Current Pre-prints in BioRxiv (lab members in bold) 

MLL3/4 Prevents Stem Cell Hyperplasia And Controls Differentiation Programs In A Planarian Cancer Stem Cell Model. Yuliana Mihaylova, Damian Kao, Samantha Hughes, Alvina Lai, Farah Jaber-Hijazi, Nobuyoshi Kosaka, Prasad Abnave, Aziz Aboobaker

doi: https://doi.org/10.1101/126540.

 

Epigenetic analyses of the planarian genome reveals conservation of bivalent promoters in animal stem cells. Damian Kao, Yuliana Mihaylova, Samantha Hughes, Alvina Lai, Aziz Aboobaker

doi: https://doi.org/10.1101/122135.

 

A platform for efficient transgenesis in Macrostomum lignano, a flatworm model organism for stem cell research. Jakub Wudarski, Daniil Simanov, Kirill Ustyantsev, Katrien de Mulder, Margriet Grelling, Magda Grudniewska, Frank Beltman, Lisa Glazenburg, Turan Demircan, Julia Wunderer, Weihong Qi, Dita B. Vizoso, Philipp M. Weissert, Daniel Olivieri, Stijn Mouton, Victor Guryev, Aziz Aboobaker, Lukas Scharer, Peter Ladurner, Eugene Berezikov

doi: https://doi.org/10.1101/151654

 

Published Papers (lab members in bold)

 

  • An X-ray shielded irradiation assay reveals EMT transcription factors control pluripotent adult stem cell migration in vivo in planarians. Prasad Abnave, Ellen Aboukhatwa, Nobuyoshi Kosaka, James Thompson, Mark Hill, and Aziz Aboobaker, Development, in press

 

  • Secrets from immortal worms: What can we learn about biological ageing from the planarian model system? Sounak Sahu, Anish Dattani and Aziz Aboobaker, Seminars in Cell and Developmental Biology, in press

 

  • Organ specific gene expression in the regenerating tail of Macrostomum lignano. Birgit Lengerer, Julia Wunderer, Robert Pjeta, Giada Carta, Damian Kao, Aziz Aboobaker, Christian Beisel, Eugene Berezikov, Willi Salvenmoser, Peter Ladurner. Developmental Biology, in press. https://doi.org/10.1016/j.ydbio.2017.07.021

 

  • Alvina Lai, Nobuyoshi Kosaka, Prasad Abnave, Sounak Sahu and Aziz Aboobaker.The Abrogation Of Condensin Function Provides Independent Evidence For Defining The Self-Renewing Population Of Pluripotent Stem Cells  Developmental Biology, in press. doi: https://doi.org/10.1016/j.ydbio.2017.07.023

 

  • Bridge KS, Shah KM, Li Y, Foxler DE, Wong SCK, Miller DC, Davidson KM, Foster JG, Rose R, Hodgkinson MR, Ribeiro PS, AboobakerAA, Yashiro K, Wang X, Graves PR, Plevin MJ, Lagos D, Sharp TV. Argonaute Utilization for miRNA Silencing Is Determined by Phosphorylation-Dependent Recruitment of LIM-Domain-Containing Proteins. Cell Rep. 2017 Jul 5;20(1):173-187. doi: 10.1016/j.celrep.2017.06.027. PMID: 28683311

 

  • Lai AG, Aboobaker AA. Comparative genomic analysis of innate immunity reveals novel and conserved components in crustacean food crop species. BMC Genomics. 2017 May 18;18(1):389. doi: 10.1186/s12864-017-3769-4. PubMed PMID: 28521727; PubMed Central PMCID: PMC5437397.

 

  • Lai AG, Pouchkina-Stantcheva N, Di Donfrancesco A, Kildisiute G, Sahu S, Aboobaker AA. The protein subunit of telomerase displays patterns of dynamic evolution and conservation across different metazoan taxa. BMC Evol Biol. 2017 Apr 26;17(1):107. doi: 10.1186/s12862-017-0949-4. PubMed PMID: 28441946; PubMed Central PMCID: PMC5405514.

 

  • Valenzano DR, Aboobaker A, Seluanov A, Gorbunova V. Non-canonical aging model systems and why we need them. EMBO J. 2017 Apr 13;36(8):959-963. doi:10.15252/embj.201796837. Epub 2017 Mar 20. PubMed PMID: 28320740; PubMed Central PMCID: PMC5391153.

