bioconductor: ArrayExpress | Projects

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: almost 16 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: over 15 years ago

10.1371/journal.pone.0008939

The Transcriptional Programme of Human Heart Valves Reveals the Natural History of Infective Endocarditis
Cited by: 29
Author(s): Marie Benoit, Franck Thuny, Yannick Le Priol, Hubert Lépidi, Sonia Bastonero, Jean‐Paul Casalta, Frédéric Collart, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0020063

Molecular Strategy for Survival at a Critical High Temperature in Eschierichia coli
Cited by: 72
Author(s): Masayuki Murata, Hiroko Fujimoto, Kaori Nishimura, Kannikar Charoensuk, Hiroshi Nagamitsu, Satish Raina, Tomoyuki Kosaka, Taku Oshima, Nagahisa Ogasawara, Mamoru Yamada
Software Mentions: 1
Published: over 14 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: almost 13 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

10.1186/2040-2392-5-21

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: almost 12 years ago

10.1371/journal.pone.0109978

Life without Oxygen: Gene Regulatory Responses of the Crucian Carp (Carassius carassius) Heart Subjected to Chronic Anoxia
Cited by: 11
Author(s): Kåre‐Olav Stensløkken, Stian Ellefsen, Olga Vasieva, Yongxiang Fang, Anthony P. Farrell, Lisa Olohan, Jarle Vaage, Göran Nilsson, Andrew R. Cossins
Software Mentions: 1
Published: over 11 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: over 9 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: about 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: almost 9 years ago

10.1186/1471-2164-11-93

Comparative transcriptome analysis coupled to X-ray CT reveals sucrose supply and growth velocity as major determinants of potato tuber starch biosynthesis
Cited by: 65
Author(s): Stephanus J. Ferreira, Melanie Senning, Sophia Sonnewald, Petra-Maria Keßling, Ralf Goldstein, Uwe Sonnewald
Software Mentions: 1
Published: about 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: about 19 years ago

10.1186/1471-2164-8-377

Optimization of cDNA microarrays procedures using criteria that do not rely on external standards
Cited by: 4
Author(s): Torunn Bruland, Endre Anderssen, Berit Doseth, Hallgeir Bergum, Vidar Beisvåg, Astrid Lægreid
Software Mentions: 1
Published: about 19 years ago

10.1371/journal.pone.0053478

Genome-Wide Alteration of Histone H3K9 Acetylation Pattern in Mouse Offspring Prenatally Exposed to Arsenic
Cited by: 83
Author(s): Andrea A. Cronican, Nicholas F. Fitz, Alexis B. Carter, Muzamil Saleem, Sruti Shiva, Aaron Barchowsky, Radosveta Koldamova, Jonathan Schug, Iliya Lefterov
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0109745

Mg2+ Effect on Argonaute and RNA Duplex by Molecular Dynamics and Bioinformatics Implications
Cited by: 9
Author(s): Seungyoon Nam, Hyojung Ryu, Won Son, Yon Hui Kim, Young Ho Kim, Curt Balch, Kenneth P. Nephew, Jinhyuk Lee
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-11-389

Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile
Cited by: 24
Author(s): Gemma Marsden, Ian J. Davis, Victoria Wright, Mohammed Sebaihia, Ed J. Kuijper, Nigel P. Minton
Software Mentions: 1
Published: over 15 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: over 10 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: over 8 years ago

10.1186/1471-2164-7-224

Development and validation of a bovine macrophage specific cDNA microarray
Cited by: 38
Author(s): Kirsty Jensen, Richard Talbot, Edith Paxton, David Waddington, Elizabeth J. Glass
Software Mentions: 1
Published: over 19 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: about 11 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: about 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: almost 12 years ago

10.1007/s10495-019-01542-y

17-Aminogeldanamycin selectively diminishes IRE1α-XBP1s pathway activity and cooperatively induces apoptosis with MEK1/2 and BRAFV600E inhibitors in melanoma cells of different genetic subtypes
Cited by: 12
Author(s): Aleksandra Mielczarek-Lewandowska, Małgorzata Sztiller-Sikorska, Marta Osrodek, Małgorzata Czyż, Mariusz L. Hartman
Software Mentions: 1
Published: almost 7 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: over 13 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: about 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: over 12 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: about 16 years ago

10.3390/ijms19071967

miR-196a Is Able to Restore the Aggressive Phenotype of Annexin A1 Knock-Out in Pancreatic Cancer Cells by CRISPR/Cas9 Genome Editing
Cited by: 26
Author(s): Raffaella Belvedere, Pasquale Saggese, Emanuela Pessolano, Domenico Memoli, Valentina Bizzarro, Francesca Rizzo, Luca Parente, Alessandro Weisz, Antonello Petrella
Software Mentions: 1
Published: over 7 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: over 16 years ago

