Edinburgh Research Explorer

Dr Anagha Joshi

(Former employee or visitor)

  1. 2018
  2. Insights into mammalian transcription control by systematic analysis of ChIP sequencing data

    Devailly, G. & Joshi, A., 20 Nov 2018, In : BMC Bioinformatics. 19, Suppl 14, p. 409

    Research output: Contribution to journalArticle

  3. Causal Transcription Regulatory Network Inference Using Enhancer Activity as a Causal Anchor

    Vipin, D., Wang, L., Devailly, G., Michoel, T. & Joshi, A., 15 Nov 2018, In : International Journal of Molecular Sciences. 19, 11

    Research output: Contribution to journalArticle

  4. LIF-dependent survival of embryonic stem cells is regulated by a novel palmitoylated Gab1 signalling protein

    Sutherland, L., Ruhe, M., Gattegno-Ho, D., Mann, K., Greaves, J., Koscielniak, M., Meek, S., Lu, Z., Waterfall, M., Taylor, R., Tsakiridis, A., Brown, H., Maciver, S., Joshi, A., Clinton, M., Chamberlain, L. H., Smith, A. & Burdon, T., Sep 2018, In : Journal of Cell Science. 131, 18, 222257.

    Research output: Contribution to journalArticle

  5. Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells

    Mantsoki, A., Devailly, G. & Joshi, A., 20 Feb 2018, In : BMC Developmental Biology. 18, 1, p. 2

    Research output: Contribution to journalArticle

  6. 2017
  7. Delineating biological and technical variance in single cell expression data

    Arzalluz-Luque, Á., Devailly, G., Mantsoki, A. & Joshi, A., Sep 2017, In : International Journal of Biochemistry and Cell Biology. 90, p. 161-166

    Research output: Contribution to journalArticle

  8. Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs

    Reyes, P. F. L., Michoel, T., Joshi, A. & Devailly, G., 26 Aug 2017, In : Computational and Structural Biotechnology Journal. 15, p. 425-432 8 p.

    Research output: Contribution to journalArticle

  9. Transcription Control in Human Cell Types by Systematic Analysis of ChIP Sequencing Data from the ENCODE

    Devailly, G. & Joshi, A., 1 Apr 2017, Lecture Notes in Computer Science. Springer, Vol. 10209. p. 315-324 Chapter 29. (Bioinformatics and Biomedical Engineering; vol. 10209).

    Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

  10. A Transcriptional switch point during hematopoietic stem and progenitor cell ontogeny

    Sugiyama, D., Joshi, A., Kulkeaw, K., Tan, K. S., Yokoo-Inoue, T., Mizuochi-Yanagi, C., Yasuda, K., Doi, A., Iino, T., Itoh, M., Nagao-Sato, S., Tani, K., Akashi, K., Hayashizaki, Y., Suzuki, H., Kawaji, H., Carninci, P. & Forrest, A. R. R., 24 Jan 2017, In : Stem Cells and Development. 26, 5, p. 314-327

    Research output: Contribution to journalArticle

  11. Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types

    Giotti, B., Joshi, A. & Freeman, T. C., 5 Jan 2017, In : BMC Genomics. 18, 1, p. 30

    Research output: Contribution to journalArticle

  12. 2016
  13. Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data

    Devailly, G., Mantsoki, A. & Joshi, A., 1 Nov 2016, In : Bioinformatics. 32, 21, p. 3354-3356

    Research output: Contribution to journalArticle

  14. Gene expression variability in mammalian embryonic stem cells using single cell RNA-seq data

    Mantsoki, A., Devailly, G. & Joshi, A., Aug 2016, In : Computational Biology and Chemistry. 63, p. 52-61

    Research output: Contribution to journalArticle

  15. Long-lived Self-renewing Bone Marrow-derived Macrophages Displace Embryo-derived Cells to Inhabit Adult Serous Cavities

    Bain, C., Hawley, C. A., Garner, H., Scott, C. L., Schridde, A., Steers, N., Mack, M., Joshi, A., Guilliams, M., Geissmann, F., Mowat, A. M. & Jenkins, S., 13 Jun 2016, In : Nature Communications. 7, ncomms11852.

