DOE Joint Genome Institute

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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News & Publications
Home › News & Publications › Scientific Posters

Scientific Posters

Note: neither these posters nor their contents may be reproduced except by permission of JGI.

Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274 (March, 2015 28th Fungal Genetics Conference) Andrei S. Steindorff

Comparative Analysis of Transcription Factors Families Across Fungal Tree of Life (March, 2015 The 10th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting) Asaf Salamov

Using the Model Perennial Grass Brachypodium sylvaticum to Engineer Resistance to Multiple Abiotic Stresses (March, 2015 The 10th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting) John Vogel

Exploration of Metagenome Assemblies with an Interactive Visualization Tool (July, 2014 Intelligent Systems for Molecular Biology BioViz Symposium 2014) Michael Cantor

Evolutionary History of Ascomyceteous Yeasts (June, 2014 the 2014 Annual Meeting of the Mycological Society of America) Sajeet Haridas

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics (June, 2014 Gordon Research Conference on Marine Microbes) Leong-Keat Chan

Genetic Control of Plant Root Colonization by the Biocontrol agent, Pseudomonas fluorescens (March, 2015 The 10th Annual DOE Joint Genome Institute Genomics of Energy & Environment Meeting) Benjamin J. Cole

Whole-Genus Sequencing: 300 Aspergilli (2015 28th Fungal Genetics Conference) Alan Kuo

Genomic Evolution of the Ascomycete Yeasts (March, 2015 28th Fungal Genetics Conference) Robert Riley

Fueling the Future with Fungal Genomics (October, 2014 Biosciences Retreat) Igor V. Grigoriev

Large Scale Sequencing of Dothideomycetes Provides Insights into Genome Evolution and Adaptation (March 2015 28th Fungal Genetics Conference) Sajeet Haridas

The effect of compost on carbon cycling and the active soil microbiota (December, 2014 American Geophysical Union – San Francisco) Esther Singer

Phytozome Comparative Plant Genomics Portal (September, 2014 Plant Genomics Conference – St. Louis, Missouri) David Goodstein

RNA-Seq Gene Expression Analysis at the Joint Genome Institute (JGI User Meeting 2014) Vasanth Singan, Anna Lipzen, James Han and Erika Lindquist

BBMap: A Fast, Accurate, Splice-Aware Aligner (JGIUM 2014) Brian Bushnell

The JGI Pipeline for Annotation of Microbial Genomes and Metagenomes (JGIUM 2014) Marcel Huntemann, Konstantinos Mavrommatis, Natalia Ivanova, Natalia Mikhailova, Galina Ovchinnikova, Andrew Schaumberg, Jim Tripp, Krishna Palaniappan, Ernest Szeto, I-Min Chen, Nikos Kyrpides, Amrita Pati

JGI Fungal Genomics Program (Fungal Genetics Conference) Igor Grigoriev

Rapid and Efficient Methods for Ribosomal RNA Removal from Plant and Metatranscriptome Samples Cindi A. Hoover and Cris Kinross

PERTRAN: Genome-guided RNA-seq Read Assembler Shengqiang Shu, David M. Goodstein, & Dan Rokhsar

Mining the Agave Microbiome for adapations to arid environment Devin Coleman-Derr, Tanja Woyke, Gretchen North, Laila Partida-Martinez, Kristen DeAngelis, Scott Clingenpeel, Stephen Gross, Susannah Tringe, Axel Visel

Microbial Dark Matter: Unusual intervening sequences in 16S rRNA genes of candidate phyla from the deep subsurface (JGIUM 2014) Jessica Jarett, Ramunas Stepanauskas, Thomas Kieft, Tullis Onstott, Tanja Woyke

High-resolution phylogenetic microbial community profiling (JGIUM 2014) Esther Singer, Devin Coleman-Derr, Brett Bowman, Patrick Schwientek, Alicia Clum, Alex Copeland, Doina Ciobanu, Jan- Fang Cheng, Esther Gies, Steve Hallam, Susannah Tringe, Tanja Woyke

