Resources

RELEVANT WEBSITES

RELEVANT PUBLICATIONS

Appenzeller T (2017) The Scientists' Apprentice. Science 357(6346):16-17

Bigelow A, Drucker S, Fisher D, Meyer M (2014) Reflections on how designers design with data. Proceedings of the 2014 International Working Conference on Advanced Visual Interfaces 17-24

Bik HM, Pitch Interactive (2014) Phinch: An interactive, exploratory data visualization framework for –Omic datasets. bioRxiv 009944

Bonneau G-P, Hege H-C, Johnson CR, Oliveira MM, Potter K, Rheingans P, Schultz T (2014) Overview and State-of-the-Art of Uncertainty Visualization. Scientific Visualization, ed Hansen C, Chen M, Johnson C, Kaufman A, Hagen H. Springer (London) p 3-27

Bradley DC (2008) Passive margins through earth history. Earth-Science Reviews 91(1-4):1-26

Bradley DC (2011) Secular trends in the geologic record and the supercontinent cycle. Earth-Science Reviews 108(1-2):16-33

Cawood PA, Hawkesworth CJ, Dhuime B (2013) The continental record and the generation of continental crust. Geological Society of America Bulletin 125(1-2):14-32

Cawood PA, Hawkesworth CJ (2013) Temporal relations between mineral deposits and global tectonic cycles. Geological Society, London, Special Publications 393:9-21

Cawood PA, Hawkesworth CJ (2014) Earth's middle age. Geology 42(6):503-506

Coltice N, Gérault M, Ulvrová M (2017) A mantle convection perspective on global tectonics. Earth-Science Reviews 165:120-150

Creer S, Deiner K, Frey S, Porazinska D, Taberlet P, Thomas WK, Potter C, Bik HM (2016) The ecologist's field guide to sequence-based identification of biodiversity. Methods in Ecology and Evolution 7(9):1008-1018

Cronin L, Walker SI (2016) Beyond prebiotic chemistry. Science 352(6290):1174-1175

Ferreiro DU, Komives EA, Wolynes PG (2018) Frustration, function and folding. Current Opinion in Structural Biology 48:68-73

Hao J, Sverjensky DA, Hazen RM (2017) Mobility of nutrients and trace metals during weathering in the late Archean. Earth and Planetary Science Letters 471:148-159

Harel A, Bromberg Y, Falkowski PG, Bhattacharya D (2014) Evolutionary history of redox metal-binding domains across the tree of life. Proceedings of the National Academy of Sciences 111(19):7042-7047

Harel A, Falkowski P, Bromberg Y (2012) TrAnsFuSE refines the search for protein function: oxidoreductases. Integrative Biology 4(7):765-777

Hazen RM, Hummer DR, Hystad G, Downs RT, Golden JJ (2016) Carbon mineral ecology: Predicting the undiscovered minerals of carbon. American Mineralogist 101(4):889-906

Hazen RM, Hystad G, Downs RT, Golden J, Pires A, Grew ES (2015) Earth’s “missing” minerals. American Mineralogist 100(10):2344-2347

Hystad G, Downs RT, Grew ES, Hazen RM (2015) Statistical analysis of mineral diversity and distribution: Earth’s mineralogy is unique. Earth and Planetary Science Letters 426:154-157

Jelen B, Giovannelli D, Falkowski PG (2016) The Role of Microbial Electron Transfer in the Coevolution of the Geosphere and Biosphere. Annual Review of Microbiology 70:45-62

Joppa LN (2017) The case for technology investments in the environment. Nature 552:325-328

Karagulle D, Frye C, Sayre R, Breyer S, Aniello P, Vaughan R, Wright D (2017) Modeling global Hammond landform regions from 250-m elevation data. Transactions in GIS 21(5):1040-1060

Kern M, Lex A, Gehlenborg N, Johnson CR (2017) Interactive visual exploration and refinement of cluster assignments. BMC Bioinformatics 18:406

Kerzner E, Lex A, Sigulinsky CL, Urness T, Jones BW, Marc RE, Meyer M (2017) Graffinity: Visualizing Connectivity in Large Graphs. Computer Graphics Forum 36(3):251-260

Kim H, Smith H, Mathis C, Raymond J, Walker S (2018) Universal scaling across biochemical networks on Earth. bioRxiv

Kirby RM, Meyer M (2013) Visualization Collaborations: What Works and Why. IEEE Computer Graphics and Applications 33(6):82-88

Lanese N (2018) Rising Ocean Temperatures Threaten Carbon-Storing Sea Grass. Eos 99

Large RR, Mukherjee I, Gregory DD, Steadman JA, Maslennikov VV, Meffre S (2017) Ocean and Atmosphere Geochemical Proxies Derived from Trace Elements in Marine Pyrite: Implications for Ore Genesis in Sedimentary Basins. Economic Geology 112(2):423-450

Large RR, Mukherjee I, Zhukova I, Corkrey R, Stepanov A, Danyushevsky LV (2018) Role of upper-most crustal composition in the evolution of the Precambrian ocean–atmosphere system. Earth and Planetary Science Letters 487:44-53

