186/s13023-014-0160-2

Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes
Cited by: 15
Author(s): Pilvi Maliniemi, Sonja Hahtola, Kristian Ovaska, Leila Jeskanen, Liisa Väkevä, Kirsi Jäntti, Rudolf Stadler, David Michonneau, Sylvie Fraïtag, Sampsa Hautaniemi, Annamari Ranki
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0030269

Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer
Cited by: 99
Author(s): Stefan Bentink, Benjamin Haibe‐Kains, Thomas S. Risch, Jian–Bing Fan, Michelle S. Hirsch, Kristina M. Holton, Renee Rubio, Craig April, Jing Chen, Eliza Wickham-Garcia, Joyce F. Liu, Aedín C. Culhane, Ronny Drapkin, John Quackenbush, Ursula A. Matulonis
Software Mentions: 1
Published: over 14 years ago

10.1016/j.molcel.2007.03.002

A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast
Cited by: 188
Author(s): Daniel H. Lackner, Traude H. Beilharz, Samuel Marguerat, Juan Mata, Stephen Watt, Falk Schubert, Thomas Preiß, Jürg Bähler
Software Mentions: 1
Published: about 19 years ago

10.1186/s12943-017-0717-5

Phospholipid Phosphatase 4 promotes proliferation and tumorigenesis, and activates Ca2+-permeable Cationic Channel in lung carcinoma cells
Cited by: 55
Author(s): Xin Zhang, Lan Zhang, Bihua Lin, Xingxing Chai, Ronggang Li, Yuehua Liao, Xing-Hui Deng, Qiongru Liu, Wenli Yang, Yubo Cai, Wei Zhou, Zhichao Lin, Wenhai Huang, Meigong Zhong, Fangyong Lei, Jiangxue Wu, Shuaishuai Yu, Xiaoping Li, Shangren Li, Yueyue Li, Jincheng Zeng, Wansheng Long, Dong Ren, Yanming Huang
Software Mentions: 1
Published: almost 9 years ago

10.1186/1471-2407-8-18

Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation
Cited by: 11
Author(s): Olivier Gevaert, Frank De Smet, Toon Van Gorp, Nathalie Pochet, Kristof Engelen, Frédéric Amant, Bart De Moor, Dirk Timmerman, Ignace Vergote
Software Mentions: 1
Published: over 18 years ago

10.1172/JCI129115

Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia
Cited by: 29
Author(s): Alhomidi Almotiri, Hamed Ahmad A. Alzahrani, Juan Bautista Menendez-Gonzalez, Ali Abdelfattah, Badi Alotaibi, Lubaid Saleh, Adelle Greene, Mia R. F. Georgiou, Alex Gibbs, Amani Salem Alsayari, Sarab Taha, Leigh-anne Thomas, Dhruv Shah, Sarah Edkins, Peter Giles, Marc P. Stemmler, Simone Brabletz, Thomas Brabletz, Ashleigh S. Boyd, Florian A. Siebzehnrübl, Neil P. Rodrigues
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2407-9-409

Impact of biospecimens handling on biomarker research in breast cancer
Cited by: 84
Author(s): Loris De Cecco, Valeria Musella, Silvia Veneroni, Vera Cappelletti, Italia Bongarzone, Maurizio Callari, Barbara Valeri, Marco A. Pierotti, Maria Grazia Daidone
Software Mentions: 1
Published: over 16 years ago

10.1093/jxb/ert337

Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
Cited by: 109
Author(s): Selahattin Danisman, Aalt D. J. van Dijk, Andrea Bimbó, Froukje van der Wal, Lars Hennig, Stefan de Folter, Gerco C. Angenent, Richard G. H. Immink
Software Mentions: 1
Published: over 12 years ago

10.1093/jxb/ert397

Overexpression ofPYL5in rice enhances drought tolerance, inhibits growth, and modulates gene expression
Cited by: 178
Author(s): Hyun-Mi Kim, Kyeyoon Lee, Hyunsik Hwang, Nikita Bhatnagar, Dool Yi Kim, In Sun Yoon, Myung-Ok Byun, Sun Tae Kim, Ki‐Hong Jung, Beom-Gi Kim
Software Mentions: 1
Published: over 12 years ago