Assembly of Repeat Content Using Next Generation Sequencing Data (JGIUM 2014) Kurt LaButti1, Alan Kuo, Igor Grigoriev, Alex Copeland

Automated Single Cell Data Decontamination Pipeline (JGIUM 2014) Kristin Tennessen, Amrita Pati

Integrated OMICs analysis in IMG and IMG/M (JGIUM 2014) Amrita Pati, Neha Varghese, I-Min Amy Chen, Marcel Huntemann, Kostas Billis, Kostas Mavrommatis, Krishna Palaniappan, Ernest Szeto, Anna Ratner, Manoj Pillay, Ken Chu, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides

The evolution of microbial species – a view through the genomic lens (JGIUM 2014) Neha Varghese, Supratim Mukherjee, Natalia Ivanova, Konstantinos Mavromatis, Konstantinos Konstantinidis, Nikos Kyrpides and Amrita Pati

Stop Codon Reassignment in the Wild (JGIUM 2014) Natalia Ivanova, Patrick Schwientek, H. James Tripp, Christian Rinke, Marcel Huntemann, Axel Visel, Tanja Woyke, Nikos Kyrpides, Edward Rubin

Promoting, understanding, recording, and utilizing metadata in genomic/metagenomic studies (JGIUM 2014) Alex Thomas, T.B.K. Reddy, Michelle Isbandi, Jyothi Mallajosyula, Dimitrios Stamatis, Jonathon Bertsch, Nikos Kyrpides

Exploring Arabidopsis thaliana Root Endophytes via Single-Cell Genomics (JGIUM 2014) Scott Clingenbeel, Derek Lundberg, Tanja Woyke, Susannah Tringe, Jeff Dangl

Genomics of “Candidatus Synechococcus spongiarum”, a Cyanobacterial Sponge Symbiont (JGIUM 2014) Beate M. Slaby, Alex Copeland, Tanja Woyke, Ute Hentschel

Microbial diversity and carbon cycling in San Francisco Bay wetlands (JGIUM 2014) Susanna Theroux, Wyatt Hartman, Shaomei He, Susannah Tringe

Transcriptional Interactome in Mouse Genome (Illumina User Meeting) Yubo ZHANG, Guoliang LI, Han XU, Fabianus Hendriyan MULAWADI, Ken SUNG Wing Kin, Xiao’an Ruan, Yijun Ruan and Chia-Lin WEI

Illumina Production Sequencing at DOE Joint Genome Institute Angela Tarver, Alison Fern, Nicole Shapiro, Mojgan Amirebrahimi, Megan Kennedy, Matthew Zane, Christopher Daum, Marie Ballon, David Gilbert, Susan Lucas, Chia-Lin Wei, Len Pennacchio

Genome-wide selective sweeps in natural bacterial populations revealed by time-series metagenomics (2014 ASM Conference) Leong-Keat Chan1, Matthew L. Bendall1, Stephanie Malfatti1, Patrick Schwientek1, Julien Tremblay1, Wendy Schackwitz1, Joel Martin1, Amrita Pati1, Brian Bushnell1, Brian Foster1, Dongwan Kang1, Suannah G. Tringe1, Stefan Bertilsson2, Mary Ann Moran3, Ashley Shade4, Ryan J. Newton5, Sarah Stevens6, Katherine D. McMahon6, and Rex Malmstrom1

Comparative Genomics of Mycorrhizal Symbiosis and Wood Decay in Forest Ecosystems (2014; France-Berkeley-Fund Meeting) Igor Grigoriev and Francis Martin

Dynamic of sequence-discrete bacterial populations inferred using metagenomes (JGIUM 2014)Sarah Stevens, Mathew Bendall, Dongwan Kang, Jeff Froula, Rob Egan, Leong-Keat Chan, Susannah Tringe, Katherine McMahon, Rex Malmstrom

FASTERp: a feature array search tool for estimating resemblance of protein sequences (JGIUM 2014) Derek N. Macklin, Rob Egan, Zhong Wang

