Project | Data Management Plan |
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Pattern and Process in Marine Bacterial, Archaeal, and Protistan Biodiversity, and Effects of Human Impacts | DMP_Fuhrman_OCE-1136818.pdf (11.73 KB) |
Principal Investigator: Jed A. Fuhrman (University of Southern California)
Co-Principal Investigator: Fengzhu Sun
Co-Principal Investigator: William C Nelson
Co-Principal Investigator: David A Caron
Co-Principal Investigator: John F Heidelberg
Deep-Sea Research I.~2011~58~Schnetzer, A., S.D. Moorthi, P.D. Countway R.J. Gast, I.C. Gilg and D.A. Caron.~~16~~~~Depth matters: microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries.~N~~~~~~
Annual Review of Marine Science~2012~4~Caron, D.A. P.D. Countway, A.C. Jones, D.Y. Kim, A. Schnetzer.~~467~~~~Marine Protistan Diversity.~N~~~~~~
Envir. Microbiol.~2012~~Chow, C-E.T., and J.A. Fuhrman.~10.1111/j.1462-2920.2012.02744.x~~~~~Seasonality and monthly dynamics of marine myovirus communities~N~~~~~~
F1000 Biology Reports~2012~4~Fuhrman, J.A.~10.3410/B4-15~15~~~~Metagenomics and its connection to microbial community organization~N~~~~~~
ISME J~2013~~Needham, David M., Cheryl-Emiliane T. Chow, Jacob A. Cram, Rohan Sachdeva, Alma Parada, Jed A. Fuhrman~doi:10.1038/ismej.20~~~~~Short-term observations of marine bacterial and viral communities: patterns, connections, and resilience.~~~~~~~
ISME Journal~2013~~Chow, Cheryl-Emiliane T., Rohan Sachdeva, Jacob A. Cram, Joshua A Steele, David M. Needham, Anand Patel, Alma E. Parada, and Jed A. Fuhrman~10.1038/ismej.2013.122~~~~~Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight.~~~~~~~
Aquat. Microb. Ecol.~2013~70~Lie, A.A.Y, D.Y Kim, A. Schnetzer, D.A. Caron~10.3354./ame01652~93~~~~Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-Series station off the coast of southern California~~~~~~~
Journal of Computational Biology~2012~19~Zhai ZY, Reinert G, Song K, Waterman MS, Luan YH, Sun FZ~PMID 22697250~839~~~~Normal and Compound Poisson Approximations for Pattern Occurrences in NGS Reads~~~~~~~
Journal of Computational Biology~2012~20~Song K, Ren J, Zhai ZY, Liu XM, Deng MH, Sun FZ~~64~~~~Alignment-Free Sequence Comparison Based on NGS Reads.~~~~~~~
BMC genomics~2013~13~Jiang B, Song K, Ren J, Deng MH, Sun FZ*, Zhang XG~~730~~~~Comparison of metagenomic samples using sequence signatures~~~~~~~
Bioinformatics~2013~29~Xia LC, Ai DM, Cram J, Fuhrman JA, Sun FZ~~230~~~~Efficient statistical significance approximation for local association analysis of high-throughput time series data.~~~~~~~
PLoS ONE~2012~7~Hao X and Chen T (2012)~10.1371/journal.pone.0049785~e49785~~~~OTU Analysis Using Metagenomic Shotgun Sequencing Data~~~~~~~
Scientific Report~2012~2~Jiang B, Liang X, Chen Y, Ma T, Liu L, Li J, Chen T, Zhang X and Li S~10.1038/srep00936~936~~~~Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome~~~~~~~
Microbial Ecology~2011~62~Kim, D.Y., P.D. Countway, R.J. Gast and D.A. Caron~~383~~~~Rapid shifts in protistan community structure and composition during bottle incubations~~~~~~~
Journal of Eukaryotic Microbiology~2013~60~Caron, D.A.~~407~~~~Towards a molecular taxonomy for protists: benefits, risks and applications in plankton ecology.~~~~~~~
Journal of Plankton Research,~2012~35~Caron, D.A. and D.A. Hutchins~~235~~~~The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps~~~~~~~
