Ecosyste.ms: Papers

10.1016/j.cell.2006.12.017

Mutations in α-Tubulin Cause Abnormal Neuronal Migration in Mice and Lissencephaly in Humans
Cited by: 396
Author(s): David A. Keays, Guoling Tian, Karine Poirier, Guo-Jen Huang, Christian Siebold, James Cleak, Peter L. Oliver, Martin Fray, Robert J. Harvey, Zoltán Molnár, Maria Carmen Piñon, Neil Dear, William Valdar, Steve Brown, Kay E. Davies, J. N. P. Rawlins, Nicholas J. Cowan, Patrick M. Nolan, Jamel Chelly, Jonathan Flint
Software Mentions: 2
Published: over 17 years ago

10.1186/s13578-021-00642-0

Metabolomic and transcriptomic profiling of adult mice and larval zebrafish leptin mutants reveal a common pattern of changes in metabolites and signaling pathways
Cited by: 4
Author(s): Yi Ding, Mariëlle C. Haks, Gabriel Forn-Cuní, Jian He, Natalia Nowik, Amy C. Harms, Thomas Hankemeier, Muhamed N. H. Eeza, Jörg Matysik, A. Alia, Herman P. Spaink
Software Mentions: 2
Published: about 3 years ago

10.3389/fncel.2021.660732

RNA-Seq Dataset From Isolated Leukocytes Following Spontaneous Intracerebral Hemorrhage in Zebrafish Larvae
Cited by: 0
Author(s): Siobhan Crilly, James W. Cooper, Lauren Bradford, Ian Prise, Siddharth Krishnan, Paul R. Kasher
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-019-5518-3

Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef
Cited by: 26
Author(s): Joel D. Leal-Gutiérrez, Mauricio A. Elzo, D. D. Johnson, Heather Hamblen, Raluca G. Mateescu
Software Mentions: 2
Published: over 5 years ago

10.1016/j.cellsig.2007.01.010

Genomic tagging of endogenous Type IIβ Phosphatidylinositol 5-phosphate 4-kinase in DT40 cells reveals a nuclear localisation
Cited by: 31
Author(s): Jonathan P. Richardson, Minchuan Wang, Jonathan H. Clarke, Ketan Patel, Robin F. Irvine
Software Mentions: 2
Published: over 17 years ago

10.1038/srep46539

Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs
Cited by: 21
Author(s): María Ballester, Yuliaxis Ramayo-Caldas, Manuel Revilla, Jordi Corominas, Anna Castelló, Jordi Estellé, Ana Fernández, Josep María Folch
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-020-07202-9

Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns
Cited by: 0
Author(s): Yuan Lu, Mikki Boswell, William Boswell, Raquel Y. Salinas, Markita Savage, José Carlos Castañeda Reyes, Sean M. Walter, R. William Marks, Trevor J. Gonzalez, Geraldo Medrano, Wesley C. Warren, Manfred Schartl, Ronald B. Walter
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0128598

Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout
Cited by: 5
Author(s): Sophie Depiereux, Bertrand De Meulder, Eric Bareke, Fabrice Berger, Florence Le Gac, Eric Depiereux, Patrick Kestemont
Software Mentions: 2
Published: about 9 years ago

10.7554/eLife.33292

Nonsense mRNA suppression via nonstop decay
Cited by: 42
Author(s): Joshua A. Arribere, Andrew Fire
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-2207-8

RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles
Cited by: 27
Author(s): Amy Webb, Audrey C. Papp, Amanda Curtis, Leslie C. Newman, Maciej Pietrzak, Michał Seweryn, Samuel K. Handelman, Grzegorz A. Rempała, Daqing Wang, Erica Graziosa, Rachel F. Tyndale, Caryn Lerman, John R. Kelsoe, Deborah C. Mash, Wolfgang Sadée
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-018-24967-y

Whole exome sequencing reveals rare variants linked to congenital pouch colon
Cited by: 16
Author(s): Praveen Mathur, Krishna Mohan Medicherla, Spandan Chaudhary, Mruduka S. Patel, Prashanth Bagali, Prashanth Suravajhala
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0217343

Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling
Cited by: 6
Author(s): Lidia Hildebrand Pulz, Camila Neri Barra, Pâmela Almeida Alexandre, Greice Cestari Huete, Karine Germano Cadrobbi, Adriana Tomoko Nishiya, Sílvio Henrique de Freitas, Heidge Fukumasu, Ricardo de Francisco Strefezzi
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0148685