Functional and comparative genomics of lignocellulose degradation by the fungus Schizophyllum commune (JGIUM 2014) Robin A. Ohm, Hanbyul Lee, Hongjae Park, Heather M. Brewer, Akiko Carver, Alex Copeland, Jane Grimwood, Erika Lindquist, Anna Lipzen, Joel Martin, Samuel O. Purvine, Wendy Schackwitz, Martin Tegelaar, Andrew Tritt, Scott Baker, In-Geol Choi, Luis G. Lugones, Han A. B. Wosten, Igor V. Grigoriev

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi (JGIUM 2014) Robert Riley, Asaf Salamov, Daren W. Brown, Laszlo G. Nagy, Dimitris Floudas, Benjamin Held, Anthony Levasseur, Vincent Lombard, Emmanuelle Morin, Robert Otillar, Erika Lindquist, Hui Sun, Kurt LaButti, Jeremy Schmutz, Dina Jabbour, Hong Luo, Scott E. Baker, Antonio Pisabarro, Jonathan D. Walton, Robert Blanchette, Bernard Henrissat, Francis Martin, Dan Cullen, David Hibbett, Igor V. Grigoriev

Single cell genomics and transcriptomics for unicellular eukaryotes (JGIUM 2014) Doina Ciobanu, Alicia Clum, Vasanth Singan, Adaf Salamov, James Han, Alex Copeland, Igor Grigoriev, Timothy James, Steven Singer, Tanja WOyke, Rex Malmstrom, Jan-Fang Cheng

Current developments in prokaryotic single cell whole genome amplification (JGIUM 2014)
Danielle Goudeau, Nandita Nath, Doina Ciobanu, Jan-Fang Cheng, Rex Malmstrom

Genome editing in Escherichia coli with Cas9 and synthetic CRISPRs (JGIUM 2014) Ze Peng, Sarah Richardson, David Robinson, Samuel Deutsch, Jan-Fang Cheng

MetaBAT: Metagenome binning based in abundance and tetranucleotide frequency (JGIUM 2014) Dongwan D. Kang, Jeff Froula, Rob Egan, Zhong Wang

Chromatin landscaping in algae reveals novel regulation pathway for biofuels production (AGBT Conference 2013) Chew Yee Ngan, Chee-Hong Wong, Cindy Choi, Abhishek Pratap, James Han, Chia-Lin Wei

Functional Encyclopedia of Bacteria and Archaea (JGIUM 2013) M. J. Blow, A. M. Deutschbauer, C. A. Hoover, J. Lamson, L.A.Pennacchio, M. N. Price, J. Waters, K. M. Wetmore, J. Bristow, A. P. Arkin

Assessment of Nextera Long Mate-Pair Libraries: A Rapid, Low-Input Method for Mate-Pair Library Construction Yields Improved Assemblies (JGIUM 2013) Cindi A. Hoover, Kevin S. Eng, Hui Sun, Jeff Froula, and Feng Chen

PacBio Only Assembly with Low Genomic DNA Input (JGIUM 2013) Zhiying Zhao, Yu-Chih Tsai, Alicia Clum, Katherine Munson, Chris Daum, Stephen W. Turner, Jonas Korlach, Len A. Pennacchio, Feng Chen

Phasing Variants in Poplar Trees using a Hybrid of Short & Long Read Technologies (JGIUM 2013) Wendy Schackwitz, Joel Martin, Anna Lipzen, Len Pennacchio, Gerald Tuskan

Annotation of Fungal Transposable Elements Jaydeep Srimani, Igor Grigoriev, Asaf Salamov

Transcriptome analysis of drough-tolerant CAM plants, Agave deserti and Agave tequilana (JGIUM 2013) Stephen M. Gross, Jeffrey A. Martin, June Simpson, Zhong Wang, and Axel Visel

Comparison of Three Cre-LoxP Based Paired-End Library Construction Methods (JGIUM 2013) Ze Peng, Nandita Nath, Andrew Tritt, Shoudan Liang, James Han, Len Pennacchio and Feng Chen

Microbial diversity in restored wetlands of San Francisco Bay (AGU 2013) Susanna Theroux, Wyatt Hartman, Shaomei He, Susannah Tringe

