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Items: 38

1.

New data from Monoplacophora and a carefully-curated dataset resolve molluscan relationships.

Kocot KM, Poustka AJ, Stöger I, Halanych KM, Schrödl M.

Sci Rep. 2020 Jan 9;10(1):101. doi: 10.1038/s41598-019-56728-w.

2.

The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes.

Hogan JD, Keenan JL, Luo L, Ibn-Salem J, Lamba A, Schatzberg D, Piacentino ML, Zuch DT, Core AB, Blumberg C, Timmermann B, Grau JH, Speranza E, Andrade-Navarro MA, Irie N, Poustka AJ, Bradham CA.

Dev Biol. 2019 Dec 6. pii: S0012-1606(19)30386-0. doi: 10.1016/j.ydbio.2019.12.002. [Epub ahead of print]

PMID:
31816285
3.

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.

Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas-Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ.

Curr Biol. 2019 Jun 3;29(11):1818-1826.e6. doi: 10.1016/j.cub.2019.04.009. Epub 2019 May 16.

PMID:
31104936
4.

Monoplacophoran mitochondrial genomes: convergent gene arrangements and little phylogenetic signal.

Stöger I, Kocot KM, Poustka AJ, Wilson NG, Ivanov D, Halanych KM, Schrödl M.

BMC Evol Biol. 2016 Dec 16;16(1):274.

5.

RNA-Seq identifies SPGs as a ventral skeletal patterning cue in sea urchins.

Piacentino ML, Zuch DT, Fishman J, Rose S, Speranza EE, Li C, Yu J, Chung O, Ramachandran J, Ferrell P, Patel V, Reyna A, Hameeduddin H, Chaves J, Hewitt FB, Bardot E, Lee D, Core AB, Hogan JD, Keenan JL, Luo L, Coulombe-Huntington J, Blute TA, Oleinik E, Ibn-Salem J, Poustka AJ, Bradham CA.

Development. 2016 Feb 15;143(4):703-14. doi: 10.1242/dev.129312. Epub 2016 Jan 11.

6.

The complete mitochondrial genome of Telmatobufo australis (Amphibia: Anura: Calyptocephalellidae).

Grau JH, Nuñez JJ, Plötner J, Poustka AJ.

Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Jul;27(4):2817-8. doi: 10.3109/19401736.2015.1053082. Epub 2015 Jun 22.

PMID:
26094990
7.

The nervous system of Xenacoelomorpha: a genomic perspective.

Perea-Atienza E, Gavilán B, Chiodin M, Abril JF, Hoff KJ, Poustka AJ, Martinez P.

J Exp Biol. 2015 Feb 15;218(Pt 4):618-28. doi: 10.1242/jeb.110379.

8.

LTR retroelements are intrinsic components of transcriptional networks in frogs.

Grau JH, Poustka AJ, Meixner M, Plötner J.

BMC Genomics. 2014 Jul 23;15:626. doi: 10.1186/1471-2164-15-626.

9.

Massively parallel RNA sequencing identifies a complex immune gene repertoire in the lophotrochozoan Mytilus edulis.

Philipp EE, Kraemer L, Melzner F, Poustka AJ, Thieme S, Findeisen U, Schreiber S, Rosenstiel P.

PLoS One. 2012;7(3):e33091. doi: 10.1371/journal.pone.0033091. Epub 2012 Mar 20.

10.

Acoelomorph flatworms are deuterostomes related to Xenoturbella.

Philippe H, Brinkmann H, Copley RR, Moroz LL, Nakano H, Poustka AJ, Wallberg A, Peterson KJ, Telford MJ.

Nature. 2011 Feb 10;470(7333):255-8. doi: 10.1038/nature09676.

11.

Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix.

Mann K, Wilt FH, Poustka AJ.

Proteome Sci. 2010 Jun 17;8:33. doi: 10.1186/1477-5956-8-33.

12.

Data integration using scanners with SQL output--the bioscanners project at sourceforge.

Groth D, Hartmann S, Friemel M, Hill N, Müller S, Poustka AJ, Panopoulou G.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-122.

PMID:
20375454
13.
14.

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention.

Hufton AL, Mathia S, Braun H, Georgi U, Lehrach H, Vingron M, Poustka AJ, Panopoulou G.

Genome Res. 2009 Nov;19(11):2036-51. doi: 10.1101/gr.093237.109. Epub 2009 Aug 24.

15.

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network.

Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ.

BMC Syst Biol. 2009 Aug 23;3:83. doi: 10.1186/1752-0509-3-83.

16.

Chordin is required for neural but not axial development in sea urchin embryos.

Bradham CA, Oikonomou C, Kühn A, Core AB, Modell JW, McClay DR, Poustka AJ.

Dev Biol. 2009 Apr 15;328(2):221-33. doi: 10.1016/j.ydbio.2009.01.027. Epub 2009 Jan 29.

17.

In-depth, high-accuracy proteomics of sea urchin tooth organic matrix.

Mann K, Poustka AJ, Mann M.

Proteome Sci. 2008 Dec 9;6:33. doi: 10.1186/1477-5956-6-33.

18.

Ca(2+) signaling occurs via second messenger release from intraorganelle synthesis sites.

Davis LC, Morgan AJ, Ruas M, Wong JL, Graeff RM, Poustka AJ, Lee HC, Wessel GM, Parrington J, Galione A.