Tetra-O-Methyl Nordihydroguaiaretic Acid Broadly Suppresses Cancer Metabolism and Synergistically Induces Strong Anticancer Activity in Combination with Etoposide, Rapamycin and UCN-01
Cited by: 18
Author(s): Kotohiko Kimura, Ru Chih C. Huang
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0182456

Acute and chronic effects of exercise on mRNA expression in the skeletal muscle of two mouse models of peripheral artery disease
Cited by: 5
Author(s): Hiroki Nagase, Shuhei Yao, Shota Ikeda
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0003369

Identification of Nuclear and Cytoplasmic mRNA Targets for the Shuttling Protein SF2/ASF
Cited by: 101
Author(s): Jeremy R. Sanford, Pedro M. Coutinho, Jim Hackett, Xin Wang, William P. Ranahan, Javier F. Cáceres
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12870-016-0782-8

Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”
Cited by: 35
Author(s): Felix Seifert, Sandra Bössow, Jochen Kumlehn, Heike Gnad, Stefan Scholten
Software Mentions: 2
Published: over 8 years ago

10.1186/1756-0381-3-4

SICTIN: Rapid footprinting of massively parallel sequencing data
Cited by: 11
Author(s): Stefan Enroth, Robin Andersson, Claes Wadelius, Jan Komorowski
Software Mentions: 2
Published: about 14 years ago

10.1093/database/bav103

WaspAtlas: aNasonia vitripennisgene database and analysis platform
Cited by: 17
Author(s): Nathaniel J. Davies, Eran Tauber
Software Mentions: 2
Published: over 9 years ago

10.1007/s00438-020-01739-w

Molecular variation among virulent and avirulent strains of the quarantine nematode Bursaphelenchus xylophilus
Cited by: 9
Author(s): Anna Filipiak, Tadeusz Malewski, Ewa Matczyńska, Marek Tomalak
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms18112295

Inter-Species Host Gene Expression Differences in Response to Human and Avian Influenza A Virus Strains
Cited by: 9
Author(s): Biruhalem Taye, David Yeo, Raphael Tze Chuen Lee, Boon Huan Tan, Richard J. Sugrue, Sebastian Maurer‐Stroh
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1000869

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading
Cited by: 293
Author(s): Anna C. Groner, Sylvain Meylan, Angela Ciuffi, Nadine Zangger, Giovanna Ambrosini, Nicolas Dénervaud, Philipp Bücher, Didier Trono
Software Mentions: 2
Published: over 14 years ago

10.3390/molecules26040966

Zincbindpredict—Prediction of Zinc Binding Sites in Proteins
Cited by: 9
Author(s): Sam M. Ireland, Andrew C.R. Martin
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-5314-5

Fine mapping chromatin contacts in capture Hi-C data
Cited by: 16
Author(s): Chris Eijsbouts, Oliver S. Burren, Paul Newcombe, Chris Wallace
Software Mentions: 2
Published: over 5 years ago

10.15252/embj.201592862

Mitochondria are required for pro‐ageing features of the senescent phenotype
Cited by: 482
Author(s): Clara Correia‐Melo, Francisco D.M. Marques, Rosaleen J. Anderson, Graeme Hewitt, Rachael N. Hewitt, John Cole, Bernadette Carroll, Soichi Miwa, Jodie Birch, Alina Merz, Michael D. Rushton, Michelle Charles, Diana Jurk, Stephen W.G. Tait, Rafal Czapiewski, Laura C. Greaves, Glyn Nelson, Mohammad Bohlooly‐Y, Sergio Rodríguez‐Cuenca, Antonio Vidal‐Puig, Derek A. Mann, Gabriele Saretzki, Giovanni Quarato, Douglas R. Green, Peter D. Adams, Thomas von Zglinicki, Viktor I. Korolchuk, João F. Passos
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0108001

Specific Gene Expression Responses to Parasite Genotypes Reveal Redundancy of Innate Immunity in Vertebrates
Cited by: 24
Author(s): David Haase, Jennifer K. Rieger, Anika Witten, Monika Stoll, Erich Bornberg‐Bauer, Martin Kalbe, Thorsten B. H. Reusch
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2105-5-131

Cited by: 9
Author(s): Thomas A. Down, Tim Hubbard
Software Mentions: 2
Published: over 20 years ago

10.3390/genes12010031

Genome-Wide Analysis of LysM-Containing Gene Family in Wheat: Structural and Phylogenetic Analysis during Development and Defense
Cited by: 13
Author(s): Zheng Chen, Zijie Shen, Zhao Da, Lei Xu, Lijun Zhang, Quan Zou
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-68141-9