10.1186/1476-4598-13-20

Oncogenic transformation of mesenchymal stem cells decreases Nrf2 expression favoring in vivo tumor growth and poorer survival
Cited by: 36
Author(s): Juan M. Funes, Stephen Henderson, Rachel Kaufman, James M. Flanagan, Mathew Robson, R. Barbara Pedley, Salvador Moncada, Chris Boshoff
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0134866

Transcriptomic Profiling of Virus-Host Cell Interactions following Chicken Anaemia Virus (CAV) Infection in an In Vivo Model
Cited by: 19
Author(s): Efstathios S. Giotis, Lisa Rothwell, Alistair Scott, Tuanjun Hu, Richard Talbot, D. Todd, David W. Burt, Elizabeth J. Glass, Pete Kaiser
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0053391

Characterization of the Humoral Immune Response during Staphylococcus aureus Bacteremia and Global Gene Expression by Staphylococcus aureus in Human Blood
Cited by: 69
Author(s): P. Martijn den Reijer, Nicole Lemmens-den Toom, Samantha Kant, Susan V. Snijders, Hélène Boelens, Mehri Tavakol, Nelianne J. Verkaik, Alex van Belkum, Henri A. Verbrugh, Willem J. B. van Wamel
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0093175

Renal Tissue Thawed for 30 Minutes Is Still Suitable for Gene Expression Analysis
Cited by: 5
Author(s): Yi Ma, Xiaonan Kang, Weijun Ding, Haozheng Yang, Ye Wang, Jin Zeng, Yiran Huang, Hongyue Dai
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0152997

Overexpression and Biological Function of Ubiquitin-Specific Protease 42 in Gastric Cancer
Cited by: 19
Author(s): Kezuo Hou, Zhihua Zhu, Yong Wang, Chunhui Zhang, Shanshan Yu, Qingqing Zhu, Bo Yan
Software Mentions: 1
Published: about 10 years ago

10.1186/1476-4598-9-88

Organ-, inflammation- and cancer specific transcriptional fingerprints of pancreatic and hepatic stellate cells
Cited by: 90
Author(s): Mert Erkan, Nadine Weis, Pan Zheng, Christian Schwager, Tamar Samkharadze, Xiaohua Jiang, Ute Wirkner, Nathalia A. Giese, Wilhelm Ansorge, Jürgen Debus, Peter E. Huber, Helmut Friess, Amir Abdollahi, Jörg Kleeff
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0040538

Temporal Profiling of Gene Networks Associated with the Late Phase of Long-Term Potentiation In Vivo
Cited by: 50
Author(s): Margaret M. Ryan, Brigid Ryan, Madeleine Kyrke-Smith, Barbara Logan, Warren P. Tate, Wickliffe C. Abraham, Joanna M. Williams
Software Mentions: 1
Published: almost 14 years ago

10.1186/1476-4598-9-123

MicroRNAs involvement in fludarabine refractory chronic lymphocytic leukemia
Cited by: 98
Author(s): Manuela Ferracin, Barbara Zagatti, Lara Rizzotto, Francesco Cavazzini, Angelo Veronese, Maria Ciccone, Elena Saccenti, Laura Lupini, Andrea Grilli, Cristiano De Angeli, Massimo Negrini, Antonio Cuneo
Software Mentions: 1
Published: about 16 years ago

10.1186/1756-6606-6-12

Synaptosomal-associated protein 25 mutation induces immaturity of the dentate granule cells of adult mice
Cited by: 51
Author(s): Koji Ohira, Katsunori Kobayashi, Keiko Toyama, Hironori Nakamura, Hirotaka Shoji, Keizo Takao, Rika Takeuchi, Shun Yamaguchi, Masakazu Kataoka, Shintaro Otsuka, Masami Takahashi, Tsuyoshi Miyakawa
Software Mentions: 1
Published: over 13 years ago

10.1186/1472-6750-5-5

Cited by: 5
Author(s): Valtteri Wirta, Anders Holmberg, Morten Lukacs, Peter Nilsson, Pierre Hilson, Mathias Uhlén, Rishikesh P. Bhalerao, Joakim Lundeberg
Software Mentions: 1
Published: over 21 years ago

