TY  - JOUR
A1  - Chipman, Ariel D.
A1  - Ferrier, David E. K.
A1  - Brena, Carlo
A1  - Qu, Jiaxin
A1  - Hughes, Daniel S. T.
A1  - Schroeder, Reinhard
A1  - Torres-Oliva, Montserrat
A1  - Znassi, Nadia
A1  - Jiang, Huaiyang
A1  - Almeida, Francisca C.
A1  - Alonso, Claudio R.
A1  - Apostolou, Zivkos
A1  - Aqrawi, Peshtewani
A1  - Arthur, Wallace
A1  - Barna, Jennifer C. J.
A1  - Blankenburg, Kerstin P.
A1  - Brites, Daniela
A1  - Capella-Gutierrez, Salvador
A1  - Coyle, Marcus
A1  - Dearden, Peter K.
A1  - Du Pasquier, Louis
A1  - Duncan, Elizabeth J.
A1  - Ebert, Dieter
A1  - Eibner, Cornelius
A1  - Erikson, Galina
A1  - Evans, Peter D.
A1  - Extavour, Cassandra G.
A1  - Francisco, Liezl
A1  - Gabaldon, Toni
A1  - Gillis, William J.
A1  - Goodwin-Horn, Elizabeth A.
A1  - Green, Jack E.
A1  - Griffiths-Jones, Sam
A1  - Grimmelikhuijzen, Cornelis J. P.
A1  - Gubbala, Sai
A1  - Guigo, Roderic
A1  - Han, Yi
A1  - Hauser, Frank
A1  - Havlak, Paul
A1  - Hayden, Luke
A1  - Helbing, Sophie
A1  - Holder, Michael
A1  - Hui, Jerome H. L.
A1  - Hunn, Julia P.
A1  - Hunnekuhl, Vera S.
A1  - Jackson, LaRonda
A1  - Javaid, Mehwish
A1  - Jhangiani, Shalini N.
A1  - Jiggins, Francis M.
A1  - Jones, Tamsin E.
A1  - Kaiser, Tobias S.
A1  - Kalra, Divya
A1  - Kenny, Nathan J.
A1  - Korchina, Viktoriya
A1  - Kovar, Christie L.
A1  - Kraus, F. Bernhard
A1  - Lapraz, Francois
A1  - Lee, Sandra L.
A1  - Lv, Jie
A1  - Mandapat, Christigale
A1  - Manning, Gerard
A1  - Mariotti, Marco
A1  - Mata, Robert
A1  - Mathew, Tittu
A1  - Neumann, Tobias
A1  - Newsham, Irene
A1  - Ngo, Dinh N.
A1  - Ninova, Maria
A1  - Okwuonu, Geoffrey
A1  - Ongeri, Fiona
A1  - Palmer, William J.
A1  - Patil, Shobha
A1  - Patraquim, Pedro
A1  - Pham, Christopher
A1  - Pu, Ling-Ling
A1  - Putman, Nicholas H.
A1  - Rabouille, Catherine
A1  - Ramos, Olivia Mendivil
A1  - Rhodes, Adelaide C.
A1  - Robertson, Helen E.
A1  - Robertson, Hugh M.
A1  - Ronshaugen, Matthew
A1  - Rozas, Julio
A1  - Saada, Nehad
A1  - Sanchez-Gracia, Alejandro
A1  - Scherer, Steven E.
A1  - Schurko, Andrew M.
A1  - Siggens, Kenneth W.
A1  - Simmons, DeNard
A1  - Stief, Anna
A1  - Stolle, Eckart
A1  - Telford, Maximilian J.
A1  - Tessmar-Raible, Kristin
A1  - Thornton, Rebecca
A1  - van der Zee, Maurijn
A1  - von Haeseler, Arndt
A1  - Williams, James M.
A1  - Willis, Judith H.
A1  - Wu, Yuanqing
A1  - Zou, Xiaoyan
A1  - Lawson, Daniel
A1  - Muzny, Donna M.
A1  - Worley, Kim C.
A1  - Gibbs, Richard A.
A1  - Akam, Michael
A1  - Richards, Stephen
T1  - The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima
JF  - PLoS biology
N2  - Myriapods (e. g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Y1  - 2014
U6  - https://doi.org/10.1371/journal.pbio.1002005
SN  - 1545-7885
VL  - 12
IS  - 11
PB  - PLoS
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Khider, D.
A1  - Emile-Geay, J.
A1  - McKay, N. P.
A1  - Gil, Y.
A1  - Garijo, D.