Curr Biol. 2008 Oct 28;18(20):1612-8. doi: 10.1016/j.cub.2008.09.024.

19.

The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes.

Mann K, Poustka AJ, Mann M.

Proteome Sci. 2008 Aug 11;6:22. doi: 10.1186/1477-5956-6-22.

20.

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement.

Hufton AL, Groth D, Vingron M, Lehrach H, Poustka AJ, Panopoulou G.

Genome Res. 2008 Oct;18(10):1582-91. doi: 10.1101/gr.080119.108. Epub 2008 Jul 14.

21.

Modeling development: spikes of the sea urchin.

Kühn C, Kühn A, Poustka AJ, Klipp E.

Genome Inform. 2007;18:75-84.

PMID:
18546476
22.

Evolution of a core gene network for skeletogenesis in chordates.

Hecht J, Stricker S, Wiecha U, Stiege A, Panopoulou G, Podsiadlowski L, Poustka AJ, Dieterich C, Ehrich S, Suvorova J, Mundlos S, Seitz V.

PLoS Genet. 2008 Mar 21;4(3):e1000025. doi: 10.1371/journal.pgen.1000025.

23.

GOblet: annotation of anonymous sequence data with gene ontology and pathway terms.

Groth D, Hartmann S, Panopoulou G, Poustka AJ, Hennig S.

J Integr Bioinform. 2008 Aug 25;5(2). doi: 10.2390/biecoll-jib-2008-104.

PMID:
20134064
24.

A global view of gene expression in lithium and zinc treated sea urchin embryos: new components of gene regulatory networks.

Poustka AJ, Kühn A, Groth D, Weise V, Yaguchi S, Burke RD, Herwig R, Lehrach H, Panopoulou G.

Genome Biol. 2007;8(5):R85.

25.

The genome of the sea urchin Strongylocentrotus purpuratus.

Sea Urchin Genome Sequencing Consortium, Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R.

Science. 2006 Nov 10;314(5801):941-52. Erratum in: Science. 2007 Feb 9;315(5813):766.

26.

Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep.

Hecht J, Kuhl H, Haas SA, Bauer S, Poustka AJ, Lienau J, Schell H, Stiege AC, Seitz V, Reinhardt R, Duda GN, Mundlos S, Robinson PN.

BMC Genomics. 2006 Jul 5;7:172.

27.

Timing and mechanism of ancient vertebrate genome duplications -- the adventure of a hypothesis.

Panopoulou G, Poustka AJ.

Trends Genet. 2005 Oct;21(10):559-67. Review.

PMID:
16099069
28.

Nodal/activin signaling establishes oral-aboral polarity in the early sea urchin embryo.

Flowers VL, Courteau GR, Poustka AJ, Weng W, Venuti JM.

Dev Dyn. 2004 Dec;231(4):727-40.

29.

On the origin of the chordate central nervous system: expression of onecut in the sea urchin embryo.

Poustka AJ, Kühn A, Radosavljevic V, Wellenreuther R, Lehrach H, Panopoulou G.

Evol Dev. 2004 Jul-Aug;6(4):227-36.

PMID:
15230963
30.

Expression of an NK2 homeodomain gene in the apical ectoderm defines a new territory in the early sea urchin embryo.

Takacs CM, Amore G, Oliveri P, Poustka AJ, Wang D, Burke RD, Peterson KJ.

Dev Biol. 2004 May 1;269(1):152-64.

31.

Cloning of a novel phospholipase C-delta isoform from pacific purple sea urchin (Strongylocentrotus purpuratus) gametes and its expression during early embryonic development.

Coward K, Owen H, Poustka AJ, Hibbitt O, Tunwell R, Kubota H, Swann K, Parrington J.

Biochem Biophys Res Commun. 2004 Jan 23;313(4):894-901.

PMID:
14706626
32.

Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters.

Poustka AJ, Groth D, Hennig S, Thamm S, Cameron A, Beck A, Reinhardt R, Herwig R, Panopoulou G, Lehrach H.

Genome Res. 2003 Dec;13(12):2736-46.

33.

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes.

Panopoulou G, Hennig S, Groth D, Krause A, Poustka AJ, Herwig R, Vingron M, Lehrach H.

Genome Res. 2003 Jun;13(6A):1056-66.

34.

A single amphioxus and sea urchin runt-gene suggests that runt-gene duplications occurred in early chordate evolution.

Stricker S, Poustka AJ, Wiecha U, Stiege A, Hecht J, Panopoulou G, Vilcinskas A, Mundlos S, Seitz V.

Dev Comp Immunol. 2003 Sep;27(8):673-84.

PMID:
12798364
35.

brachyury Target genes in the early sea urchin embryo isolated by differential macroarray screening.

Rast JP, Cameron RA, Poustka AJ, Davidson EH.

Dev Biol. 2002 Jun 1;246(1):191-208.

36.

A sea urchin genome project: sequence scan, virtual map, and additional resources.

Cameron RA, Mahairas G, Rast JP, Martinez P, Biondi TR, Swartzell S, Wallace JC, Poustka AJ, Livingston BT, Wray GA, Ettensohn CA, Lehrach H, Britten RJ, Davidson EH, Hood L.

Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9514-8.

37.

Large-scale clustering of cDNA-fingerprinting data.

Herwig R, Poustka AJ, Müller C, Bull C, Lehrach H, O'Brien J.

Genome Res. 1999 Nov;9(11):1093-105.

38.

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