10.1371/journal.pone.0187920

Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization
Cited by: 15
Author(s): Thiago Jonas Nakayama, Fabiana Aparecida Rodrigues, N. Neumaier, Juliana Marcolino-Gomes, Hugo Bruno Correa Molinari, Thaís Ribeiro Santiago, Eduardo Fernandes Formighieri, Marcos Fernando Basso, J. R. B. Farias, Beatriz Marti Emygdio, A. Oliveira, Ângela Diniz Campos, Aluízio Borém, Frank G. Harmon, L. M. Mertz-Henning, Alexandre Lima Nepomuceno
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0008408

Expression Profiling the Temperature-Dependent Amphibian Response to Infection by Batrachochytrium dendrobatidis
Cited by: 144
Author(s): Laia Ribas, Mingshi Li, Benjamin J. Doddington, Jacques Robert, Judith A. Seidel, J. Simon Kroll, Lyle B. Zimmerman, Nicholas C Grassly, Trenton W. J. Garner, Matthew C. Fisher
Software Mentions: 1
Published: over 16 years ago

10.1093/molbev/msu299

Expression Profile and Gene Age Jointly Shaped the Genome-Wide Distribution of Premature Termination Codons in a Drosophila melanogaster Population
Cited by: 19
Author(s): Haiwang Yang, Bin He, Huijing Ma, Shun-Chern Tsaur, Chenyu Ma, Ying Wu, Chau‐Ti Ting, Yong E. Zhang
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0026985

Transcriptomics Responses in Marine Diatom Thalassiosira pseudonana Exposed to the Polycyclic Aromatic Hydrocarbon Benzo[a]pyrene
Cited by: 51
Author(s): Ralph Carvalho, Stephanie K. Bopp, Teresa Lettieri
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0017154

Human Primary Adipocytes Exhibit Immune Cell Function: Adipocytes Prime Inflammation Independent of Macrophages
Cited by: 170
Author(s): Kees Meijer, Marcel P. de Vries, Saad Al-Lahham, Marcel Bruinenberg, Desireé Weening, Martijn Dijkstra, Niels J. Kloosterhuis, Roelof Jan van der Leij, H van der Want, Bart-Jan Kroesen, Roel J. Vonk, Farhad Rezaee
Software Mentions: 1
Published: about 15 years ago

10.1186/2040-2392-5-21

Altered brain gene expression but not steroid biochemistry in a genetic mouse model of neurodevelopmental disorder
Cited by: 20
Author(s): Simon Trent, JP Fry, Obah A. Ojarikre, William Davies
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0009748

Cardiac Deletion of Smyd2 Is Dispensable for Mouse Heart Development
Cited by: 68
Author(s): Florian Diehl, Mark A. Brown, Machteld J. van Amerongen, Tatyana Novoyatleva, Astrid Wietelmann, June V. Harriss, Fulvia Ferrazzi, Thomas Boettger, Richard P. Harvey, Philip W. Tucker, Felix B. Engel
Software Mentions: 1
Published: about 16 years ago

10.1016/j.kint.2018.11.040

Lrig2 and Hpse2, mutated in urofacial syndrome, pattern nerves in the urinary bladder
Cited by: 25
Author(s): Neil Roberts, Emma Hilton, Filipa Lopes, Subir Singh, Michael J. Randles, Natalie J. Gardiner, Karl Chopra, Riccardo Coletta, Zunera Bajwa, Robert J. Hall, Wyatt W. Yue, Franz Schaefer, Stefanie Weber, Roger Henriksson, Helen M. Stuart, Håkan Hedman, William G. Newman, Adrian S. Woolf
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0064483

Identification of Novel Tissue-Specific Genes by Analysis of Microarray Databases: A Human and Mouse Model
Cited by: 36
Author(s): Yan Song, Jinsoo Ahn, Young Ho Suh, Michael Davis, Kichoon Lee
Software Mentions: 1
Published: about 13 years ago