    Research output: Contribution to journalArticle

  16. Corrigendum: CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells

    Mantsoki, A., Devailly, G. & Joshi, A., 23 May 2016, In : Scientific Reports. 6, p. 25682

    Research output: Contribution to journalComment/debate

  17. Functional transcription factor target discovery via compendia of binding and expression profiles

    Banks, C. J., Joshi, A. & Michoel, T., 2016, In : Scientific Reports. 6, 10 p., 20649.

    Research output: Contribution to journalArticle

  18. 2015
  19. Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource

    Devailly, G., Mantsoki, A., Michoel, T. & Joshi, A., 21 Dec 2015, In : FEBS Letters. 589, 24, part B, p. 3866–3870

    Research output: Contribution to journalArticle

  20. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

    Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R., FANTOM consortium & Huminiecki, L., 18 Dec 2015, In : PLoS Biology. 13, 12, e1002315.

    Research output: Contribution to journalArticle

  21. CpG island erosion, polycomb occupancy and sequence motif enrichment at bivalent promoters in mammalian embryonic stem cells

    Mantsoki, A., Devailly, G. & Joshi, A., 20 Nov 2015, In : Scientific Reports. 5, 16791.

    Research output: Contribution to journalArticle

  22. Deducing the stage of origin of Wilms tumours from a developmental series of Wt1 mutants

    Berry, R. L., Ozdemir, D. D., Aronow, B., Lindstrom, N., Dudnakova, T., Thornburn, A., Perry, P., Baldock, R., Armit, C., Joshi, A., Jeanpierre, C., Shan, J., Vainio, S., Baily, J., Brownstein, D., Davies, J., Hastie, N. D. & Hohenstein, P., Aug 2015, In : Disease Models & Mechanisms. 8, 8, p. 903-17 15 p.

    Research output: Contribution to journalArticle

  23. Comparative Analysis of Bivalent Domains in Mammalian Embryonic Stem Cells

    Mantsoki, A. & Joshi, A., 15 Apr 2015, Bioinformatics and Biomedical Engineering. Springer International Publishing, p. 391-402

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

  24. Multi-species network inference improves gene regulatory network reconstruction for early embryonic development in Drosophila

    Joshi, A., Beck, Y. & Michoel, T., Apr 2015, In : Journal of Computational Biology. 22, 4, p. 253-65 13 p.

    Research output: Contribution to journalArticle

  25. Technical advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

    Joshi, A., Pooley, C., Freeman, T. C., Lennartsson, A., Babina, M., Schmidl, C., Geijtenbeek, T., Michoel, T., Severin, J., Itoh, M., Lassmann, T., Kawaji, H., Hayashizaki, Y., Carninci, P., Forrest, A. R. R., Rehli, M., Hume, D. A. & the FANTOM Consortium, 25 Feb 2015, In : Journal of Leukocyte Biology. 97, 5, p. 985-995

    Research output: Contribution to journalArticle

  26. 2014
  27. Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms

    Joshi, A. & Gottgens, B., 18 Aug 2014, In : Molecular BioSystems. 10, 11, p. 2935-2941

    Research output: Contribution to journalArticle

  28. TRES predicts transcription control in embryonic stem cells

    Pooley, C., Ruau, D., Lombard, P., Gottgens, B. & Joshi, A., 23 Jun 2014, In : Bioinformatics. 30, 20, p. 2983-2985

    Research output: Contribution to journalArticle

  29. Dysregulation of ubiquitin homeostasis and beta-catenin signaling promote spinal muscular atrophy

    Wishart, T. M., Mutsaers, C. A., Riessland, M., Reimer, M. M., Hunter, G., Hannam, M. L., Eaton, S. L., Fuller, H. R., Roche, S. L., Somers, E., Morse, R., Young, P. J., Lamont, D. J., Hammerschmidt, M., Joshi, A., Hohenstein, P., Morris, G. E., Parson, S. H., Skehel, P. A., Becker, T. & 4 othersRobinson, I. M., Becker, C. G., Wirth, B. & Gillingwater, T. H., Apr 2014, In : Journal of Clinical Investigation. 124, 4, p. 1821-1834

    Research output: Contribution to journalArticle

  30. A promoter-level mammalian expression atlas

    Forrest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., de Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jorgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U. & 32 othersMedvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Fisher, M. E., Ha, T. J., Joshi, A., Meynert, A., Prendergast, J. G. D., Summers, K. M., Freeman, T. C., Taylor, M. S., Hume, D. A., FANTOM Consortium & RIKEN PMI CLST DGT, 27 Mar 2014, In : Nature. 507, 7493, p. 462-+ 22 p.