10.1038/s41598-018-21915-8

Morphine induces changes in the gut microbiome and metabolome in a morphine dependence model
Cited by: 144
Author(s): Fuyuan Wang, Jingjing Meng, Li Zhang, Timothy J. Johnson, Chi Chen, Sabita Roy
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2148-9-59

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation
Cited by: 53
Author(s): Arne W. Nolte, Sébastien Renaut, Louis Bernatchez
Software Mentions: 1
Published: about 17 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: almost 12 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: over 8 years ago

10.1186/1479-5876-8-6

Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity
Cited by: 4
Author(s): Kelly L. Brown, Reza Falsafi, Winnie W. S. Kum, Pamela Hamill, Jennifer L. Gardy, Donald J. Davidson, Stuart E. Turvey, B. Brett Finlay, David P. Speert, Robert E. W. Hancock
Software Mentions: 1
Published: about 16 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: about 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: over 12 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: over 12 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

10.1038/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: about 7 years ago

10.1038/s42003-019-0281-1

SnRK2 protein kinases represent an ancient system in plants for adaptation to a terrestrial environment
Cited by: 69
Author(s): Akihisa Shinozawa, Ryoko Otake, Daisuke Takezawa, Taishi Umezawa, Kenji Kono, Keisuke Tanaka, Anna Amagai, Shin-nosuke Ishikawa, Yusuke Hara, Yasuko Kamisugi, Andrew C. Cuming, Koichi Hori, Hiroyuki Ohta, Fumiyuki Takahashi, Kazuo Shinozaki, Takahisa Hayashi, Teruaki Taji, Yoichi Sakata
Software Mentions: 1
Published: about 7 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: almost 7 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: over 7 years ago

10.1186/2001-1326-3-7

Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development
Cited by: 108
Author(s): Maria Frantzi, Akshay Bhat, Agnieszka Latosinska
Software Mentions: 1
Published: almost 12 years ago

10.3389/fbioe.2015.00058

SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human
Cited by: 13
Author(s): Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Software Mentions: 1
Published: almost 11 years ago

10.3389/fnbeh.2019.00103

Autonomic and Redox Imbalance Correlates With T-Lymphocyte Inflammation in a Model of Chronic Social Defeat Stress
Cited by: 23
Author(s): Cassandra Moshfegh, Safwan Elkhatib, Christopher W. Collins, Allison J. Kohl, Adam J. Case
Software Mentions: 1
Published: over 6 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: over 9 years ago

10.1111/1574-6968.12230

An attenuated mutant of the Rv1747 ATP-binding cassette transporter ofMycobacterium tuberculosisand a mutant of its cognate kinase, PknF, show increased expression of the efflux pump-relatediniBACoperon
Cited by: 6
Author(s): Vicky L. Spivey, Rachael H. Whalan, Elizabeth Hirst, Stephen J. Smerdon, Roger S. Buxton
Software Mentions: 1
Published: over 12 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

10.1038/cti.2015.17

Expression profiling pre‐diabetic mice to uncover drugs with clinical application to type 1 diabetes
Cited by: 2
Author(s): Dimeng Pang, Katharine M. Irvine, Ahmed M. Mehdi, Helen E. Thomas, Mark Harris, Emma E. Hamilton‐Williams, Ranjeny Thomas
Software Mentions: 1
Published: over 10 years ago

10.3390/cells9010142

Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity
Cited by: 41
Author(s): Mariusz L. Hartman, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Małgorzata Czyż
Software Mentions: 1
Published: about 6 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: about 22 years ago

10.1093/cid/ciaa503

The Current Status of Enteric Fever Diagnostics and Implications for Disease Control
Cited by: 2
Author(s): Stephen Baker, Christoph J. Blohmke, Mailis Maes, Peter I Johnston, Thomas C. Darton
Software Mentions: 1
Published: over 5 years ago

10.1002/2211-5463.12082

Cryptochrome 2 extensively regulates transcription of the chloroplast genome in tomato
Cited by: 14
Author(s): Paolo Facella, Fabrizio Carbone, Antonio Placido, Gaetano Perrotta
Software Mentions: 1
Published: almost 9 years ago

10.12688/f1000research.7911.1

Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources
Cited by: 14
Author(s): David Bousfield, Johanna McEntyre, Sameer Velankar, George Papadatos, Alex Bateman, Guy Cochrane, Jee-Hyub Kim, Florian Graef, Vid Vartak, Blaise T. F. Alako, Niklas Blomberg
Software Mentions: 1
Published: almost 10 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: over 7 years ago