10.3390/ijms21061941

Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells
Cited by: 1
Author(s): Torsten Thalheim, Lydia Hopp, Maria Herberg, Susann Siebert, Christiane Kerner, Marianne Quaas, Michal R. Schweiger, Gabriela Aust, Joerg Galle
Software Mentions: 1
Published: over 6 years ago

10.3390/genes9060275

Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson’s Disease Data
Cited by: 16
Author(s): Elisa Mariani, Lorenza Lombardini, Federica Facchin, Fabrizio Pizzetti, Flavia Frabetti, Andrea Tarozzi, Raffaella Casadei
Software Mentions: 1
Published: about 8 years ago

10.3390/genes10050341

Genetical Genomics of Tonic Immobility in the Chicken
Cited by: 19
Author(s): Jesper Fogelholm, Samuel Eguasi Inkabi, Andrey Höglund, Robin N. Abbey-Lee, Martin Johnsson, Per Jensen, Rie Henriksen, I. A. Wright
Software Mentions: 1
Published: about 7 years ago

10.1038/s41436-018-0015-7

A homozygous FANCM frameshift pathogenic variant causes male infertility
Cited by: 61
Author(s): Hong Yin, Hui Ma, Sajjad Hussain, Huan Zhang, Xuefeng Xie, Long Jiang, Xiaohua Jiang, Furhan Iqbal, Ihtisham Bukhari, Hanwei Jiang, Asim Ali, Liangwen Zhong, Tao Li, Suixing Fan, Beibei Zhang, Jianing Gao, Yang Li, Nazish Jabeen, Teka Khan, Manan Khan, Muhammad Zubair, Qiaomei Hao, Hui Fang, Jun Huang, Mahmoud Huleihel, Jiahao Sha, Tej K. Pandita, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12711-020-00587-x

Genomic regions and signaling pathways associated with indicator traits for feed efficiency in juvenile Atlantic salmon (Salmo salar)
Cited by: 8
Author(s): Hanne Dvergedal, Thomas Nelson Harvey, Yang Jin, Jørgen Ødegård, Lars Grønvold, Simen Rød Sandve, Dag Inge Våge, Thomas Moen, G. Klemetsdal
Software Mentions: 1
Published: over 5 years ago

10.1534/genetics.116.197376

Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function
Cited by: 11
Author(s): Tai‐Di Chen, Maxime Rotival, Ling-Yin Chiu, Marta Bagnati, Jeong‐Hun Ko, Prashant K. Srivastava, Enrico Petretto, Charles D. Pusey, Ping-Chin Lai, Timothy J. Aitman, H. Terence Cook, Jacques Behmoaras
Software Mentions: 1
Published: about 9 years ago

10.1534/genetics.119.302493

Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue of Heliconius Butterflies
Cited by: 28
Author(s): Ana Catalán, Adriana D. Briscoe, Sebastian Höhna
Software Mentions: 1
Published: over 6 years ago

10.1016/j.gdata.2014.10.016

Transcriptional ontogeny of first trimester human fetal and placental mesenchymal stem cells: Gestational age versus niche
Cited by: 5
Author(s): Jennifer Ryan, Nicholas Matigian, Rebecca A. Pelekanos, Samuel Jesuadian, Christine A. Wells, Nicholas M. Fisk
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2005-6-11-r94

Cited by: 155
Author(s): Bregje Wertheim, Alex R. Kraaijeveld, Eugene F. Schuster, Eric Blanc, Meirion Hopkins, Scott D. Pletcher, Michael R. Strand, Linda Partridge, H. C. J. Godfray
Software Mentions: 1
Published: over 21 years ago

10.1186/gb-2005-6-7-r56

Cited by: 41
Author(s): Shiri Freilich, Tim Massingham, Sumit Bhattacharyya, Hannes Ponstingl, Paul Lyons, Tom C. Freeman, Janet M. Thornton
Software Mentions: 1
Published: over 21 years ago

10.1186/gb-2006-7-3-r26

Cited by: 40
Author(s): Colin C. Pritchard, David A. Coil, Sarah Hawley, Li Hsu, Peter S. Nelson
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-6-r46

Cited by: 39
Author(s): Emma Laing, Vassilis Mersinias, Colin P. Smith, Simon J. Hubbard
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-12-r114