Environmental Microbiology~2012~91~Kim, D.Y., P.D. Countway, W. Yamashito and D.A. Caron~~527~~~~"A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method.~~~~~~~
Journal of Plankton Research.~2013~35~Caron, D.A. and D.A. Hutchins~~235~~~~The effects of changing climate on microzooplankton grazing and community structure: drivers, predictions and knowledge gaps.~~~~~~~
ISME Journal~2013~8~Chow, Cheryl-Emiliane T., Diane Y. Kim, Rohan Sachdeva, David A. Caron, and Jed A. Fuhrman.~10.1038/ismej.2013.199~816~~~~Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists.~~~~~~~
ISME Journal,~2014~~Cram, Jacob A., Cheryl-Emiliane T. Chow, Rohan Sachdeva, David M. Needham, Alma E. Parada, Joshua A. Steele, Jed A. Fuhrman.~10.1038/ismej.2014.153~~~~~Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years.~~~~~~~
Limnology and Oceanography.~2014~59~Howard, M.D.A., M. Sutula, D.A. Caron, Y. Chao, J.D. Farrara, H. Frenzel, B. Jones, G. Robertson, K. McLaughlin and A. Sengupta.~~285~~~~Anthropogenic nutrient sources rival natural sources on small scales in the coastal waters of the Southern California Bight.~~~~~~~
The ISME Journal~2014~8~Kim, D.Y., P.D. Countway, A.C. Jones, A. Schnetzer, W. Yamashita, C. Tung and D.A. Caron.~~515~~~~Monthly, seasonal and interannual variability of microbial eukaryote assemblages within and below the euphotic zone in the eastern North Pacific.~~~~~~~
Aquatic Microbial Ecology~2013~70~Lie, A.A.Y., D.Y. Kim, A. Schnetzer and D.A. Caron.~~93~~~~Small-scale temporal and spatial variations in protistan community composition at the San Pedro Ocean Time-series station off the coast of southern California.~~~~~~~
Bioinformatics~2013~29~Ren J, Song K, Sun FZ, Deng MH, Reinert R*~PMID 23990418~2690~~~~Multiple Alignment-free Sequence Comparison~~~~~~~
Briefings in Bioinformatics~2013~15~Song K, Ren J, Reinert G, Deng MH, Waterman MS*, Sun FS*~~343~~~~New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.~~~~~~~
PLoS ONE~2014~9~Wang Y*, Liu L, Chen LN, Chen T, Sun FZ*~~e84348~~~~Comparison of metatranscriptomic samples based on k-tuple frequencies.~~~~~~~
Nucleic Acid Research. 1-13, doi:~2013~~Zeng F, Jiang R and Chen T~10.1093/nar/gkt372~~~~~PyroHMMSNP: a SNP caller for Ion Torrent and 454 Sequencing Data.~~~~~~~
Bioinformatics~2013~~Zeng F, Jiang R and Chen T~10.1093/bioinformatics/btt512.~~~~~PyroHMMvar: an accurate and sensitive SNP and short indel caller for Ion Torrent and 454 Sequencing Data.~~~~~~~
The ISME Journal.~2015~~Cram JA*, Xia LC, Needham DM, Sachdeva R, Sun FZ, Fuhrman JA~10.1038/ismej.2015.76~~~~~Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes.~~~~~~~
International Journal of Robotics Research.~2015~~Das, J., F. Py, J. Harvey, J. Ryan, A. Gellene, R. Grahamk, D.A. Caron, K. Rajan and G,S. Sukhatme.~10.1177/0278364915587723.~~~~~Data-driven robotic sampling for marine ecosystem monitoring.~~~~~~~
Nature Reviews Microbiology,~2015~13~Fuhrman, Jed A, Jacob Cram, David M. Needham.~10.1038/nrmicro3417~133~~~~Marine microbial dynamics and their ecological interpretation.~~~~~~~
Journal of Eukaryotic Microbiology.~2015~~Hu, S., Z. Liu, A.A. Y. Lie, P.D. Countway, D.Y. Kim, A.C. Jones, R.J. Gast, E.B. Sherr, B.F. Sherr, S.C. Cary and D.A. Caron.~10.1111/jeu.12217.~~~~~Marine microbial eukaryote diversity and biogeography inferred from three different approaches for processing DNA information.~~~~~~~
