A core transcriptional network for early mesoderm development in Drosophila melanogaster
Sandmann, Thomas, Girardot, Charles, Brehme, Marc, Tongprasit, Waraporn, Stolc, Viktor, Furlong, Eileen E.M.·2007·Genes & Development
Cited by (286)
Items 101–200 of 286
- TSHZ1-dependent gene regulation is essential for olfactory bulb development and olfactionDaniela Ragancokova, Elena Rocca, Anne M.M. Oonk, Herbert Schulz, Elvira Rohde, Jan Bednarsch, Ilse Feenstra, Ronald J. E. Pennings, Hagen Wende, Alistair N. Garratt · 2014 · Journal of Clinical Investigation
- Diversification of Muscle Types in DrosophilaCyrille de Joussineau, Laetitia Bataillé, Teresa Jagla, Krzysztof Jagla · 2012 · Current topics in developmental biology/Current Topics in Developmental Biology
- Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin StateBartek Wilczyński, Ya-Hsin Liu, Zhen Xuan Yeo, Eileen E. M. Furlong · 2012 · PLoS Computational Biology
- Understanding transcriptional regulatory networks using computational modelsBing He, Kai Tan · 2016 · Current Opinion in Genetics & Development
- Tissue development and RNA control: “HOW” is it coordinated?Talila Volk, David Israeli, Ronit Nir, Hila Toledano · 2008 · Trends in Genetics
- Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activityKhoueiry, Pierre, Girardot, Charles, Ciglar, Lucia, Peng, Pei-Chen, Gustafson, E Hilary, Sinha, Saurabh, Furlong, Eileen EM · 2017 · eLife
- Genome Wide Analysis Reveals Zic3 Interaction with Distal Regulatory Elements of Stage Specific Developmental Genes in ZebrafishCecilia Lanny Winata, Igor Kondrychyn, Vibhor Kumar, Kandhadayar Gopalan Srinivasan, Yuriy Lvovich Orlov, Ashwini Ravishankar, Shyam Prabhakar, Lawrence Walter Stanton, Vladimir P. Korzh, Sinnakaruppan Mathavan · 2013 · PLoS Genetics
- Dynamic CRM occupancy reflects a temporal map of developmental progressionWilczyński, Bartek, Furlong, Eileen E M · 2010 · Molecular Systems Biology
- Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous insectLena Sachs, Yen-Ta Chen, Axel Drechsler, Jeremy Lynch, Kristen A. Panfilio, Michael Lässig, Johannes Berg, Siegfried Roth · 2015 · eLife
- Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneumJessica Cande, Vivek S. Chopra, Michael Levine · 2009 · Development
- Multi-step control of muscle diversity by Hox proteins in the Drosophila embryoJonathan Enriquez, Hadi Boukhatmi, Laurence Dubois, Anthony Philippakis, Martha L. Bulyk, Alan M. Michelson, Michèle Crozatier, Alain Vincent · 2010 · Development
- Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA OccupancyQiong Cheng, Majid Kazemian, Hannah Pham, Charles A. Blatti, S Celniker, Scot A. Wolfe, Michael H. Brodsky, Saurabh Sinha · 2013 · PLoS Genetics
- Unexpected functional redundancy between Twist and Slug (Snail2) and their feedback regulation of NF-κB via Nodal and CerberusChi Zhang, Michael W. Klymkowsky · 2009 · Developmental Biology
- Roles of Lineage-Determining Transcription Factors in Establishing Open Chromatin: Lessons From High-Throughput StudiesSven Heinz, Christopher K. Glass · 2011 · Current topics in microbiology and immunology
- Dorsoventral Polarity of the Nasonia Embryo Primarily Relies on a BMP Gradient Formed without Input from TollOrhan Özüak, Thomas Buchta, Siegfried Roth, Jeremy Lynch · 2014 · Current Biology
- A protocol for unraveling gene regulatory networksStefan C. Materna, Paola Oliveri · 2008 · Nature Protocols
- Myocyte Enhancer Factor 2 Transcription Factors in Heart Development and DiseaseBrian L. Black, Richard M. Cripps · 2010 · Elsevier eBooks
- Toward a systems-level understanding of developmental regulatory networksBrian W. Busser, Martha L. Bulyk, Alan M. Michelson · 2008 · Current Opinion in Genetics & Development
- Quantitative Single-Embryo Profile ofDrosophilaGenome Activation and the Dorsal–Ventral Patterning NetworkJeremy E. Sandler, Angelike Stathopoulos · 2016 · Genetics
- Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing dataChengwei Li, Bor‐Sen Chen · 2016 · Cell Cycle
- Discoidin-domain receptor coordinates cell-matrix adhesion and collective polarity in migratory cardiopharyngeal progenitorsYelena Y. Bernadskaya, Saahil Brahmbhatt, Stephanie E. Gline, Wei Wang, Lionel Christiaen · 2018 · Nature Communications
- Extremely rapid and reversible optogenetic perturbation of nuclear proteins in living embryosAnna C. Kögler, Yacine Kherdjemil, Katharina Bender, Adam H. Rabinowitz, Raquel Marco-Ferreres, Eileen E. M. Furlong · 2021 · Developmental Cell
- BTB-Zinc Finger Oncogenes Are Required for Ras and Notch-Driven Tumorigenesis in DrosophilaKaren Doggett, Nezaket Türkel, Lee F. Willoughby, Jason Ellul, Michael J. Murray, Helena E. Richardson, Anthony M. Brumby · 2015 · PLoS ONE
- Conserved regulatory sequences inAtoh7mediate non-conserved regulatory responses in retina ontogenesisDorota Skowronska‐Krawczyk, Florence Chiodini, Martin Ebeling, Christine Alliod, Adam Kundzewicz, Diogo S. Castro, Marc Ballivet, François Guillemot, Lidia Matter-Sadzinski, Jean‐Marc Matter · 2009 · Development
- Involvement of the transcription factor twist in phenotype alteration through epithelial–mesenchymal transition in lung cancer cellsHarunori Nakashima, Naozumi Hashimoto, Daisuke Aoyama, Takashi Kohnoh, Koji Sakamoto, Masaaki Kusunose, Kazuyoshi Imaizumi, Yoshihiro Takeyama, Mitsuo Sato, Tsutomu Kawabe et al. · 2011 · Molecular Carcinogenesis
- A Machine Learning Approach for Identifying Novel Cell Type–Specific Transcriptional Regulators of MyogenesisBrian W. Busser, Leila Taher, Yongsok Kim, Terese R. Tansey, Molly J. Bloom, Ivan Ovcharenko, Alan M. Michelson · 2012 · PLoS Genetics
- Genetic control of muscle development: learning from DrosophilaTariq Maqbool, Krzysztof Jagla · 2007 · Journal of Muscle Research and Cell Motility
- Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAiYasuhiro Tomaru, Misato Nakanishi, Hisashi Miura, Yasumasa Kimura, Hiroki Ohkawa, Yusuke Ohta, Yoshihide Hayashizaki, Masanori Suzuki · 2009 · Nucleic Acids Research
- JAK/Stat signaling regulates heart precursor diversification inDrosophilaAaron N. Johnson, Mayssa H. Mokalled, Tom N. Haden, Eric N. Olson · 2011 · Development
- Complex functions of Mef2 splice variants in the differentiation of endoderm and of a neuronal cell type in a sea anemoneGrigory Genikhovich, Ulrich Technau · 2011 · Development
- A Cdx4-Sall4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic HematopoiesisElizabeth J. Paik, Shaun Mahony, Richard Mark White, Emily Price, Anthony DiBiase, Bilguujin Dorjsuren, Christian Mosimann, Alan James Davidson, David Kenneth Gifford, Leonard Ira Zon · 2013 · Stem Cell Reports
- HLH54Fis required for the specification and migration of longitudinal gut muscle founders from the caudal mesoderm ofDrosophilaAfshan Ismat, Christoph Schaub, Ingolf Reim, Katharina Kirchner, Dorothea Schultheis, Manfred Frasch · 2010 · Development
- Role for Traf4 in Polarizing Adherens Junctions as a Prerequisite for Efficient Cell Shape ChangesSam J. Mathew, Martina Rembold, Maria Leptin · 2011 · Molecular and Cellular Biology
- Initial deployment of the cardiogenic gene regulatory network in the basal chordate, Ciona intestinalisArielle Woznica, Maximilian Haeussler, Ella Starobinska, Jessica Jemmett, Younan Li, David W. Mount, Brad Davidson · 2012 · Developmental Biology
- Twist-BRD4 Complex: Potential Drug Target for Basal-like Breast CancerJian Shi, Jingying Cao, Binhua Peter Zhou · 2015 · Current Pharmaceutical Design
- The developmental expression dynamics of Drosophila melanogastertranscription factorsBoris Adryan, Sarah Amalia Teichmann · 2010 · Genome biology
- Mef2d Acts Upstream of Muscle Identity Genes and Couples Lateral Myogenesis to Dermomyotome Formation in Xenopus laevisBruno Della Gaspera, Anne‐Sophie Armand, Sylvie Lécolle, Frédéric Charbonnier, Christophe Chanoine · 2012 · PLoS ONE