A1  - Ratnakar, V
A1  - Alonso-Garcia, M.
A1  - Bertrand, S.
A1  - Bothe, O.
A1  - Brewer, P.
A1  - Bunn, A.
A1  - Chevalier, M.
A1  - Comas-Bru, L.
A1  - Csank, A.
A1  - Dassie, E.
A1  - DeLong, K.
A1  - Felis, T.
A1  - Francus, P.
A1  - Frappier, A.
A1  - Gray, W.
A1  - Goring, S.
A1  - Jonkers, L.
A1  - Kahle, M.
A1  - Kaufman, D.
A1  - Kehrwald, N. M.
A1  - Martrat, B.
A1  - McGregor, H.
A1  - Richey, J.
A1  - Schmittner, A.
A1  - Scroxton, N.
A1  - Sutherland, E.
A1  - Thirumalai, Kaustubh
A1  - Allen, K.
A1  - Arnaud, F.
A1  - Axford, Y.
A1  - Barrows, T.
A1  - Bazin, L.
A1  - Birch, S. E. Pilaar
A1  - Bradley, E.
A1  - Bregy, J.
A1  - Capron, E.
A1  - Cartapanis, O.
A1  - Chiang, H-W
A1  - Cobb, K. M.
A1  - Debret, M.
A1  - Dommain, Réne
A1  - Du, J.
A1  - Dyez, K.
A1  - Emerick, S.
A1  - Erb, M. P.
A1  - Falster, G.
A1  - Finsinger, W.
A1  - Fortier, D.
A1  - Gauthier, Nicolas
A1  - George, S.
A1  - Grimm, E.
A1  - Hertzberg, J.
A1  - Hibbert, F.
A1  - Hillman, A.
A1  - Hobbs, W.
A1  - Huber, M.
A1  - Hughes, A. L. C.
A1  - Jaccard, S.
A1  - Ruan, J.
A1  - Kienast, M.
A1  - Konecky, B.
A1  - Le Roux, G.
A1  - Lyubchich, V
A1  - Novello, V. F.
A1  - Olaka, L.
A1  - Partin, J. W.
A1  - Pearce, C.
A1  - Phipps, S. J.
A1  - Pignol, C.
A1  - Piotrowska, N.
A1  - Poli, M-S
A1  - Prokopenko, A.
A1  - Schwanck, F.
A1  - Stepanek, C.
A1  - Swann, G. E. A.
A1  - Telford, R.
A1  - Thomas, E.
A1  - Thomas, Z.
A1  - Truebe, S.
A1  - von Gunten, L.
A1  - Waite, A.
A1  - Weitzel, N.
A1  - Wilhelm, B.
A1  - Williams, J.
A1  - Winstrup, M.
A1  - Zhao, N.
A1  - Zhou, Y.
T1  - PaCTS 1.0: A Crowdsourced Reporting Standard for Paleoclimate Data
JF  - Paleoceanography and paleoclimatology
N2  - The progress of science is tied to the standardization of measurements, instruments, and data. This is especially true in the Big Data age, where analyzing large data volumes critically hinges on the data being standardized. Accordingly, the lack of community-sanctioned data standards in paleoclimatology has largely precluded the benefits of Big Data advances in the field. Building upon recent efforts to standardize the format and terminology of paleoclimate data, this article describes the Paleoclimate Community reporTing Standard (PaCTS), a crowdsourced reporting standard for such data. PaCTS captures which information should be included when reporting paleoclimate data, with the goal of maximizing the reuse value of paleoclimate data sets, particularly for synthesis work and comparison to climate model simulations. Initiated by the LinkedEarth project, the process to elicit a reporting standard involved an international workshop in 2016, various forms of digital community engagement over the next few years, and grassroots working groups. Participants in this process identified important properties across paleoclimate archives, in addition to the reporting of uncertainties and chronologies; they also identified archive-specific properties and distinguished reporting standards for new versus legacy data sets. This work shows that at least 135 respondents overwhelmingly support a drastic increase in the amount of metadata accompanying paleoclimate data sets. Since such goals are at odds with present practices, we discuss a transparent path toward implementing or revising these recommendations in the near future, using both bottom-up and top-down approaches.
KW  - standards
KW  - FAIR
KW  - paleoclimate
KW  - paleoceanography
KW  - data
KW  - best practices
Y1  - 2019
U6  - https://doi.org/10.1029/2019PA003632
SN  - 2572-4517
SN  - 2572-4525
VL  - 34
IS  - 10
SP  - 1570
EP  - 1596
PB  - American Geophysical Union
CY  - Washington
ER  -