Cited by: 56
Author(s): Hanni Willenbrock, Carsten Friis, Agnieszka Sierakowska Juncker, David W. Ussery
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-9-r84

Cited by: 140
Author(s): Katleen De Preter, Jo Vandesompele, Pierre Heimann, Nurten Yigit, Siv Beckman, Alexander Schramm, Angelika Eggert, Raymond L. Stallings, Yves Benoît, Marleen Renard, Anne De Paepe, Geneviève Laureys, Sven Påhlman, Franki Speleman
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-10-r99

Cited by: 78
Author(s): Anders F. Andersson, Magnus Lundgren, Stefan Eriksson, Magnus Rosenlund, Rolf Bernander, Peter Nilsson
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-10-r89

Cited by: 25
Author(s): Shiri Freilich, Tim Massingham, Eric Blanc, Leon Goldovsky, Janet M. Thornton
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2006-7-11-r107

Cited by: 211
Author(s): Birgitte Regenberg, Thomas Grotkjær, Ole Winther, Anders Fausbøll, Mats Åkesson, Christoffer Bro, Lars Kai Hansen, Søren Brunak, Jens Nielsen
Software Mentions: 1
Published: over 20 years ago

10.1186/gb-2007-8-5-r74

Threshold-free high-power methods for the ontological analysis of genome-wide gene-expression studies
Cited by: 23
Author(s): Björn Nilsson, Petra Håkansson, Mikael Johansson, Sven Nelander, Thoas Fioretos
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2007-8-10-r229

Simplified ontologies allowing comparison of developmental mammalian gene expression
Cited by: 13
Author(s): Adéle Kruger, Oliver Hofmann, Piero Carninci, Yoshihide Hayashizaki, Winston Hide
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2007-8-7-r148

Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres
Cited by: 74
Author(s): Alicia Alonso, Björn Fritz, Dan Hasson, György Abrusán, Fanny Cheung, Kinya Yoda, Bernhard Radlwimmer, Andreas G. Ladurner, Peter E. Warburton
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2008-9-2-r32

Temporal regulation of expression of immediate early and second phase transcripts by endothelin-1 in cardiomyocytes
Cited by: 47
Author(s): Timothy E. Cullingford, Thomais Markou, Stephen J. Fuller, Alejandro Giraldo, Sampsa Pikkarainen, Georgia Zoumpoulidou, Ali Alsafi, Collins Ekere, Timothy J. Kemp, Jayne L. Dennis, Laurence Gamé, Peter H. Sugden, Angela Clerk
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2007-8-9-r179

Genomic analysis reveals the major driving forces of bacterial life in the rhizosphere
Cited by: 190
Author(s): Miguel A. Matilla, Manuel Espinosa‐Urgel, José J. Rodríguez‐Herva, Juan L. Ramos, Marı́a Isabel Ramos-González
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2007-8-9-r200

Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis
Cited by: 212
Author(s): Robert Kleemann, Lars Verschuren, Marjan J. van Erk, Yuri Nikolsky, N.H.P. Cnubben, Elwin Verheij, Age K. Smilde, H. Hendriks, Susanne Zadelaar, Graham J. Smith, Valery Kaznacheev, Tatiana Nikolskaya, А. С. Мельников, Eva Hurt-Camejo, J. van der Greef, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: over 19 years ago

10.1186/gb-2008-9-1-r19

Translational control plays a prominent role in the hepatocytic differentiation of HepaRG liver progenitor cells
Cited by: 33
Author(s): Romain Parent, Laura Beretta
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2008-9-5-r82

Individual mRNA expression profiles reveal the effects of specific microRNAs
Cited by: 47
Author(s): Amit Arora, David Simpson
Software Mentions: 1
Published: over 18 years ago

10.1186/gb-2009-10-8-r87

Depletion of T-cell intracellular antigen proteins promotes cell proliferation
Cited by: 47
Author(s): Raquel Ruz Reyes, José Alcalde, José M. Izquierdo
Software Mentions: 1
Published: over 17 years ago