- Immune-metabolic interaction in DrosophilaMarc Dionne · 2014 · Fly
- Conservation and divergence in developmental networks: a view from Drosophila myogenesisLucia Ciglar, Eileen E. M. Furlong · 2009 · Current Opinion in Cell Biology
- Mesoderm patterning and morphogenesis in the polychaete Alitta virens (Spiralia, Annelida): Expression of mesodermal markers Twist , Mox , Evx and functional role for MAP kinase signalingВиталий Владиславович Козин, Daria Filimonova, E. E. Kupriashova, Roman P. Kostyuchenko · 2016 · Mechanisms of Development
- Regulation of p21 by TWIST2 contributes to its tumor-suppressor function in human acute myeloid leukemiaXueguang Zhang, Wenxue Ma, Juanjuan Cui, Hong Yao, Haixia Zhou, Yan Ge, Liying Xiao, Xing Hu, B-H Liu, Jing Yang et al. · 2014 · Oncogene
- Mechanical competition alters the cellular interpretation of an endogenous genetic programSourabh Bhide, Denisa Gombalova, Gregor Mönke, Johannes Stegmaier, Valentyna Zinchenko, Anna Kreshuk, Julio Monti Belmonte, Maria Leptin · 2021 · The Journal of Cell Biology
- An Org-1–Tup transcriptional cascade reveals different types of alary muscles connecting internal organs in DrosophilaHadi Boukhatmi, Christoph Schaub, Laetitia Bataillé, Ingolf Reim, Jean‐Louis Frendo, Manfred Frasch, Alain Vincent · 2014 · Development
- Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesisLucia Ciglar, Charles Girardot, Bartek Wilczyński, Martina Maria Braun, Eileen E. M. Furlong · 2014 · Development
- Parameter estimation for robust HMM analysis of ChIP-chip dataPeter Humburg, David W. Bulger, Glenn Stone · 2008 · BMC Bioinformatics
- Tup/Islet1 integrates time and position to specify muscle identity in DrosophilaHadi Boukhatmi, Jean‐Louis Frendo, Jonathan Enriquez, Michèle Crozatier, Laurence Dubois, Alain Vincent · 2012 · Development
- Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learningLujing Zheng, Zhenhuan Liu, Yang Yang, Hong‐Bin Shen · 2021 · Bioinformatics
- Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemiaLi Wei Chang, Jacqueline E. Payton, Wenlin Yuan, Timothy James Ley, Rakesh Nagarajan, Gary D. Stormo · 2008 · Genome biology
- Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activityMichael Chambers, Wiam Turki-Judeh, Min Woo Kim, Kenny Chen, Sean D. Gallaher, Albert J. Courey · 2017 · BMC Genomics
- The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in DrosophilaKatrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga V. Ermakova, Maria Polychronidou, Ingrid Lohmann · 2019 · eLife
- Differential roles of the Drosophila EMT-inducing transcription factors Snail and Serpent in driving primary tumour growthKyra Campbell, Gaëlle Lebreton, Xavier Franch‐Marro, Jordi Casanova · 2018 · PLoS Genetics
- Human genetic variation within neural crest enhancers: molecular and phenotypic implicationsRada-Iglesias, Alvaro, Prescott, Sara L., Wysocka, Joanna · 2013 · Philosophical Transactions of the Royal Society B Biological Sciences
- Stripe formation in the early fly embryo: principles, models, and networksDmitri Papatsenko · 2009 · BioEssays
- Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory networkBrian W. Busser, Di Huang, Kevin R. Rogacki, Elizabeth A. Lane, Leila Shokri, Ting Ni, Caitlin E. Gamble, Stephen S. Gisselbrecht, Jun Zhu, Martha L. Bulyk et al. · 2012 · Proceedings of the National Academy of Sciences
- Functional genomic approaches to elucidate the role of enhancers during developmentGenevieve E. Ryan, Emma K. Farley · 2019 · WIREs Systems Biology and Medicine
- Chapter 5 Drosophila MycPeter Gallant · 2009 · Advances in cancer research
- Daughterless dictates Twist activity in a context-dependent manner during somatic myogenesisMing‐Ching Wong, Irinka Castanon, Mary K. Baylies · 2008 · Developmental Biology
- Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracyHamutal Arbel, Sumanta Basu, William W. Fisher, Ann S. Hammonds, Kenneth H. Wan, Soo Hyung Park, Richard Weiszmann, Benjamin W. Booth, Soile V.E. Keränen, Clara Henriquez et al. · 2018 · Proceedings of the National Academy of Sciences
- Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cellsJakke Neiro, Divya Sridhar, Anish Dattani, Aziz A. Aboobaker · 2022 · eLife
- Influence of the Twist gene on the invasion and metastasis of colon cancerDuowei Wang, Bikash Rai, Feng Qi, Tong Liu, Jinmiao Wang, Xiaodong Wang, Bozhao Ma · 2017 · Oncology Reports
- Formation, interpretation, and regulation of the Drosophila Dorsal/NF-κB gradientAllison E. Schloop, Prasad U. Bandodkar, Gregory T. Reeves · 2019 · Current topics in developmental biology/Current Topics in Developmental Biology
- Neofunctionalization of Toll Signaling in Insects: From Immunity to Dorsoventral PatterningSiegfried Roth · 2023 · Annual Review of Cell and Developmental Biology
- Emerging Role of Mechanical Forces in Cell Fate AcquisitionYanina D. Álvarez, Michael Smutny · 2022 · Frontiers in Cell and Developmental Biology
- Dynamic patterning by morphogens illuminated by cis-regulatory studiesJihyun Irizarry, Angelike Stathopoulos · 2021 · Development
- Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemiaMd Almamun, Olha Kholod, Alexei J. Stuckel, Benjamin T Levinson, Nathan T. Johnson, Gerald L. Arthur, J. Wade Davis, Kristen H. Taylor · 2017 · Leukemia & lymphoma/Leukemia and lymphoma
- TRAP-rc, Translating Ribosome Affinity Purification from Rare Cell Populations of Drosophila EmbryosBenjamin Bertin, Yoan Renaud, Rajaguru Aradhya, Krzysztof Jagla, Guillaume Junion · 2015 · Journal of Visualized Experiments
- Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logicPeter A. Combs, Hunter B. Fraser · 2018 · PLoS Genetics
- Dynamic Interactions of Transcription Factors and Enhancer Reprogramming in Cancer ProgressionEmily Kate Zboril, Hannah Yoo, Lizhen Chen, Zhijie Liu · 2021 · Frontiers in Oncology
- The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal GradientMichael D. O’Connell, Gregory T. Reeves · 2015 · PLoS Computational Biology
- Development of Tribolium castaneumSiegfried Roth, Volker Hartenstein · 2008 · Development Genes and Evolution
- Coacting enhancers can have complementary functions within gene regulatory networks and promote canalizationLeslie Dunipace, Zsuzsa Ákos, Angelike Stathopoulos · 2019 · PLoS Genetics
- Inference of dynamic spatial GRN models with multi-GPU evolutionary computationReza Mousavi, Sri Harsha Konuru, Daniel Lobo · 2021 · Briefings in Bioinformatics
- A Systematic Phenotypic Screen of F-box Genes Through a Tissue-specific RNAi-based Approach in DrosophilaWen Dui, Wei Lü, Jun Ma, Renjie Jiao · 2012 · Journal of genetics and genomics/Journal of Genetics and Genomics
- A directional recombination cloning system for restriction- and ligation-free construction of GFP, DsRed, and lacZ transgenic Drosophila reportersChristina I. Swanson, Trish Hinrichs, Lisa A. Johnson, Ying Zhao, Scott Barolo · 2007 · Gene
- Analyzing Transcription Factor Occupancy During Embryo Development Using ChIP-seqYad Ghavi-Helm, Eileen E. M. Furlong · 2011 · Methods in molecular biology
- The Role of Chromatin Accessibility in cis-Regulatory EvolutionPei-Chen Peng, Pierre Khoueiry, Charles Girardot, James P. Reddington, David A Garfield, Eileen E. M. Furlong, Saurabh Sinha · 2019 · Genome Biology and Evolution
- Profiling a Caenorhabditis elegans behavioral parametric dataset with a supervised K-means clustering algorithm identifies genetic networks regulating locomotionShijie Zhang, Wei Jin, Ying Huang, Wei Su, Jiong Yang, Zhaoyang Feng · 2011 · Journal of Neuroscience Methods
- FGF signaling acts on different levels of mesoderm development within SpiraliaCarmen Andrikou, Andreas Hejnol · 2021 · Development
- NK-2 Class Homeodomain ProteinsDavid A. Elliott, Edwin Philip Kirk, Daniel Schaft, Richard Paul Harvey · 2010 · Elsevier eBooks