Leach DL, Bradley DC, Huston D, Pisarevsky SA, Taylor RD, Gardoll SJ (2010) Sediment-Hosted Lead-Zinc Deposits in Earth History. Economic Geology 105(3):593-625

Liu C, Knoll A, Hazen RM (2017) Geochemical and mineralogical evidence that Rodinian assembly was unique. Nature Communications 8:1950

Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jørgensen BB (2013) Predominant archaea in marine sediments degrade detrital proteins. Nature 496:215-218

Ma X, Hummer D, Golden JJ, Fox PA, Hazen RM, Morrison SM, Downs RT, Madhikarmi BL, Wang C, Meyer MB (2017) Using Visual Exploratory Data Analysis to Facilitate Collaboration and Hypothesis Generation in Cross-Disciplinary Research. ISPRS International Journal of Geo-Information 6(11):368

Miller M, Zhu C, Bromberg Y (2017) clubber: removing the bioinformatics bottleneck in big data analyses. Journal of Integrative Bioinformatics 14(2):20170020

Moore EK, Hao J, Prabhu A, Zhong H, Jelen BI, Meyer M, Hazen RM, Falkowski PG (2018) Geological and Chemical Factors that Impacted the Biological Utilization of Cobalt in the Archean Eon. Journal of Geophysical Research: Biogeosciences 123(3):743-759

Moore EK, Jelen BI, Giovannelli D, Raanan H, Falkowski PG (2017) Metal availability and the expanding network of microbial metabolisms in the Archaean eon. Nature Geoscience 10:629-636

Morrison SM, Liu C, Eleish A, Prabhu A, Lic C, Ralph J, Downs RT, Golden JJ, Fox P, Hazen RM (2017) Network analysis of mineralogical systems. American Mineralogist 102(8):1588-1596

Müller RD, Dutkiewicz A (2018) Oceanic crustal carbon cycle drives 26-million-year atmospheric carbon dioxide periodicities. Science Advances 4(2):eaaq0500

Parra RG, Espada R, Sánchez IE, Sippl MJ, Ferreiro DU (2013) Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space. The Journal of Physical Chemistry B 117(42):12887-12897

Partl C, Gratzl S, Streit M, Wassermann AM, Pfister H, Schmalstieg D, Lex A (2016) Pathfinder: Visual Analysis of Paths in Graphs. Computer Graphics Forum 35(3):71-80

Potter K, Rosen P, Johnson CR (2012) From Quantification to Visualization: A Taxonomy of Uncertainty Visualization Approaches. Uncertainty Quantification in Scientific Computing, ed Dienstfrey AM, Boisvert RF. IFIP Advances in Information and Communication Technology 377:226-249

Sayre R, Dangermond J, Frye C, Vaughan R, Aniello P, Breyer SP, Cribbs D, Hopkins D, Nauman R, Derrenbacher W, Wright DJ, Brown C, Convis C, Smith JH, Benson L, Van Sistine  D, Warner H, Cress JJ, Danielson JJ, Hamann SL, Cecere T, Reddy AD, Burton D, Grosse A, True D, Metzger M, Hartmann J, Moosdorf N, Durr H, Paganini M, Defourny P, Arino O, Maynard S, Anderson M, Comer P (2014) A new map of global ecological land units—An ecophysiographic stratification approach. Association of American Geographers, 46 p

Sayre RG, Wright DJ, Breyer SP, Butler KA, Van Graafeiland K, Costello MJ, Harris PT, Goodin KL, Guinotte JM, Basher Z, Kavanaugh MT, Halpin PN, Monaco ME, Cressie N, Aniello P, Frye CE, Stephens D (2017) A Three-Dimensional Mapping of the Ocean Based on Environmental Data. Oceanography 30(1):90-103

Senn S, Nanda V, Falkowski PG, Bromberg Y (2014) Function-based assessment of structural similarity measurements using metal co-factor orientation. Proteins 82(4):648-656

Stall S, Robinson E, Wyborn L, Yarmey LR, Parsons MA, Lehnert K, Cutcher-Gershenfeld J, Nosek B, Hanson B (2017) Enabling FAIR data across the Earth and space sciences. Eos 98

Stuart D, Baynes G, Hrynaszkiewicz I, Allin K, Penny D, Lucraft M, Astell M (2018) Whitepaper: Practical challenges for researchers in data sharing. figshare

Wright DJ (2016) Toward a digital resilience. Elementa Science of the Anthropocene 4:82

 

Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B (2014) PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Research 42(W1):W337-W343
 

Zhu C, Delmont TO, Vogel TM, Bromberg Y (2015) Functional Basis of Microorganism Classification. PLoS Computational Biology 11(8):e1004472

Zhu C, Mahlich Y, Miller M, Bromberg Y (2017) fusion DB: assessing microbial diversity and environmental preferences via functional similarity networks. Nucleic Acids Research 46(D1):D535-D541


Zhu C, Miller M, Marpaka S, Vaysberg P, Rühlemann MC, Wu G, Heinsen FA, Tempel M, Zhao L, Lieb W, Franke A, Bromberg Y (2017) Functional sequencing read annotation for high precision microbiome analysis. Nucleic acids research 46(4):e23
 

 

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