10.1186/gb-2009-10-12-r139

Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods
Cited by: 136
Author(s): Priit Adler, Raivo Kolde, Meelis Kull, Александр Георгиевич Ткаченко, Hedi Peterson, Jüri Reimand, Jaak Vilo
Software Mentions: 1
Published: over 17 years ago

10.1186/gb-2009-10-11-r125

High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians
Cited by: 55
Author(s): Hajime Matsuzaki, Peihua Wang, Jing Hu, Rich Rava, Glenn K. Fu
Software Mentions: 1
Published: over 17 years ago

10.1186/gb-2011-12-6-r53

Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
Cited by: 141
Author(s): Wei Li, Long Yan, Tai Wang
Software Mentions: 1
Published: about 15 years ago

10.1186/gb-2011-12-8-r82

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast
Cited by: 39
Author(s): Brian T. Wilhelm, Samuel Marguerat, Sofia Aligianni, Sandra Codlin, Stephen Watt, Jürg Bähler
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-12-r127

Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera
Cited by: 31
Author(s): Tom A. Mendum, Jane Newcombe, Ahmad A. Mannan, Andrzej M. Kierzek, Johnjoe McFadden
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2013-14-12-r132

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B
Cited by: 133
Author(s): Elinor K. Karlsson, Snaevar Sigurðsson, Emma Ivansson, Rachael Thomas, Ingegerd Elvers, Jason Wright, Cédric Howald, Noriko Tonomura, Michele Perloski, Ross Swofford, Tara Biagi, Sarah Fryc, Nathan Anderson, Céline Courtay-Cahen, Lisa Youell, Sally L. Ricketts, Sarah Mandlebaum, Patricio Rivera, Henrik von Euler, William C. Kisseberth, Cheryl A. London, Eric S. Lander, Guillermo Couto, Kenine E. Comstock, Mike Starkey, Jaime F. Modiano, Matthew Breen, Kerstin Lindblad‐Toh
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2014-15-4-r54

DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
Cited by: 314
Author(s): Kaie Lokk, Vijayachitra Modhukur, Balaji Rajashekar, Kaspar Märtens, Reedik Mägi, Raivo Kolde, Marina Koltšina, Torbjörn Nilsson, Jaak Vilo, Andres Salumets, Neeme Tõnisson
Software Mentions: 1
Published: about 12 years ago

10.1186/gb-2014-15-1-r13

Constitutive patterns of gene expression regulated by RNA-binding proteins
Cited by: 34
Author(s): Davide Cirillo, Domenica Marchese, Antonella Federico, Carmen Maria Livi, Teresa Botta-Orfila, Gian Gaetano Tartaglia
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2013-14-6-r63

Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle
Cited by: 106
Author(s): Julietta Jupe, Remco Stam, Andrew J. M. Howden, Jenny Morris, Runxuan Zhang, Pete E. Hedley, Edgar Huitema
Software Mentions: 1
Published: about 13 years ago

10.1186/gb-2013-14-6-r65

Thermal stress effects on grain yield in Brachypodium distachyon occur via H2A.Z-nucleosomes
Cited by: 71
Author(s): Scott A. Boden, Monika Kavanová, E. Jean Finnegan, Philip A. Wigge
Software Mentions: 1
Published: about 13 years ago

10.1186/s13059-016-0996-y

Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data
Cited by: 17
Author(s): Thomas Rensch, Diego Villar, Julie E. Horvath, Duncan T. Odom, Paul Flicek
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13059-016-1064-3

Correlation of an epigenetic mitotic clock with cancer risk
Cited by: 183
Author(s): Zhen Yang, Andrew Wong, Diana Kuh, Dirk S. Paul, Vardhman K. Rakyan, Richard Leslie, Shiqing Zheng, Martin Widschwendter, Stephan Beck, Andrew E. Teschendorff
Software Mentions: 1
Published: over 9 years ago

10.1186/gb-2004-6-1-r1

Cited by: 33
Author(s): Jeffrey G. Mandell, Jürg Bähler, Thomas A. Volpe, Robert A. Martienssen, Thomas R. Cech
Software Mentions: 1
Published: over 22 years ago