Proteomic and transcriptomic profiling identifies mediators of anchorage-independent growth and roles of inhibitor of differentiation proteins in invasive lobular carcinoma
Cited by: 16
Author(s): Nilgun Tasdemir, Kai Ding, Laura Savariau, Kevin M. Levine, Tian Du, Ashuvinee Elangovan, Emily A. Bossart, Adrian V. Lee, Nancy E. Davidson
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-019-43983-0

Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples
Cited by: 19
Author(s): Marie-Ange Palomares, Cyril Dalmasso, Eric Bonnet, Céline Derbois, Solène Brohard, Christophe Ambroise, Christophe Battail, Jean‐François Deleuze, Robert Olaso
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-021-83913-7

CIBERSORT analysis of TCGA and METABRIC identifies subgroups with better outcomes in triple negative breast cancer
Cited by: 47
Author(s): Kelly E. Craven, Yesim Gökmen‐Polar, Sunil Badve
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0000169

Vertebrate Vitellogenin Gene Duplication in Relation to the “3R Hypothesis”: Correlation to the Pelagic Egg and the Oceanic Radiation of Teleosts
Cited by: 181
Author(s): Roderick Nigel Finn, Børge André Kristoffersen
Software Mentions: 2
Published: over 17 years ago

10.1093/molbev/msy243

Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds
Cited by: 36
Author(s): Marjolaine Rousselle, Alexandre Laverré, Emeric Figuet, Benoît Nabholz, Nicolas Galtier
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0147046

Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.)
Cited by: 24
Author(s): Simerjeet Kaur, Kanwarpal S. Dhugga, Kulvinder S. Gill, Jaswinder Singh
Software Mentions: 2
Published: over 8 years ago

10.1186/1742-4682-10-61

Exploring evolution of brain genes involved in microcephaly through phylogeny and synteny analysis
Cited by: 0
Author(s): Sobiah Rauf, Asif Mir
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-018-4997-y

Fasting and time of day independently modulate circadian rhythm relevant gene expression in adipose and skin tissue
Cited by: 6
Author(s): Alexessander Couto Alves, Craig A. Glastonbury, Julia S. El-Sayed Moustafa, Kerrin S. Small
Software Mentions: 2
Published: about 6 years ago

10.1186/s12862-020-1591-0

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life
Cited by: 29
Author(s): Elias Dohmen, Steffen Klasberg, Erich Bornberg‐Bauer, Sören W. Perrey, Carsten Kemena
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2148-12-110

Functional characterization and evolution of PTH/PTHrP receptors: insights from the chicken
Cited by: 66
Author(s): Pedro L C Pinheiro, João C. R. Cardoso, Deborah M. Power, Adelino V.M. Canário
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2105-6-S1-S12

Data preparation and interannotator agreement: BioCreAtIvE Task 1B
Cited by: 34
Author(s): Marc E. Colosimo, Alexander A. Morgan, Alexander Yeh, Jeffrey B. Colombe, Lynette Hirschman
Software Mentions: 1
Published: over 19 years ago

10.3389/fmolb.2021.696319

Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes
Cited by: 1
Author(s): Kai‐Lu Zhang, Jian Zhou, Jing‐Fang Yang, Yuzhen Zhao, Debatosh Das, Ge‐Fei Hao, Caie Wu, Jianhua Zhang, Feng Zhu, Moxian Chen, Shiwei Zhou
Software Mentions: 1
Published: about 3 years ago

10.1186/1471-2148-7-113

Molecular cloning and analysis of zebrafish voltage-gated sodium channel beta subunit genes: implications for the evolution of electrical signaling in vertebrates
Cited by: 38
Author(s): Sameer Chopra, Hiroshi Watanabe, Tao Zhong, Dan M. Roden
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2148-9-2

Evolution and differential expression of a vertebrate vitellogenin gene cluster
Cited by: 58
Author(s): Roderick Nigel Finn, Jelena Kolarevic, Heidi Kongshaug, Frank Nilsen
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2148-7-178

Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes
Cited by: 84
Author(s): Tsukasa Kawahara, J. David Lambeth
Software Mentions: 1
Published: over 17 years ago

10.3390/genes12020134

A SINE Insertion in F8 Gene Leads to Severe Form of Hemophilia A in a Family of Rhodesian Ridgebacks
Cited by: 4
Author(s): Alexandra Kehl, Anita Haug Haaland, Ines Langbein‐Detsch, Elisabeth Mueller
Software Mentions: 1
Published: over 3 years ago