Applied and Environmental Microbiology~2014~80~Lie, A.A.Y., Z. Liu, S. Hu, A.C. Jones, D.Y. Kim, P.D. Countway, L.A. Amaral-Zettler, R.J. Gast, E.B. Sherr, B.F. Sherr, S.C. Cary and D.A. Caron.~~436~~~~Investigating microbial eukaryote diversity: Insights from a comparison of pyrotag and full-length sequences of 18S rDNA from a global survey.~~~~~~~
Envir. Microbiol.~2015~~Parada, Alma, David M. Needham, and Jed A. Fuhrman.~10.1111/1462-2920.13023~~~~~Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples.~~~~~~~
Bioinformatics~2015~online~Ren J, Song K, Deng MH, Reinert G, Cannon CH, Sun FZ*~~~~~~Inference of Markovian Properties of Molecular Sequences from NGS Data and Applications to Comparative Genomics~~~~~~~
BMC Bioinformatics~2015~16~Xia, LC, Ai DM, Cram JA, Liang XY, Fuhrman JA, Fengzhu Sun FZ~~~~~~Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains.~~~~~~~
Marine Ecology Progress Series~2015~~Bialonski, S., D.A. Caron, U. Feudel, H. Kantz and S.D. Moorthi.~~~~~~Time-series dataset of phytoplankton indicates a complex mixture of transport and ecology in a coastal ecosystem.~~~~~~2016-09-28 13:40:31.816~
Nature Microbiology Needham, David M., and J. A. Fuhrman. 2016. Pronounced daily succession of bloom associated phytoplankton, archaea, & bacteria. Nature Microbiology 1, 16005. 29 February 2016 doi:~2016~1~David Needham and Jed Fuhrman~10.1038/nmicrobiol.2016.5~16005. 29~~~~Pronounced daily succession of bloom associated phytoplankton, archaea, & bacteria.~~~~~~2016-09-28 13:40:31.833~
Envir. Microbiol. (5)~2016~18~Parada, Alma, David M. Needham, and Jed A. Fuhrman.~10.1111/1462-29~1403~~~~Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples~~~~~~2016-09-28 13:40:31.840~
BMC Bioinformatics~2015~16~Xia, Li Charlie, Dongmei Ai, Jacob Cram, Xiaoyi Liang, Jed A Fuhrman, Fengzhu Sun~10.1186/s12859-015-0732-8~301~~~~Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains~~~~~~2016-09-28 13:40:31.843~
mSystems~2015~1~Walters, William, Embriette R. Hyde, Donna Berg-Lyons, Gail Ackermann, Greg Humphrey, Alma Parada, Jack Gilbert, Janet K. Jansson, Greg Caporaso, Jed A. Fuhrman, Amy Apprill, Rob Knight.~10.1128/mSystems.00009-15~~~~~Improved V4, V4-5, and ITS marker gene primers for microbial community survey. mSystems~~~~~~2016-09-28 13:40:31.850~
Limnol. Oceanogr~2016~61~Cram, Jacob A., Alma E. Parada and Jed A. Fuhrman~10.1002/lno.10259~889~~~~Dilution reveals how viral lysis and grazing shape microbial communities~~~~~~2016-09-28 13:40:31.853~
ISME J.~2016~10,~Weiss S., Van Treuren W., Lozupone C., Faust K., Friedman J., Deng Y., Xia L.C., Xu Z.Z., Ursell L., Alm E.J., Birmingham A., Cram J.A., Fuhrman J.A., Raes J., Sun F., Zhou J., Knight R.~10.1038/ismej.2015.235~1669~~~~Correlation detection strategies in microbial datasets vary widely in sensitivity and precision~~~~~~2016-09-28 13:40:31.856~
Journal of Eukaryotic Microbiology~2015~~Hu, S., Z. Liu, A.A. Y. Lie, P.D. Countway, D.Y. Kim, A.C. Jones, R.J. Gast, E.B. Sherr, B.F. Sherr, S.C. Cary and D.A. Caron.~DOI: 10.1111/jeu.12217.~~~~~Marine microbial eukaryote diversity and biogeography inferred from three different approaches for processing DNA information. .~~~~~~2016-09-28 13:40:31.866~