10.1038/s12276-018-0162-6

The E3 ubiquitin ligase TRIM25 regulates adipocyte differentiation via proteasome-mediated degradation of PPARγ
Cited by: 17
Author(s): Jae Min Lee, Sun Sil Choi, Yo Han Lee, Keon Woo Khim, Susan A. Yoon, Byung-gyu Kim, Dougu Nam, Pann‐Ghill Suh, Kyungjae Myung, Jang Hyun Choi
Software Mentions: 1
Published: over 7 years ago

10.1016/j.exer.2021.108553

ON-bipolar cell gene expression during retinal degeneration: Implications for optogenetic visual restoration
Cited by: 13
Author(s): Michael James Gilhooley, Doron Hickey, Moritz Lindner, Teele Palumaa, Steven Hughes, Stuart N. Peirson, Robert E. MacLaren, Mark W. Hankins
Software Mentions: 1
Published: over 4 years ago

10.1186/1756-8935-3-6

A paucity of heterochromatin at functional human neocentromeres
Cited by: 86
Author(s): Alicia Alonso, Dan Hasson, Fanny Cheung, Peter E. Warburton
Software Mentions: 1
Published: almost 16 years ago

10.1186/s13072-016-0078-0

Chromatin variation associated with liver metabolism is mediated by transposable elements
Cited by: 30
Author(s): Juan Du, Amy Leung, Candi Trac, Michael Lee, Brian W. Parks, Aldons J. Lusis, Rama Natarajan, Dustin E. Schones
Software Mentions: 1
Published: over 9 years ago

10.1186/s13072-015-0018-4

Role of Ccr4-Not complex in heterochromatin formation at meiotic genes and subtelomeres in fission yeast
Cited by: 40
Author(s): Cristina Cotobal, María Rodríguez-López, Caia D. S. Duncan, Ayesha Hasan, Akira Yamashita, Masayuki Yamamoto, Jürg Bähler, Juan Mata
Software Mentions: 1
Published: over 10 years ago

10.1111/j.1462-2920.2011.02461.x

Genomic variations define divergence of water/wildlife‐associated Campylobacter jejuni niche specialists from common clonal complexes
Cited by: 54
Author(s): Philip J. Hepworth, Kevin E. Ashelford, Jason Hinds, Katherine A. Gould, Adam A. Witney, Nicola Williams, Howard Leatherbarrow, Nigel P. French, Richard J. Birtles, Chriselle Mendonca, Nick Dorrell, Brendan W. Wren, Paul Wigley, Neil Hall, Craig Winstanley
Software Mentions: 1
Published: almost 15 years ago

10.1007/s10585-016-9810-1

Prognostic value of 5-microRNA based signature in T2-T3N0 colon cancer
Cited by: 49
Author(s): Maciej Bobowicz, Marcin Skrzypski, Piotr Czapiewski, Michał Marczyk, Agnieszka Maciejewska, Michał Jankowski, Anna Szulgo-Paczkowska, Wojciech Zegarski, Ryszard Pawłowski, Joanna Polańska, Wojciech Biernat, Janusz Jaśkiewicz, Jacek Jassem
Software Mentions: 1
Published: over 9 years ago

10.1111/1462-2920.12726

Adaptation of anaerobic cultures ofEscherichia coli K-12 in response to environmental trimethylamine-N-oxide
Cited by: 9
Author(s): Katie J. Denby, Matthew D. Rolfe, Ellen Crick, Guido Sanguinetti, Robert K. Poole, Jeffrey Green
Software Mentions: 1
Published: about 11 years ago

10.1530/ERC-17-0399

GnRH antagonist treatment of malignant adrenocortical tumors
Cited by: 14
Author(s): Milena Doroszko, Marcin Chruściel, Joanna Stelmaszewska, T. Ślęzak, Sławomir Anisimowicz, Ursula Plöckinger, Marcus Quinkler, Marco Bonomi, Sławomir Wołczyński, Ilpo Huhtaniemi, Jorma Toppari, Nafis Rahman
Software Mentions: 1
Published: about 7 years ago

10.1530/ERC-13-0098

Clinical and functional impact of TARBP2 over-expression in adrenocortical carcinoma
Cited by: 51
Author(s): Stefano Caramuta, Linkiat Lee, Deniz M. Özata, Pınar Akçakaya, Hong Xie, Anders Höög, Jan Zedenius, Martin Bäckdahl, Catharina Larsson, Weng‐Onn Lui
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.24644