10.3390/genes12030410

Evaluation of a Custom Design Gene Panel as a Diagnostic Tool for Human Non-Syndromic Infertility
Cited by: 3
Author(s): Özlem Okutman, Julien Tarabeux, Jean Muller, Stéphane Viville
Software Mentions: 1
Published: over 3 years ago

10.1590/1678-4685-GMB-2019-0383

Rho guanine nucleotide exchange factor 39 increases the viability, migration and invasion of clear cell renal cell carcinoma cells via the activation of the AKT/ERK signaling pathway
Cited by: 1
Author(s): Shuzhong Wang, Yanmei Wang, Chuanyun Wang
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2148-10-38

The zebrafish genome encodes the largest vertebrate repertoire of functional aquaporins with dual paralogy and substrate specificities similar to mammals
Cited by: 145
Author(s): Angèle Tingaud‐Sequeira, Magdalena Całusińska, Roderick Nigel Finn, François Chauvigné, Juan José Lozano, Joan Cerdà
Software Mentions: 1
Published: over 14 years ago

10.1186/s13073-017-0430-4

Lost in translation: returning germline genetic results in genome-scale cancer research
Cited by: 25
Author(s): Amber Johns, Skye McKay, Jeremy L. Humphris, Mark Pinese, Lorraine A. Chantrill, R. Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda High, Kátia Nones, Ann‐Marie Patch, Neil D. Merrett, Nick Pavlakis, Karin S. Kassahn, Jaswinder S. Samra, David Miller, David K. Chang, Marina Pajic, John V. Pearson, Sean M. Grimmond, Nicola Waddell, Nikolajs Zeps, Anthony J. Gill, Andrew V. Biankin
Software Mentions: 1
Published: over 7 years ago

10.1186/s13027-019-0262-5

Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans
Cited by: 8
Author(s): Ekaterina Matyunina, Alexander Emelyanov, T. V. Kurbatova, A. A. Makashov, I. V. Mizgirev, А. P. Kozlov
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13023-016-0545-5

Rett syndrome – biological pathways leading from MECP2 to disorder phenotypes
Cited by: 58
Author(s): Friederike Ehrhart, Susan L. Coort, Elisa Cirillo, Eric Smeets, Chris T. Evelo, Leopold Curfs
Software Mentions: 1
Published: almost 8 years ago

10.1074/jbc.M113.540906

The Methyltransferase WBSCR22/Merm1 Enhances Glucocorticoid Receptor Function and Is Regulated in Lung Inflammation and Cancer
Cited by: 33
Author(s): Maryam Jangani, Toryn Poolman, Laura Matthews, Nan Yang, Stuart N. Farrow, Andrew Berry, Neil A. Hanley, Andrew J.K. Williamson, Anthony D. Whetton, Rachelle Donn, David Ray
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2148-11-302

Accelerated evolution of 3'avian FOXE1 genes, and thyroid and feather specific expression of chicken FoxE1
Cited by: 2
Author(s): Sergey Yaklichkin, Diana K. Darnell, Maricela Pier, Parker B. Antin, Sridhar Hannenhalli
Software Mentions: 1
Published: almost 13 years ago

10.1186/1465-9921-9-46

Could a defective epithelial sodium channel lead to bronchiectasis
Cited by: 33
Author(s): Isabelle Fajac, Marion Viel, Sébastien Sublemontier, D. Hubert, Thierry Bienvenu
Software Mentions: 1
Published: over 16 years ago

10.1038/sdata.2016.52

Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR
Cited by: 5
Author(s): Pieter Mestdagh, Steve Lefever, Pieter-Jan Volders, Stefaan Derveaux, Jan Hellemans, Jo Vandesompele
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-017-11898-3

Novel pathogenic mutations in C1QTNF5 support a dominant negative disease mechanism in late-onset retinal degeneration
Cited by: 26
Author(s): Chloe Stanton, Shyamanga Borooah, Camilla Drake, Joseph A. Marsh, Susan Campbell, Alan Lennon, Dinesh C. Soares, Neeru A. Vallabh, Jayashree Sahni, Artur V. Cideciyan, Baljean Dhillon, Véronique Vitart, Samuel G. Jacobson, Alan F. Wright, Caroline Hayward
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2148-6-26

Multiple lineage specific expansions within the guanylyl cyclase gene family
Cited by: 42
Author(s): David A. Fitzpatrick, Damien M. O’Halloran, Ann M. Burnell
Software Mentions: 1
Published: over 18 years ago