International Journal of Robotics Research.~2015~~Das, J., F. Py, J. Harvey, J. Ryan, A. Gellene, R. Grahamk, D.A. Caron, K. Rajan and G,S. Sukhatme.~10.1177/0278364915587723~~~~~Data-driven robotic sampling for marine ecosystem monitoring~~~~~~2016-09-28 13:40:31.870~
FEMS Microbiology Ecology~2016~~Hu, S.K., V. Campbell, P. Connell, A.G. Gellene, Z. Liu, R. Terrado, D.A. Caron.~http://dx.doi.org/10.1093/femsec/fiw050.~~~~~Protistan diversity and activity inferred from rRNA and rDNA at a coastal ocean site in the eastern North Pacific~~~~~~2016-09-28 13:40:31.873~
Protist~2016~167~Mitra, A., K.J. Flynn, U. Tillmann, J. Raven, D. Caron, D. Stoecker, F. Not, P. Hansen, G. Hallegraeff, R. Sanders, S. Wilken, G. McManus, M. Johnson, P. Pitta, S. Våge, R. Berje, A. Calbet, F. Thingstad, J.J. Jeong, J. Burkholder, P. Glibert, E. Granéli~~10~~~~Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition; incorporation of diverse mixotrophic strategies~~~~~~2016-09-28 13:40:31.876~
Bioinformatics (online first, June 30, 2016)~2016~~YY Lu, T Chen, JA Fuhrman, F Sun~~~~~~COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge~~~~~~2016-09-28 13:40:31.893~
Nucleic Acids Research~2017~45~Ahlgren, Nathan, Jie Ren, Yang Lu, Jed A. Fuhrman, Fengzhu Sun~10.1093/nar/gkw1002~39~~~~Alignment-free d2? oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.~~~~~~2017-06-21 19:17:07.916~
Deep-Sea Research I.~2017~121~Caron, D.A., P. Connell, R.A. Schaffner, A. Schnetzer, J.A. Fuhrman, P.D. Countway, D.Y. Kim.~~14~~~~Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial Abundance and Biomass~~~~~~2017-06-21 19:17:07.956~
Deep-Sea Research I~2017~121~Connell, P., D.Caron et al.~~21~~~~Planktonic food web structure at a coastal time-series site: II. Spatiotemporal variability of microbial trophic activities.~~~~~~2017-06-21 19:17:07.960~
Scientific Reports~2016~6~Liao WN, Ren J, Wang K, Wang S, Zeng F, Wang Y, Sun FZ~~37243~~~~Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains~~~~~~2017-06-21 19:17:07.976~
Limnology and Oceanography.~2016~61~Martiny, A.C., A. Talarmin, C. Mouginot, J. Lee, J. Huang, A. Gellene and D.A. Caron.~10.1002/lno.10233~531~~~~Biogeochemical interactions control a temporal succession in the elemental composition of marine communities.~~~~~~2017-06-21 19:17:08.20~
ISME Journal~2017~Advance~Needham, David M., Rohan Sachdeva, Jed A. Fuhrman.~10.1038/ismej.2017.29~~~~~Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters.~~~~~~2017-06-21 19:17:08.36~
Annual Reviews of Marine Sciences~2017~9~Stoecker, D.K, P.J. Hanse, D.A. Caron and A. Mitra.~10.1146/annurev-marine-010816-060617~311~~~~Mixotrophy in the marine Plankton.~~~~~~2017-06-21 19:17:08.53~
ISME J~2016~10~Weiss S., Van Treuren W., Lozupone C., Faust K., Friedman J., Deng Y., Xia L.C., Xu Z.Z., Ursell L., Alm E.J., Birmingham A., Cram J.A., Fuhrman J.A., Raes J., Sun F., Zhou J., Knight R.~10.1038/ismej.2015.235~1669~~~~Correlation detection strategies in microbial datasets vary widely in sensitivity and precision.~~~~~~2017-06-21 19:17:08.70~
BMC Bioinformatics~2017~18~Zhang MG, Yang LP, Ren J, Ahlgren NA, Fuhrman JA, Sun FZ~~60~~~~Prediction of virus-host infectious association by supervised learning methods.~~~~~~2017-06-21 19:17:08.90~