 

  • Kao D, Lai AG, Stamataki E, Rosic S, Konstantinides N, Jarvis E, Di Donfrancesco A, Pouchkina-Stancheva N, Semon M, Grillo M, Bruce H, Kumar S, Siwanowicz I, Le A, Lemire A, Eisen MB, Extavour C, Browne WE, Wolff C, Averof M, Patel NH, Sarkies P, Pavlopoulos A, Aboobaker A. The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion. Elife. 2016 Nov 16;5. pii: e20062. doi: 10.7554/eLife.20062. PubMed PMID: 27849518; PubMed Central PMCID: PMC5111886.

 

  • Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker AA, Blaxter M. No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini. Proc Natl Acad Sci U S A. 2016 May 3;113(18):5053-8. doi: 10.1073/pnas.1600338113. Epub 2016 Mar 24. PubMed PMID: 27035985; PubMed Central PMCID: PMC4983863.

 

  • Mangel M, Bonsall MB, Aboobaker A. Feedback control in planarian stem cell systems. BMC Syst Biol. 2016 Feb 13;10:17. doi: 10.1186/s12918-016-0261-8. PubMed PMID: 26873593; PubMed Central PMCID: PMC4752765.

 

  • Tejada-Romero B, Carter JM, Mihaylova Y, Neumann B, Aboobaker AA. JNK signalling is necessary for a Wnt- and stem cell-dependent regeneration programme. Development. 2015 Jul 15;142(14):2413-24. doi: 10.1242/dev.115139. Epub 2015 Jun 10. PubMed PMID: 26062938; PubMed Central PMCID: PMC4510858.

 

  • Moreton J, Malla S, Aboobaker AA, Tarlinton RE, Emes RD. Characterisation of the horse transcriptome from immunologically active tissues. PeerJ. 2014 May 6;2:e382. doi: 10.7717/peerj.382. eCollection 2014. PubMed PMID: 24860704; PubMed Central PMCID: PMC4017814.

 

  • Solana J, Gamberi C, Mihaylova Y, Grosswendt S, Chen C, Lasko P, Rajewsky N, Aboobaker AA. The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation. PLoS Genet. 2013;9(12):e1004003. doi: 10.1371/journal.pgen.1004003. Epub 2013 Dec 19. PubMed PMID: 24367277; PubMed Central PMCID: PMC3868585.

 

  • Kao D, Felix D, Aboobaker A. The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics. 2013 Nov 16;14:797. doi: 10.1186/1471-2164-14-797. PubMed PMID: 24238224; PubMed Central PMCID: PMC4046745.

 

  • Jaber-Hijazi F, Lo PJ, Mihaylova Y, Foster JM, Benner JS, Tejada Romero B, Chen C, Malla S, Solana J, Ruzov A, Aziz Aboobaker. Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation. Dev Biol. 2013 Dec 1;384(1):141-53. doi: 10.1016/j.ydbio.2013.09.020. Epub 2013 Sep 21. PubMed PMID: 24063805; PubMed Central PMCID: PMC3824064

 

  • Liu MM, Davey JW, Banerjee R, Han J, Yang F, Aboobaker A, Blaxter ML, Davison A. Fine mapping of the pond snail left-right asymmetry (chirality) locus using RAD-Seq and fibre-FISH. PLoS One. 2013 Aug 12;8(8):e71067. doi: 10.1371/journal.pone.0071067. eCollection 2013. PubMed PMID: 23951082; PubMed Central PMCID: PMC3741322.

 

  • Ketley A, Warren A, Holmes E, Gering M, Aboobaker AA, Brook JD. The miR-30 microRNA family targets smoothened to regulate hedgehog signalling in zebrafish early muscle development. PLoS One. 2013 Jun 5;8(6):e65170. doi: 10.1371/journal.pone.0065170. Print 2013. Erratum in: PLoS One. 2013;8(11). doi:10.1371/annotation/4e68e9f8-74c0-4c45-828f-7d51786c13e2. PubMed PMID: 23755189; PubMed Central PMCID: PMC3673911.

 

  • Mihaylova Y, Aboobaker AA. What is it about ‘eye of newt’? Genome Biol. 2013 Feb 20;14(2):106. doi: 10.1186/gb-2013-14-2-106. PubMed PMID: 23425551; PubMed Central PMCID: PMC3663091.

 

  • Blassberg RA, Felix DA, Tejada-Romero B, Aboobaker AA. PBX/extradenticle is required to re-establish axial structures and polarity during planarian regeneration. Development. 2013 Feb;140(4):730-9. doi: 10.1242/dev.082982. Epub 2013 Jan 14. PubMed PMID: 23318635; PubMed Central PMCID: PMC3557773.