10.1002/yea.3515

Genome‐wide effect of tetracycline, doxycycline and 4‐epidoxycycline on gene expression in<scp><i>Saccharomyces cerevisiae</i></scp>
Cited by: 6
Author(s): Guadalupe Sánchez, Samuel C. Linde, Joseph D. Coolon
Software Mentions: 1
Published: about 4 years ago

10.1007/s11103-014-0187-8

Genome-wide transcriptomic analysis of response to low temperature reveals candidate genes determining divergent cold-sensitivity of maize inbred lines
Cited by: 46
Author(s): Alicja Sobkowiak, Maciej Jończyk, Emilia Jarochowska, Przemysław Biecek, Joanna Trzcińska-Danielewicz, Jörg Leipner, Jan Fronk, Paweł Sowiński
Software Mentions: 1
Published: over 10 years ago

10.3390/v7031238

Human Endogenous Retrovirus Group E and Its Involvement in Diseases
Cited by: 32
Author(s): Christelle Le Dantec, Sophie Vallet, Wesley H. Brooks, Yves Renaudineau
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-018-33527-3

Transposon mutagenesis screen in mice identifies TM9SF2 as a novel colorectal cancer oncogene
Cited by: 11
Author(s): Christopher Clark, Makayla Maile, Patrick Blaney, Stefano R. Hellweg, Anna Strauss, Wilaiwan Durose, Sambhawa Priya, Jüri Habicht, Michael B. Burns, Ran Blekhman, Juan E. Abrahante, Timothy K. Starr
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.0020150

The Evolution of Word Composition in Metazoan Promoter Sequence
Cited by: 11
Author(s): Eliot C. Bush, Bruce T. Lahn
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pgen.1000914

Deletion of the WD40 Domain of LRRK2 in Zebrafish Causes Parkinsonism-Like Loss of Neurons and Locomotive Defect
Cited by: 116
Author(s): Donglai Sheng, Dianbo Qu, Ken Hon Hung Kwok, Seok Shin Ng, Adrian Yin Ming Lim, Sharon Siqi Aw, Charlie Wah Heng Lee, Wing-Kin Sung, Eng King Tan, Thomas Lufkin, Suresh Jesuthasan, Sinnakaruppan Mathavan, Jianjun Li
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1005097

Mutations of Human NARS2, Encoding the Mitochondrial Asparaginyl-tRNA Synthetase, Cause Nonsyndromic Deafness and Leigh Syndrome
Cited by: 92
Author(s): Mariella Simon, E. Richard, Xinjian Wang, Mohsin Shahzad, Vincent Huang, Tanveer Ahmed Qaiser, Prasanth Potluri, Sarah E. Mahl, Antonio Dávila, Sabiha Nazli, Saege Hancock, Margret Yu, J. Jay Gargus, Richard Y. Chang, Nada Al-Sheqaih, William G. Newman, José E. Abdenur, Arnold Starr, Rashmi S. Hegde, Thomas Dorn, Anke Busch, Eddie Park, Jie Wu, Hagen Schwenzer, Adrian Flierl, Catherine Florentz, Marie Sissler, Shaheen N. Khan, Ronghua Li, Min‐Xin Guan, Thomas B. Friedman, Doris K. Wu, Vincent Procaccio, Sheikh Riazuddin, Douglas C. Wallace, Zubair M. Ahmed, Taosheng Huang, Saima Riazuddin
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pgen.1002711

Prdm5 Regulates Collagen Gene Transcription by Association with RNA Polymerase II in Developing Bone
Cited by: 51
Author(s): Giorgio Galli, Kristian Honnens de Lichtenberg, Matteo Carrara, Wolfgang Hans, Manuela Wuelling, Bettina Mentz, Hinke A.B. Multhaupt, Cathrine K. Fog, Kjeld Truberg Jensen, Juri Rappsilber, Andrea Vortkamp, Les Coulton, Helmut Fuchs, Valérie Gailus‐Durner, Martin Hrabé de Angelis, Raffaele Calogero, John R. Couchman, Anders H. Lund
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-018-35375-7

Genome-wide identification and analysis of non-specific Lipid Transfer Proteins in hexaploid wheat
Cited by: 12
Author(s): Allan Kouidri, Ryan Whitford, Radosław Suchecki, Elena Kalashyan, Ute Baumann
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pgen.1006560

Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans
Cited by: 79
Author(s): Kimberly F. McManus, Angela M. Taravella, Brenna M. Henn, Carlos D. Bustamante, Martin Sikora, Omar E. Cornejo
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0160463

Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers
Cited by: 6
Author(s): Xudong Wu, Guohui Li
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0077819

Complex Patterns of Chromosome 11 Aberrations in Myeloid Malignancies Target CBL, MLL, DDB1 and LMO2
Cited by: 9
Author(s): Thorsten Klampfl, Jelena D. Milosevic, Ana Puda, Andreas Schönegger, Klaudia Bagienski, Tiina Berg, Ashot S. Harutyunyan, Bettina Gisslinger, Elisa Rumi, Luca Malcovati, Daniela Pietra, Chiara Elena, Matteo Giovanni Della Porta, Lisa Pieri, Paola Guglielmelli, Christoph Bock, Michael Doubek, Dana Dvořáková, Nada Suvajdžić, Dragica Tomin, Nataša Tos̆ić, Zdeněk Ráčil, Michael Steurer, Sonja Pavlović, Alessandro M. Vannucchi, Mario Cazzola, Heinz Gisslinger, Róbert Královics
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0014814

The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions
Cited by: 23
Author(s): Cara Woodwark, Alex Bateman
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0107202

Analysis of Tumor Suppressor Genes Based on Gene Ontology and the KEGG Pathway
Cited by: 42
Author(s): Jing Yang, Chen Lei, Xiangyin Kong, Tao Huang, Yu-Dong Cai
Software Mentions: 1
Published: about 10 years ago

10.1111/mec.15313

Genomic footprints of a biological invasion: Introduction from Asia and dispersal in Europe of the topmouth gudgeon (<i>Pseudorasbora parva</i>)
Cited by: 11
Author(s): Miguel Baltazar‐Soares, Simon Blanchet, Julien Côté, Ali Serhan Tarkan, Eva Záhorská, Rodolphe E. Gozlan, Christophe Eizaguirre
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0022691

Evolution of Trefoil Factor(s): Genetic and Spatio-Temporal Expression of Trefoil Factor 2 in the Chicken (Gallus Gallus Domesticus)
Cited by: 7
Author(s): Zhengyu Jiang, Amy C. Lossie, T. J. Applegate
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0067801

Gene Expression Analysis of Zebrafish Melanocytes, Iridophores, and Retinal Pigmented Epithelium Reveals Indicators of Biological Function and Developmental Origin
Cited by: 84
Author(s): Charles W. Higdon, Robi D. Mitra, Stephen L. Johnson
Software Mentions: 1
Published: about 11 years ago

10.1186/s12862-019-1517-x

Natriuretic peptides appeared after their receptors in vertebrates
Cited by: 3
Author(s): Anna Grandchamp, Shifa Tahir, Philippe Monget
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0004933

The Role of Genomic Data in the Discovery, Annotation and Evolutionary Interpretation of the Interferon-Lambda Family
Cited by: 66
Author(s): Brian Fox, Paul O. Sheppard, Patrick J. O׳Hara
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0180465

A functional approach to understanding the role of NCKX5 in Xenopus pigmentation
Cited by: 11
Author(s): Ruth M. Williams, Robert J. Winkfein, Rebecca S. Ginger, Martin R. Green, Paul P. M. Schnetkamp, Grant N. Wheeler
Software Mentions: 1
Published: about 7 years ago

10.1186/s13058-015-0532-0

Integrative analyses identify modulators of response to neoadjuvant aromatase inhibitors in patients with early breast cancer
Cited by: 8
Author(s): Elena López-Knowles, Paul M. Wilkerson, Ricardo Ribas, Helén Anderson, Alan Mackay, Zara Ghazoui, Aradhana Rani, Peter Osin, A Nerurkar, Lorna Renshaw, Alexey Larionov, William R. Miller, JM Dixon, Jorge S. Reis‐Filho, Anita K. Dunbier, Lesley-Ann Martin, Mitch Dowsett
Software Mentions: 1
Published: over 9 years ago

10.1111/j.1365-2826.2012.02310.x

The Prolactin Gene: A Paradigm of Tissue‐Specific Gene Regulation with Complex Temporal Transcription Dynamics
Cited by: 38
Author(s): Karen Featherstone, Mike White, John R. Davis
Software Mentions: 1
Published: over 12 years ago

10.1038/s41598-019-54058-5

Characterizing renal involvement in Hermansky-Pudlak Syndrome in a zebrafish model
Cited by: 5
Author(s): Heiko Schenk, Janina Müller-Deile, Patricia Schröder, Patricia Bolaños-Palmieri, Lynne Beverly-Staggs, Richard M. White, Jan Hinrich Bräsen, Hermann Haller, Mario Schiffer
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2202-7-S1-S8