MiR-21 over-expression and Programmed Cell Death 4 down-regulation features malignant pleural mesothelioma
Cited by: 12
Author(s): Lorenzo Nicolè, Rocco Cappellesso, Tiziana Sanavia, Vincenza Guzzardo, Ambrogio Fassina
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: over 9 years ago

10.1080/22221751.2019.1645572

Inter- and intra-lineage genetic diversity of wild-type Zika viruses reveals both common and distinctive nucleotide variants and clusters of genomic diversity
Cited by: 19
Author(s): Natalie D. Collins, Steven G. Widen, Li Li, Daniele M. Swetnam, Pei–Yong Shi, Robert B. Tesh, Vanessa V. Sarathy
Software Mentions: 1
Published: about 7 years ago

10.15252/emmm.201708163

An <scp>FGFR</scp> 3/ <scp>MYC</scp> positive feedback loop provides new opportunities for targeted therapies in bladder cancers
Cited by: 40
Author(s): Mélanie Mahé, Florent Dufour, Hélène Neyret–Kahn, Aura Ileana Moreno-Vega, C Béraud, Ming Shi, Iméne Hamaidi, Virginia Sánchez-Quiles, Clémentine Krucker, Marion Dorland‐Galliot, Élodie Chapeaublanc, Rémy Nicolle, Hervé Lang, Célio Pouponnot, Thierry Massfelder, François Radvanyi, Isabelle Bernard‐Pierrot
Software Mentions: 1
Published: almost 8 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: about 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: almost 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

10.1016/j.drudis.2012.07.014

Transcriptional data: a new gateway to drug repositioning?
Cited by: 193
Author(s): Francesco Iorio, Timothy Rittman, Hong Ge, Michael P. Menden, Julio Sáez-Rodríguez
Software Mentions: 1
Published: almost 13 years ago

10.1242/dmm.021626

Pulmonary transcriptome analysis in the rabbit model of surgically-induced diaphragmatic hernia treated with fetal tracheal occlusion
Cited by: 17
Author(s): Alexander C. Engels, Paul Brady, Molka Kammoun, Julio Finalet Ferreiro, Philip DeKoninck, Masayuki Endo, Jaan Toelen, Joris Robert Vermeesch, Jan Deprest
Software Mentions: 1
Published: about 10 years ago

10.1242/dev.112623

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo
Cited by: 53
Author(s): Isabel Olivera-Martínez, Nicholas J. Schurch, Roman A. Li, Junfang Song, Pamela A. Halley, Raman M Das, David W. Burt, Geoffrey J. Barton, Kate G. Storey
Software Mentions: 1
Published: over 11 years ago

10.1242/dev.168146

Postnatal liver functional maturation requires Cnot complex-mediated decay of mRNAs encoding cell cycle and immature liver genes
Cited by: 17
Author(s): Toru Suzuki, Chisato Kikuguchi, Saori Nishijima, Takeshi Nagashima, Akinori Takahashi, Mariko Okada, Tadashi Yamamoto
Software Mentions: 1
Published: about 7 years ago

10.1016/j.devcel.2014.12.024

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State
Cited by: 70
Author(s): Shilu Amin, Ian J. Donaldson, Denise A. Zannino, James Hensman, Magnus Rattray, Marta Losa, François Spitz, Franck Ladam, Charles G. Sagerström, Nicoletta Bobola
Software Mentions: 1
Published: about 11 years ago

10.1016/j.devcel.2016.10.015

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances
Cited by: 188
Author(s): Orsolya Symmons, Leslie Pan, Silvia Remeseiro, Tuğçe Aktaş, Felix A. Klein, Wolfgang Huber, François Spitz
Software Mentions: 1
Published: about 9 years ago

10.18632/oncotarget.25736

A k-mer based transcriptomics approach for antisense drug discovery targeting the Ewing’s family of tumors
Cited by: 3
Author(s): Andrew J. Annalora, Shawn T. O’Neil, Jeremy D Bushman, James Summerton, Carol S. Marcus, Patrick L. Iversen
Software Mentions: 1
Published: over 7 years ago

10.1093/database/baaa073

A curated database reveals trends in single-cell transcriptomics
Cited by: 130
Author(s): Valentine Svensson, Eduardo da Veiga Beltrame, Lior Pachter
Software Mentions: 1
Published: about 6 years ago

10.1093/database/bat074

HypoxiaDB: a database of hypoxia-regulated proteins
Cited by: 29
Author(s): Pankaj Khurana, R. Sugadev, Jaspreet Jain, Shashi Bala Singh
Software Mentions: 1
Published: about 13 years ago