 

  • Romero BT, Evans DJ, Aboobaker AA. FACS analysis of the planarian stem cell compartment as a tool to understand regenerative mechanisms. Methods Mol Biol. 2012;916:167-79. doi: 10.1007/978-1-61779-980-8_13. PubMed PMID: 22914940.

 

  • Delmas S, Pullan ST, Gaddipati S, Kokolski M, Malla S, Blythe MJ, Ibbett R, Campbell M, Liddell S, Aboobaker A, Tucker GA, Archer DB. Uncovering the genome-wide transcriptional responses of the filamentous fungus Aspergillus niger to lignocellulose using RNA sequencing. PLoS Genet. 2012;8(8):e1002875. doi: 10.1371/journal.pgen.1002875. Epub 2012 Aug 9. PubMed PMID: 22912594; PubMed Central PMCID: PMC3415456.

 

  • Brown K, Moreton J, Malla S, Aboobaker AA, Emes RD, Tarlinton RE. Characterisation of retroviruses in the horse genome and their transcriptional activity via transcriptome sequencing. Virology. 2012 Nov 10;433(1):55-63. doi: 10.1016/j.virol.2012.07.010. Epub 2012 Aug 4. PubMed PMID: 22868041.

 

  • Aboobaker AA, Kao D. A lack of commitment for over 500 million years: conserved animal stem cell pluripotency. EMBO J. 2012 Jun 13;31(12):2747-9. doi: 1038/emboj.2012.131. Epub 2012 May 4. PubMed PMID: 22562151; PubMed Central PMCID: PMC3380215.

 

  • González-Estévez C, Felix DA, Smith MD, Paps J, Morley SJ, James V, Sharp TV, Aboobaker AA. SMG-1 and mTORC1 act antagonistically to regulate response to injury and growth in planarians. PLoS Genet. 2012;8(3):e1002619. doi: 10.1371/journal.pgen.1002619. Epub 2012 Mar 29. PubMed PMID: 22479207; PubMed Central PMCID: PMC3315482.

 

  • Blythe MJ, Malla S, Everall R, Shih YH, Lemay V, Moreton J, Wilson R, Aboobaker AA. High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies. PLoS One. 2012;7(3):e33784. doi: 10.1371/journal.pone.0033784. Epub 2012 Mar 20. PubMed PMID: 22448274; PubMed Central PMCID: PMC3309017.

 

  • Solana J, Kao D, Mihaylova Y, Jaber-Hijazi F, Malla S, Wilson R, Aboobaker A. Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach. Genome Biol. 2012;13(3):R19. doi: 10.1186/gb-2012-13-3-r19. PubMed PMID: 22439894; PubMed Central PMCID: PMC3439970.

 

  • Tan TC, Rahman R, Jaber-Hijazi F, Felix DA, Chen C, Louis EJ, Aboobaker A. Telomere maintenance and telomerase activity are differentially regulated in asexual and sexual worms. Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4209-14. doi: 10.1073/pnas.1118885109. Epub 2012 Feb 27. PubMed PMID: 22371573; PubMed Central PMCID: PMC3306686.

 

  • González-Estévez C, Felix DA, Rodríguez-Esteban G, Aboobaker AA. Decreased neoblast progeny and increased cell death during starvation-induced planarian degrowth. Int J Dev Biol. 2012;56(1-3):83-91. doi: 10.1387/ijdb.113452cg. PubMed PMID: 22252539.

 

  • Evans DJ, Owlarn S, Tejada Romero B, Chen C, Aboobaker AA. Combining classical and molecular approaches elaborates on the complexity of mechanisms underpinning anterior regeneration. PLoS One. 2011;6(11):e27927. doi: 10.1371/journal.pone.0027927. Epub 2011 Nov 18. PubMed PMID: 22125640; PubMed Central PMCID: PMC3220713.

 

  • Iglesias M, Almuedo-Castillo M, Aboobaker AA, Saló E. Early planarian brain regeneration is independent of blastema polarity mediated by the Wnt/β-catenin pathway. Dev Biol. 2011 Oct 1;358(1):68-78. doi: 10.1016/j.ydbio.2011.07.013. Epub 2011 Jul 20. PubMed PMID: 21806978.

 

  • Aboobaker AA. Planarian stem cells: a simple paradigm for regeneration. Trends Cell Biol. 2011 May;21(5):304-11. doi: 10.1016/j.tcb.2011.01.005. Epub 2011 Feb 25. Review. PubMed PMID: 21353778.

