@article{ChipmanFerrierBrenaetal.2014,
  author    = {Chipman, Ariel D. and Ferrier, David E. K. and Brena, Carlo and Qu, Jiaxin and Hughes, Daniel S. T. and Schroeder, Reinhard and Torres-Oliva, Montserrat and Znassi, Nadia and Jiang, Huaiyang and Almeida, Francisca C. and Alonso, Claudio R. and Apostolou, Zivkos and Aqrawi, Peshtewani and Arthur, Wallace and Barna, Jennifer C. J. and Blankenburg, Kerstin P. and Brites, Daniela and Capella-Gutierrez, Salvador and Coyle, Marcus and Dearden, Peter K. and Du Pasquier, Louis and Duncan, Elizabeth J. and Ebert, Dieter and Eibner, Cornelius and Erikson, Galina and Evans, Peter D. and Extavour, Cassandra G. and Francisco, Liezl and Gabaldon, Toni and Gillis, William J. and Goodwin-Horn, Elizabeth A. and Green, Jack E. and Griffiths-Jones, Sam and Grimmelikhuijzen, Cornelis J. P. and Gubbala, Sai and Guigo, Roderic and Han, Yi and Hauser, Frank and Havlak, Paul and Hayden, Luke and Helbing, Sophie and Holder, Michael and Hui, Jerome H. L. and Hunn, Julia P. and Hunnekuhl, Vera S. and Jackson, LaRonda and Javaid, Mehwish and Jhangiani, Shalini N. and Jiggins, Francis M. and Jones, Tamsin E. and Kaiser, Tobias S. and Kalra, Divya and Kenny, Nathan J. and Korchina, Viktoriya and Kovar, Christie L. and Kraus, F. Bernhard and Lapraz, Francois and Lee, Sandra L. and Lv, Jie and Mandapat, Christigale and Manning, Gerard and Mariotti, Marco and Mata, Robert and Mathew, Tittu and Neumann, Tobias and Newsham, Irene and Ngo, Dinh N. and Ninova, Maria and Okwuonu, Geoffrey and Ongeri, Fiona and Palmer, William J. and Patil, Shobha and Patraquim, Pedro and Pham, Christopher and Pu, Ling-Ling and Putman, Nicholas H. and Rabouille, Catherine and Ramos, Olivia Mendivil and Rhodes, Adelaide C. and Robertson, Helen E. and Robertson, Hugh M. and Ronshaugen, Matthew and Rozas, Julio and Saada, Nehad and Sanchez-Gracia, Alejandro and Scherer, Steven E. and Schurko, Andrew M. and Siggens, Kenneth W. and Simmons, DeNard and Stief, Anna and Stolle, Eckart and Telford, Maximilian J. and Tessmar-Raible, Kristin and Thornton, Rebecca and van der Zee, Maurijn and von Haeseler, Arndt and Williams, James M. and Willis, Judith H. and Wu, Yuanqing and Zou, Xiaoyan and Lawson, Daniel and Muzny, Donna M. and Worley, Kim C. and Gibbs, Richard A. and Akam, Michael and Richards, Stephen},
  title     = {The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima},
  series = {PLoS biology},
  volume    = {12},
  journal   = {PLoS biology},
  number    = {11},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1545-7885},
  doi       = {10.1371/journal.pbio.1002005},
  pages     = {24},
  year      = {2014},
  abstract  = {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.},
  language  = {en}
}
@article{KhiderEmileGeayMcKayetal.2019,
  author    = {Khider, D. and Emile-Geay, J. and McKay, N. P. and Gil, Y. and Garijo, D. and Ratnakar, V and Alonso-Garcia, M. and Bertrand, S. and Bothe, O. and Brewer, P. and Bunn, A. and Chevalier, M. and Comas-Bru, L. and Csank, A. and Dassie, E. and DeLong, K. and Felis, T. and Francus, P. and Frappier, A. and Gray, W. and Goring, S. and Jonkers, L. and Kahle, M. and Kaufman, D. and Kehrwald, N. M. and Martrat, B. and McGregor, H. and Richey, J. and Schmittner, A. and Scroxton, N. and Sutherland, E. and Thirumalai, Kaustubh and Allen, K. and Arnaud, F. and Axford, Y. and Barrows, T. and Bazin, L. and Birch, S. E. Pilaar and Bradley, E. and Bregy, J. and Capron, E. and Cartapanis, O. and Chiang, H-W and Cobb, K. M. and Debret, M. and Dommain, R{\´e}ne and Du, J. and Dyez, K. and Emerick, S. and Erb, M. P. and Falster, G. and Finsinger, W. and Fortier, D. and Gauthier, Nicolas and George, S. and Grimm, E. and Hertzberg, J. and Hibbert, F. and Hillman, A. and Hobbs, W. and Huber, M. and Hughes, A. L. C. and Jaccard, S. and Ruan, J. and Kienast, M. and Konecky, B. and Le Roux, G. and Lyubchich, V and Novello, V. F. and Olaka, L. and Partin, J. W. and Pearce, C. and Phipps, S. J. and Pignol, C. and Piotrowska, N. and Poli, M-S and Prokopenko, A. and Schwanck, F. and Stepanek, C. and Swann, G. E. A. and Telford, R. and Thomas, E. and Thomas, Z. and Truebe, S. and von Gunten, L. and Waite, A. and Weitzel, N. and Wilhelm, B. and Williams, J. and Winstrup, M. and Zhao, N. and Zhou, Y.},
  title     = {PaCTS 1.0: A Crowdsourced Reporting Standard for Paleoclimate Data},
  series = {Paleoceanography and paleoclimatology},
  volume    = {34},
  journal   = {Paleoceanography and paleoclimatology},
  number    = {10},
  publisher = {American Geophysical Union},
  address   = {Washington},
  issn      = {2572-4517},
  doi       = {10.1029/2019PA003632},
  pages     = {1570 -- 1596},
  year      = {2019},
  abstract  = {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.},
  language  = {en}
}