10.18632/oncotarget.26330

Whole genome duplication is an early event leading to aneuploidy in IDH-wild type glioblastoma
Cited by: 15
Author(s): Blandine Boisselier, Frédéric Dugay, Marc‐Antoine Belaud‐Rotureau, Anne Coutolleau, Emmanuel Garcion, Philippe Meneï, Philippe Guardiola, Audrey Rousseau
Software Mentions: 1
Published: about 7 years ago

10.1093/database/bav022

Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer
Cited by: 4
Author(s): Ji Hyun Lee, Sungyong You, Do Young Hyeon, Byeongsoo Kang, Hyerim Kim, Kyoung Mii Park, Byung-Woo Han, Daehee Hwang, Sung Hoon Kim
Software Mentions: 1
Published: almost 11 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: about 5 years ago

10.1002/path.5335

Overactivity or blockade of transforming growth factor‐β each generate a specific ureter malformation
Cited by: 11
Author(s): Filipa Lopes, Neil Roberts, Leo Zeef, Natalie J. Gardiner, Adrian S. Woolf
Software Mentions: 1
Published: over 6 years ago

10.1093/database/bay059

IsopiRBank: a research resource for tracking piRNA isoforms
Cited by: 14
Author(s): Huan Zhang, Asim Ali, Jianing Gao, Rongjun Ban, Xiaohua Jiang, Yuanwei Zhang, Qinghua Shi
Software Mentions: 1
Published: about 8 years ago

10.1093/database/baz023

YESdb: integrative analysis of environmental stress in yeast
Cited by: 1
Author(s): Evi Berchtold, Gergely Csaba, Ralf Zimmer
Software Mentions: 1
Published: about 7 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: over 12 years ago

10.1093/database/bay054

RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins
Cited by: 4
Author(s): Jin Li, Su-Ping Deng, Jacob Vieira, James Thomas, Valerio Costa, Ching-San Tseng, Franjo Ivankovic, Alfredo Ciccodicola, Peng Yu
Software Mentions: 1
Published: about 8 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: about 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: about 11 years ago

10.1093/database/bax098

PCOSBase: a manually curated database of polycystic ovarian syndrome
Cited by: 9
Author(s): Nor Afiqah‐Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti‐Azura Mohamed‐Hussein
Software Mentions: 1
Published: about 9 years ago

10.1093/database/bay116

YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast
Cited by: 1
Author(s): Wei Wu, Hao Ping Tu, Yu Chu, Torbjörn E. M. Nordling, Yan Yuan Tseng, Hungjiun Liaw
Software Mentions: 1
Published: about 8 years ago

10.1002/cjp2.138

High immune cytolytic activity in tumor‐free tongue tissue confers better prognosis in patients with squamous cell carcinoma of the oral tongue
Cited by: 13
Author(s): Xiaolian Gu, Linda Boldrup, Philip J. Coates, Robin Fåhræus, Lixiao Wang, Torben Wilms, Lena Norberg‐Spaak, Nicola Sgaramella, Karin Nylander
Software Mentions: 1
Published: over 6 years ago

10.1093/database/baz058

Chickspress: a resource for chicken gene expression
Cited by: 15
Author(s): Fiona M. McCarthy, Ken Pendarvis, Amanda M. Cooksey, Cathy Gresham, Matt Bomhoff, Sean Davey, Eric Lyons, Tad S. Sonstegard, Susan M. Bridges, Shane C. Burgess
Software Mentions: 1
Published: about 7 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: about 16 years ago

10.1093/database/bax071

SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets
Cited by: 12
Author(s): Jin Li, Ching-San Tseng, Antonio Federico, Franjo Ivankovic, Yu-Shan Huang, Alfredo Ciccodicola, Maurice S. Swanson, Peng Yu
Software Mentions: 1
Published: about 9 years ago

10.1186/2041-1480-5-25

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
Cited by: 60
Author(s): James Malone, Andy Brown, Allyson L. Lister, Jon C. Ison, Duncan Hull, Helen Parkinson, Robert Stevens
Software Mentions: 1
Published: over 11 years ago

10.1186/s13148-020-00851-3

Genome-wide DNA methylation profiles of low- and high-grade adenoma reveals potential biomarkers for early detection of colorectal carcinoma
Cited by: 32
Author(s): Fan Jian, Jun Li, Shicheng Guo, Chengcheng Tao, Haikun Zhang, Wenjing Wang, Ying Zhang, Dake Zhang, Shigang Ding, Changqing Zeng
Software Mentions: 1
Published: almost 6 years ago

Projects: bioconductor: ArrayExpress

Science Score: 83/100

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Penalties:

Papers Mentioning ArrayExpress 1,962