    Research output: Contribution to journalArticle

  31. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes

    Hasegawa, Y., Tang, D., Takahashi, N., Hayashizaki, Y., Forrest, A. R. R., Suzuki, H., FANTOM Consortium & Joshi, A., 2014, In : Scientific Reports. 4, 5228.

    Research output: Contribution to journalArticle

  32. 2013
  33. HOX-mediated LMO2 expression in embryonic mesoderm is recapitulated in acute leukaemias

    Calero-Nieto, F. J., Joshi, A., Bonadies, N., Kinston, S., Chan, W-I., Gudgin, E., Pridans, C., Landry, J-R., Kikuchi, J., Huntly, B. J. & Gottgens, B., 27 May 2013, In : Oncogene.

    Research output: Contribution to journalArticle

  34. Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

    Moignard, V., Macaulay, I. C., Swiers, G., Buettner, F., Schütte, J., Calero-Nieto, F. J., Kinston, S., Joshi, A., Hannah, R., Theis, F. J., Jacobsen, S. E., de Bruijn, M. F. & Göttgens, B., Apr 2013, In : Nature Cell Biology. 15, 4, p. 363-72 10 p.

    Research output: Contribution to journalArticle

  35. Cognition and amyloid load in Alzheimer disease imaged with florbetapir F 18 (AV-45) positron emission tomography

    Rosenberg, P. B., Wong, D. F., Edell, S. L., Ross, J. S., Joshi, A. D., Brašić, J. R., Zhou, Y., Raymont, V., Kumar, A., Ravert, H. T., Dannals, R. F., Pontecorvo, M. J., Skovronsky, D. M. & Lyketsos, C. G., Mar 2013, In : American Journal of Geriatric Psychiatry. 21, 3, p. 272-278 7 p.

    Research output: Contribution to journalArticle

  36. Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level

    Swiers, G., Baumann, C., O'Rourke, J., Giannoulatou, E., Taylor, S., Joshi, A., Moignard, V., Pina, C., Bee, T., Kokkaliaris, K. D., Yoshimoto, M., Yoder, M. C., Frampton, J., Schroeder, T., Enver, T., Göttgens, B. & de Bruijn, M. F. T. R., 2013, In : Nature Communications. 4, p. 2924

    Research output: Contribution to journalArticle

  37. Exploring the abomasal lymph node transcriptome for genes associated with resistance to the sheep nematode Teladorsagia circumcincta

    Gossner, A., Wilkie, H., Joshi, A. & Hopkins, J., 2013, In : Veterinary Research. 44, 13 p., 68.

    Research output: Contribution to journalArticle

  38. Gene set control analysis predicts hematopoietic control mechanisms from genome-wide transcription factor binding data

    Joshi, A., Hannah, R., Diamanti, E. & Göttgens, B., 2013, In : Experimental Hematology. E-pub 4 December

    Research output: Contribution to journalArticle

  39. 2012
  40. ESRRB Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

    Martello, G., Sugimoto, T., Diamanti, E., Joshi, A., Hannah, R., Ohtsuka, S., Goettgens, B., Niwa, H. & Smith, A., 5 Oct 2012, In : Cell Stem Cell. 11, 4, p. 491-504 14 p.

    Research output: Contribution to journalArticle

  41. The transcriptional programme controlled by Runx1 during early embryonic blood development

    Tanaka, Y., Joshi, A., Wilson, N. K., Kinston, S., Nishikawa, S. & Goettgens, B., 15 Jun 2012, In : Developmental Biology. 366, 2, p. 404-419 16 p.

    Research output: Contribution to journalArticle

  42. A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses

    Mutasa-Goettgens, E. S., Joshi, A., Holmes, H. F., Hedden, P. & Goettgens, B., 19 Mar 2012, In : BMC Genomics. 13, 1, p. - 18 p., 99.