Computational framework for the prediction of transcription factor binding sites by multiple data integration
Cited by: 3
Author(s): Alberto Ambesi-Impiombato, Mukesh Bansal, Píetro Lió, Diego di Bernardo
Software Mentions: 1
Published: almost 18 years ago

10.1371/journal.pone.0135799

Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol
Cited by: 10
Author(s): Sophie Depiereux, Florence Le Gac, Bertrand De Meulder, Michael St.Pierre, Raphaël Helaers, Yann Guiguen, Patrick Kestemont, Eric Depiereux
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0175638

A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma
Cited by: 27
Author(s): Tajana Tešan Tomić, Josefin Olausson, Annica Wilzén, Magnus Sabel, Katarina Truvé, Helene Sjögren, Sándor Dósa, Magnus Tisell, Birgitta Lannering, Fredrik Enlund, Tommy Martinsson, Pierre Åman, Frida Abel
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0082486

Phylodynamics of the Emergence of Influenza Viruses after Cross-Species Transmission
Cited by: 4
Author(s): Leila Rahnama, Stéphane Aris‐Brosou
Software Mentions: 1
Published: almost 11 years ago

10.1186/1755-8794-5-21

Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers
Cited by: 48
Author(s): Guoqing Wang, Zhibo Xu, Rui Wang, ‪Mohammed Al-Hijji, Jacqueline Salit, Yael Strulovici-Barel, Ann E. Tilley, Jason G. Mezey, Ronald G. Crystal
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0010162

Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules
Cited by: 50
Author(s): Eric Bonnet, Marianthi Tatari, Anagha Joshi, Tom Michoel, Kathleen Marchal, Geert Berx, Yves Van de Peer
Software Mentions: 1
Published: over 14 years ago

10.1186/s12885-015-1192-2

DNA copy number analysis of metastatic urothelial carcinoma with comparison to primary tumors
Cited by: 25
Author(s): Richard Bambury, Ami S. Bhatt, Markus Riester, Chandra Sekhar Pedamallu, Fujiko Duke, Joaquim Bellmunt, Edward C. Stack, Lillian Werner, Rachel Park, Gopa Iyer, Massimo Loda, Philip W. Kantoff, Franziska Michor, Matthew Meyerson, Jonathan E. Rosenberg
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0113686

The Lineage-Specific Evolution of Aquaporin Gene Clusters Facilitated Tetrapod Terrestrial Adaptation
Cited by: 113
Author(s): Roderick Nigel Finn, François Chauvigné, Jón Baldur Hlidberg, Christopher P. Cutler, Joan Cerdà
Software Mentions: 1
Published: almost 10 years ago

10.18632/oncotarget.16500

Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1α axis inhibition
Cited by: 7
Author(s): Aurélia Nguyen, François Marie Moussallieh, Alan Mackay, A. Ercüment Çiçek, Andrés Coca, M.P. Chenard, Noëlle Weingertner, Benoît Lhermitte, Éric Letouzé, Éric Guérin, Erwan Pencreach, Sarah Jannier, Dominique Guenot, Izzie Jacques Namer, Chris Jones, Natacha Entz‐Werlé
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0255006

An insight on the impact of teleost whole genome duplication on the regulation of the molecular networks controlling skeletal muscle growth
Cited by: 5
Author(s): Bruno Oliveira da Silva Duran, Daniel García de la serrana, Bruna Tereza Thomazini Zanella, Érika Stefani Perez, Edson Assunção Mareco, Vander Bruno dos Santos, Robson Francisco Carvalho, Maeli Dal-Pai-Silva
Software Mentions: 1
Published: about 3 years ago

10.1038/s41598-020-62843-w

Identification of microRNAs in bovine faeces and their potential as biomarkers of Johne’s Disease
Cited by: 16
Author(s): Ronan G. Shaughnessy, DJ Farrell, Bojan Stojkovic, John A. Browne, Kevin Kenny, Stephen V. Gordon
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0214144

Fatty acid-binding protein 1 increases steer fat deposition by facilitating the synthesis and secretion of triacylglycerol in liver
Cited by: 11
Author(s): Yujuan Wang, Kai-Fu Tang, Wei Zhang, Wenli Guo, Yaning Wang, Zan Liu, Wenguang Yang
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2350-8-23