10.1186/s13059-018-1472-7

Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance
Cited by: 9
Author(s): Jeyaraman Rajaraman, Dimitar Douchkov, Stefanie Lück, Goetz Hensel, Daniela Nowara, Maria Pogoda, Twan Rutten, Tobias Meitzel, Jonathan Brassac, Caroline Höfle, Ralph Hückelhoven, Jörn Klinkenberg, Marco Trujillo, Eva Bauer, Thomas Schmutzer, Axel Himmelbach, Martin Mascher, Barbara Lazzari, Nils Stein, Jochen Kumlehn, Patrick Schweizer
Software Mentions: 1
Published: almost 8 years ago

10.1186/s13073-016-0329-5

Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network
Cited by: 15
Author(s): Alison F. Richard, James E. Peters, James C. Lee, Golnaz Vahedi, Alejandro A. Schäffer, Richard M. Siegel, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 1
Published: almost 10 years ago

10.1016/j.gpb.2019.10.003

Schizophrenia-associated MicroRNA–Gene Interactions in the Dorsolateral Prefrontal Cortex
Cited by: 21
Author(s): Danielle M. Santarelli, Adam P. Carroll, Heath M. Cairns, Paul A. Tooney, Murray J. Cairns
Software Mentions: 1
Published: over 6 years ago

10.1186/s13742-015-0064-7

Investigation into the annotation of protocol sequencing steps in the sequence read archive
Cited by: 20
Author(s): Jamie J. Alnasir, H. P. Shanahan
Software Mentions: 1
Published: about 11 years ago

10.1186/2047-217X-2-14

Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description
Cited by: 6
Author(s): Scott Edmunds, Chris Hunter, Vincent Smith, Pavel Stoev, Lyubomir Penev
Software Mentions: 1
Published: over 12 years ago

10.1172/jci.insight.143643

CMTM6 drives cisplatin resistance by regulating Wnt signaling through ENO-1/AKT/GSK3β axis
Cited by: 21
Author(s): Pallavi Mohapatra, Omprakash Shriwas, Sibasish Mohanty, Arup Ghosh, Shuchi Smita, Sandeep Rai Kaushik, Rakesh Arya, Rachna Rath, Saroj Kumar Das Majumdar, Dillip Kumar Muduly, Sunil K. Raghav, Ranjan Kumar Nanda, Rupesh Dash
Software Mentions: 1
Published: over 5 years ago

10.1128/JB.00473-13

The agr Locus Regulates Virulence and Colonization Genes in Clostridium difficile 027
Cited by: 95
Author(s): Melissa J. Martin, Simon Clare, David Goulding, Alexandra Faulds-Pain, Lars Barquist, Hilary P. Browne, Laura J. Pettit, Gordon Dougan, Trevor D. Lawley, Brendan W. Wren
Software Mentions: 1
Published: almost 13 years ago

10.1186/jbiol54

Growth control of the eukaryote cell: a systems biology study in yeast
Cited by: 244
Author(s): Juan I. Castrillo, Leo Zeef, David C. Hoyle, Nianshu Zhang, Andrew Hayes, David C. Gardner, Michael Cornell, June Petty, Luke Hakes, Leanne Wardleworth, Bharat Rash, Marie Brown, Warwick B. Dunn, David Broadhurst, Kerry O'Donoghue, Svenja Hester, Tom Dunkley, Sarah R. Hart, Neil Swainston, Peter Li, Simon J. Gaskell, Norman W. Paton, Kathryn S. Lilley, Douglas B. Kell, Stephen G. Oliver
Software Mentions: 1
Published: over 19 years ago

10.1074/jbc.M114.598300

Cross-talk between Two Nucleotide-signaling Pathways in Staphylococcus aureus
Cited by: 103
Author(s): Rebecca M. Corrigan, Lisa Bowman, Alexandra R. Willis, Volkhard Kaever, Angelika Gründling
Software Mentions: 1
Published: over 11 years ago

10.1186/2041-1480-1-S1-S1

Building a biomedical ontology recommender web service
Cited by: 68
Author(s): Clément Jonquet, Mark A. Musen, Nigam H. Shah
Software Mentions: 1
Published: over 16 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

Bonuses:

Penalties:

Papers Mentioning ArrayExpress 1,962