    Research output: Contribution to journalArticle

  43. Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals

    Joshi, A., Beck, Y. & Michoel, T., 2012, In : Febs Journal. 279, 18, p. 3501-3512 12 p.

    Research output: Contribution to journalArticle

  44. 2011
  45. Structural and functional organization of RNA regulons in the post-transcriptional regulatory network of yeast

    Joshi, A., Van de Peer, Y. & Michoel, T., Nov 2011, In : Nucleic Acids Research. 39, 21, p. 9108-9117 10 p.

    Research output: Contribution to journalArticle

  46. Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators

    Tijssen, M. R., Cvejic, A., Joshi, A., Hannah, R. L., Ferreira, R., Forrai, A., Bellissimo, D. C., Oram, S. H., Smethurst, P. A., Wilson, N. K., Wang, X., Ottersbach, K., Stemple, D. L., Green, A. R., Ouwehand, W. H. & Goettgens, B., 17 May 2011, In : Developmental Cell. 20, 5, p. 597-609 13 p.

    Research output: Contribution to journalArticle

  47. Maximum parsimony analysis of gene expression profiles permits the reconstruction of developmental cell lineage trees

    Joshi, A. & Goettgens, B., 15 May 2011, In : Developmental Biology. 353, 2, p. 440-447 8 p.

    Research output: Contribution to journalArticle

  48. A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms

    Hannah, R., Joshi, A., Wilson, N. K., Kinston, S. & Goettgens, B., May 2011, In : Experimental Hematology. 39, 5, p. 531-541 11 p.

    Research output: Contribution to journalArticle

  49. Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks

    Michoel, T., Joshi, A., Nachtergaele, B. & Van de Peer, Y., 2011, In : Molecular BioSystems. 7, 10, p. 2769-2778 10 p.

    Research output: Contribution to journalArticle

  50. The transcriptional coactivator Cbp regulates self-renewal and differentiation in adult hematopoietic stem cells.

    Chan, WI., Hannah, RL., Dawson, MA., Pridans, C., Foster, D., Joshi, A., Gottgens, B., Van Deursen, JM. & Huntly, BJP., 2011, In : Molecular and Cellular Biology. 31, 24, p. 5046-5060

    Research output: Contribution to journalArticle

  51. 2010
  52. Module Network Inference from a Cancer Gene Expression Data Set Identifies MicroRNA Regulated Modules

    Bonnet, E., Tatari, M., Joshi, A., Michoel, T., Marchal, K., Berx, G. & de Peer, Y. V., 14 Apr 2010, In : PLoS ONE. 5, 4, p. 1-10 10 p., e10162.

    Research output: Contribution to journalArticle

  53. Software. Characterizing regulatory path motifs in integrated networks using perturbational data

    Joshi, A., Van Parys, T., Van de Peer, Y. & Michoel, T., 2010, In : Genome Biology. 11, 3, p. 1-14 14 p., R32.

    Research output: Contribution to journalArticle

  54. Towards system level modeling of functional modules and regulatory pathways using genome-scale data

    Michoel, T., Joshi, A., Bonnet, E., Vermeirssen, V. & Van de Peer, Y., 2010, Seventh International Workshop on Computational Systems Biology, WCSB 2010, June 16–18, 2010, Luxembourg. Nykter, M., Ruusuvuori, P., Carlberg, C. & Yli-Harja, O. (eds.). Tampere: Tampere International Center for Signal Processing, p. 71-74 (TICSP Series; no. 51).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  55. 2009
  56. Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

    Michoel, T., De Smet, R., Joshi, A., de Peer, Y. V. & Marchal, K., 7 May 2009, In : BMC Systems Biology. 3, 49, p. - 13 p.

    Research output: Contribution to journalArticle

  57. Module networks revisited: computational assessment and prioritization of model predictions

    Joshi, A., De Smet, R., Marchal, K., Van de Peer, Y. & Michoel, T., 15 Feb 2009, In : Bioinformatics. 25, 4, p. 490-496 7 p.

    Research output: Contribution to journalArticle

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