- Stepwise Progression of Embryonic PatterningJeremy E. Sandler, Angelike Stathopoulos · 2016 · Trends in Genetics
- Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expressionThomas Butts, Peter W. H. Holland, David E. K. Ferrier · 2010 · Proceedings of the Royal Society B Biological Sciences
- The bHLH Transcription Factor Hand Regulates the Expression of Genes Critical to Heart and Muscle Function in Drosophila melanogasterBenjamin Hallier, Julia Hoffmann, Thomas Roeder, Markus Tögel, Heiko Meyer, Achim Paululat · 2015 · PLoS ONE
- Systems biology of embryogenesisLucas B. Edelman, Sriram Chandrasekaran, Nathan D. Price · 2009 · Reproduction Fertility and Development
- Erroneous attribution of relevant transcription factor binding sites despite successful prediction of cis-regulatory modulesMarc S. Halfon, Qianqian Zhu, Elizabeth R Brennan, Yiyun Zhou · 2011 · BMC Genomics
- Interleukin-31 Receptor α Is Required for Basal-Like Breast Cancer ProgressionYanling He, Xinyuan Zhang, Weijun Pan, Fang Tai, Li Liang, Jian Shi · 2020 · Frontiers in Oncology
- Identification of singles bar as a direct transcriptional target of Drosophila Myocyte enhancer factor-2 and a regulator of adult myoblast fusionTonya M. Brunetti, Brayon J. Fremin, Richard M. Cripps · 2015 · Developmental Biology
- Evolutionary soft co-clustering: formulations, algorithms, and applicationsWenlu Zhang, Rongjian Li, Daming Feng, Andrey N. Chernikov, Nikos P. Chrisochoides, Christopher J. Osgood, Shuiwang Ji · 2014 · Data Mining and Knowledge Discovery
- Global analysis of dorsoventral patterning in the wasp Nasonia reveals extensive incorporation of novelty in a regulatory networkDaniel Pers, Thomas Buchta, Orhan Özüak, Selma Wolff, Jessica Pietsch, Mohammad Bilal Memon, Siegfried Roth, Jeremy Lynch · 2016 · BMC Biology
- CDX4 regulates the progression of neural maturation in the spinal cordPiyush K. Joshi, Andrew J. Darr, Isaac Skromne · 2019 · Developmental Biology
- The Hox Transcription Factor Ubx Ensures Somatic Myogenesis by Suppressing the Mesodermal Master Regulator TwistKatrin Domsch, Julia Schröder, Matthias Janeschik, Christoph Schaub, Ingrid Lohmann · 2021 · Cell Reports
- Gene Regulatory NetworksMartha L. Bulyk, Albertha J.M. Walhout · 2012 · Elsevier eBooks
- Identification of cis-regulatory modules encoding temporal dynamics during developmentDelphine Potier, Denis Seyres, Céline Guichard, Magali Torres, Stein Aerts, Carl Herrmann, Laurent Perrin · 2014 · BMC Genomics
- Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancersJoseph C. Pearson, Daniel J. McKay, Jason D. Lieb, Stephen T. Crews · 2016 · Development
- Experimental advances in the characterization of metazoan gene regulatory networksBart Deplancke · 2008 · Briefings in Functional Genomics and Proteomics
- Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processesZheng Kuang, Zhicheng Ji, Jef D. Boeke, Hongkai Ji · 2017 · Nucleic Acids Research
- Intrinsic control of muscle attachment sites matchingAlexandre Carayon, Laetitia Bataillé, Gaëlle Lebreton, Laurence Dubois, Aurore Pelletier, Yannick Carrier, Antoine Wystrach, Alain Vincent, Jean‐Louis Frendo · 2020 · eLife
- Evolution of Somite Compartmentalization: A View From XenopusBruno Della Gaspera, Laure Weill, Christophe Chanoine · 2022 · Frontiers in Cell and Developmental Biology
- Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory NetworksMathilde de Taffin, Yannick Carrier, Laurence Dubois, Laetitia Bataillé, Anaïs Painset, Stéphanie Le Gras, Bernard Jost, Michèle Crozatier, Alain Vincent · 2015 · PLoS ONE
- Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor ModelsIulian Pruteanu-Malinici, Daniel Mace, Uwe Ohler · 2011 · PLoS Computational Biology
- [Overexpression of histone deacetylase 11 suppresses basal-like breast cancer cell invasion and metastasis].Yi Zhang, Luo Wenwen, Kun Wang, Shi Jian · 2019 · Europe PMC (PubMed Central)