Screening of the transcriptional regulatory regions of vascular endothelial growth factor receptor 2 (VEGFR2) in amyotrophic lateral sclerosis
Cited by: 13
Author(s): Alice Brockington, B.H.A. Wokke, Hannah Nixon, Judith Hartley, Pamela J. Shaw
Software Mentions: 1
Published: over 17 years ago

10.3390/cancers12051285

Genome-Wide Association Meta-Analysis of Single-Nucleotide Polymorphisms and Symptomatic Venous Thromboembolism during Therapy for Acute Lymphoblastic Leukemia and Lymphoma in Caucasian Children
Cited by: 5
Author(s): Marion K. Mateos, Morten Tulstrup, Michael C. Quinn, Ruta Tuckuviene, Glenn M. Marshall, Ramneek Gupta, Chelsea Mayoh, Benjamin Ole Wolthers, Pasquale Barbaro, Ellen Ruud, Rosemary Sutton, Pasi Huttunen, Tamás Révész, Sonata Šaulytė Trakymienė, Draga Barbaric, Ulf Tedgård, Jodie E. Giles, Frank Alvaro, Ólafur G. Jónsson, Françoise Méchinaud, Kadri Saks, Daniel Catchpoole, Rishi S. Kotecha, Luciano Dalla‐Pozza, Georgia Chenevix-Trench, Toby N. Trahair, Stuart MacGregor, Kjeld Schmiegelow
Software Mentions: 1
Published: over 4 years ago

10.3390/cells8091062

New Rat Model of Advanced NASH Mimicking Pathophysiological Features and Transcriptomic Signature of The Human Disease
Cited by: 15
Author(s): Raquel Maeso‐Díaz, Zoe Boyer‐Díaz, Juan José Lozano, Martí Ortega‐Ribera, Carmen Peralta, Jaime Bosch, Jordi Gracia‐Sancho
Software Mentions: 1
Published: about 5 years ago

10.1186/s13148-021-01086-6

Weight loss after Roux-En-Y gastric bypass surgery reveals skeletal muscle DNA methylation changes
Cited by: 6
Author(s): Luis Garcı́a, Samantha E. Day, Richard L. Coletta, Baltazar Campos, Tonya R. Benjamin, Eleanna De Filippis, James A. Madura, Lawrence J. Mandarino, Lori R. Roust, Dawn K. Coletta
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-8-475

Surviving extreme polar winters by desiccation: clues from Arctic springtail (Onychiurus arcticus) EST libraries
Cited by: 65
Author(s): Melody S. Clark, Michael A. S. Thorne, Jelena Purać, Gordana Grubor-Lajšić, Michael Kube, Richard Reinhardt, M. R. Worland
Software Mentions: 1
Published: over 17 years ago

10.1186/s12864-018-4842-3

An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells
Cited by: 34
Author(s): Elizabeth M. Kennedy, George N. Goehring, Michael H. Nichols, Chloe Robins, Divya Mehta, Torsten Klengel, Eleazar Eskin, Alicia K. Smith, Karen N. Conneely
Software Mentions: 1
Published: over 6 years ago

10.1155/2012/284786

Predictive Models of Gene Regulation from High-Throughput Epigenomics Data
Cited by: 9
Author(s): Sonja Althammer, Amadís Pagès, Eduardo Eyras
Software Mentions: 1
Published: over 12 years ago

10.1016/j.dib.2016.05.040

Gene expression profiling and pathway analysis data in MCF-7 and MDA-MB-231 human breast cancer cell lines treated with dioscin
Cited by: 6
Author(s): Pranapda Aumsuwan, Shabana I. Khan, Ikhlas A. Khan, Larry Walker, Asok K. Dasmahapatra
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-68350-2

The pharmaceutical solvent N-methyl-2-pyrollidone (NMP) attenuates inflammation through Krüppel-like factor 2 activation to reduce atherogenesis
Cited by: 19
Author(s): Marta Roche-Molina, B. Hardwick, Cristina Sánchez‐Ramos, D. Sanz-Rosa, Dirk R. Gewert, Francisco M. Cruz, Andrés González-Guerra, Vicente Andrés, Joaquin A. Palma, Borja Ibáñez, Grahame J. McKenzie, Juan A. Bernal
Software Mentions: 1
Published: about 4 years ago

10.15252/embj.201798449

A novel form of JARID2 is required for differentiation in lineage‐committed cells
Cited by: 13
Author(s): Diaa Al‐Raawi, Rhian Jones, Susanne N. Wijesinghe, John Halsall, Marija Petrić, Sally Roberts, Neil A. Hotchin, Aditi Kanhere
Software Mentions: 1
Published: over 5 years ago