 

  • Blythe MJ, Kao D, Malla S, Rowsell J, Wilson R, Evans D, Jowett J, Hall A, Lemay V, Lam S, Aboobaker AA. A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One. 2010 Dec 14;5(12):e15617. doi: 10.1371/journal.pone.0015617. PubMed PMID: 21179477; PubMed Central PMCID: PMC3001875.

 

  • Aboobaker A, Blaxter M. The nematode story: Hox gene loss and rapid evolution. Adv Exp Med Biol. 2010;689:101-10. PubMed PMID: 20795325.

 

  • Felix DA, Aboobaker AA. The TALE class homeobox gene Smed-prep defines the anterior compartment for head regeneration. PLoS Genet. 2010 Apr 22;6(4):e1000915. doi: 10.1371/journal.pgen.1000915. PubMed PMID: 20422023; PubMed Central PMCID: PMC2858555.

 

  • González-Estévez C, Arseni V, Thambyrajah RS, Felix DA, Aboobaker AA. Diverse miRNA spatial expression patterns suggest important roles in homeostasis and regeneration in planarians. Int J Dev Biol. 2009;53(4):493-505. doi:10.1387/ijdb.082825cg. PubMed PMID: 19247960.

 

  • Pleass RJ, Aboobaker AA, Schmitt AO. Piggybacking schistosome invasion: similarities are only skin deep. Trends Parasitol. 2008 Apr;24(4):153-6. doi: 10.1016/j.pt.2008.01.003. Epub 2008 Mar 7. PubMed PMID: 18329340.

 

  • González-Estévez C, Felix DA, Aboobaker AA, Saló E. Gtdap-1 and the role of autophagy during planarian regeneration and starvation. Autophagy. 2007 Nov-Dec;3(6):640-2. Epub 2007 Aug 24. PubMed PMID: 17786038.

 

  • González-Estévez C, Felix DA, Aboobaker AA, Saló E. Gtdap-1 promotes autophagy and is required for planarian remodeling during regeneration and starvation. Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13373-8. Epub 2007 Aug 8. PubMed PMID: 17686979; PubMed Central PMCID: PMC1948951.

 

  • Prochnik SE, Rokhsar DS, Aboobaker AA. Evidence for a microRNA expansion in the bilaterian ancestor. Dev Genes Evol. 2007 Jan;217(1):73-7. Epub 2006 Nov 14. PubMed PMID: 17103184.

 

  • Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC. Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. ProcNatl Acad Sci U S A. 2005 Dec 13;102(50):18017-22. Epub 2005 Dec 5. PubMed PMID: 16330759; PubMed Central PMCID: PMC1306796.

 

  • Aboobaker AA, Blaxter ML. Functional genomics for parasitic nematodes and platyhelminths. Trends Parasitol. 2004 Apr;20(4):178-84. Review. PubMed PMID:15099557.

 

  • Aboobaker A, Blaxter M. Hox gene evolution in nematodes: novelty conserved. Curr Opin Genet Dev. 2003 Dec;13(6):593-8. Review. PubMed PMID: 14638320.

 

  • Aboobaker AA, Blaxter ML. Use of RNA interference to investigate gene function in the human filarial nematode parasite Brugia malayi. Mol Biochem Parasitol. 2003 Jun;129(1):41-51. PubMed PMID: 12798505.

 

  • Aboobaker AA, Blaxter ML. Hox Gene Loss during Dynamic Evolution of the Nematode Cluster. Curr Biol. 2003 Jan 8;13(1):37-40. PubMed PMID: 12526742.

 

  • Foster JM, Kamal IH, Daub J, Swan MC, Ingram JR, Ganatra M, Ware J, Guiliano D, Aboobaker A, Moran L, Blaxter M, Slatko BE. Hybridization to high-density filter arrays of a Brugia malayi BAC library with biotinylated oligonucleotides and PCR products. Biotechniques. 2001 Jun;30(6):1216-8, 1220, 1222 passim. PubMed PMID: 11414208.

 

  • Aboobaker AA, Blaxter ML. Medical significance of Caenorhabditis elegans. Ann Med. 2000 Feb;32(1):23-30. PubMed PMID: 10711574.

 

  • Harder JA, Aboobaker AA, Hodgetts TC, Ridley RM. Learning impairments induced by glutamate blockade using dizocilpine (MK-801) in monkeys. Br J Pharmacol. 1998 Nov;125(5):1013-8. PubMed PMID: 9846639; PubMed Central PMCID: PMC1565679.