DNA Synthesis and Assembly Pipeline (JGIUM 2013) Samuel Deutsch, Sarah Richardson, Angela Tarver, Matthew Hamilton, David Robinson, Sangeeta Nath, Matthew Bendall, Miranda Harmon-Smith, Lisa Simirenko, Nathan J Hillson, and Jan-Fang Cheng

Chromatin landscaping in algae reveals novel regulation pathway for biofuels production (AGBT Conference, 2013) Chew Yee Ngan, Chee-Hong Wong, Cindy Choi, Abhishek Pratap, James Han, Chia-Lin Wei

Transcriptomic and Metagenomic Exploration of Agave Drought and Stress Tolerance (CSHL, Biology of Genomes, 2012) Stephen Gross, Jeffrey Martin, June Simpson, Laila Partida-Martínez, Gretchen North, Yuri Peña-Ramirez, Aidee Orozco-Hernandez, Kristen DeAngelis, Tanja Woyke, Scott Clingenpeel, Susannah Tringe, Zhong Wang, and Axel Visel

Multiple Long Mate Pair Approaches to Facilitate Short read based de novo Genome Assembly (Sequencing, Finishing and Analysis in the Future, 2012) Julianna Chow, Jaya Rajamani, James Han, Alicia Clum, Alex Copeland, Shweta Deshpande and Chia-Lin Wei

Identification of ionic liquids tolerant cellulases for biomass processing (JGIUM 2012) Tao Zhang, Supratim Datta, Jerry Eichler, Natalia Ivanova, Seth D. Axen, Cheryl A. Kerfeld, Feng Chen, Nikos Kyrpides, Philip Hugenholtz, Jan-Fang Cheng, Kenneth L. Sale, Blake Simmons and Eddy Rubin

Barcode labeling of short reads for detection of large scale genomic variations (JGIUM 2012) Tao Zhang, Kevin Eng, Jeff Froula, Kanwar Singh, Matt Blow, Zhong Wang, Len Pennacchio and Feng Chen

BioPig – A Hadoop-based Analytic Toolkit for Large Scale Sequence Data (JGIUM 2012) Kai Wang and Henrik Nordberg

Agave transcriptomes and microbiomes for bioenergy research (JGIUM 2012) Stephen Gross, Jeffrey Martin, June Simpson, Laila Partida-Martínez, Gretchen North, Yuri Peña-Ramirez, Aidee Orozco-Hernandez, Kristen DeAngelis, Tanja Woyke, Scott Clingenpeel, Susannah Tringe, Zhong Wang, and Axel Visel

Sequencing and Data Analysis of Prokaryotic 5’-Transcrept Ends. (JGIUM 2012) Ze Peng, Jeff Froula, Cindi Hoover, Xiandong Meng, Zhong Wang and Feng Chen

Detecting genome-wide DNA methylation patterns in Shewanella oneidensis MR-1 (JGIUM 2012) Rex R. Malmstrom, Matthew Bendall, Khai Luong, Matthew Blow, Jonas Korlach, and Adam Deutschbauer

Deep sequencing of a plant transcriptome (JGIUM 2012) Jeffrey Martin, Stephen Gross, James Schnable, Cindy Choi, Mei Wang, Kanwar Singh, Erika Lindquist, Feng Chen, Chia-Lin Wei, Zhong Wang

RNA-Seq Pipeline in Galaxy (JGIUM 2012) Xiandong Meng, Jeffrey Martin, Edward Kirton, and Zhong Wang

Resequencing: The Untold Story Recognizing False Positives, False Negatives and Structural Variation in User Data (Sequencing, Finishing and Analysis in the Future, 2012) Authors: Anna Lipzen, Wendy Schackwitz, Joel Martin, Len A. Pennacchio

The JGI Times – Portal 6.0 Released!! (unknown 2011) Michael Cantor and Tatyana Smirnova

Metagenomic gene annotation by a homology independent approach (unknown 2011) Changbin Du, Jeff Froula, Tao Zhang, Annette Salmeen, Matthias Hess, Cheryl A. Kerfeld, Zhong Wang

Sequencing the Algal Tree of Life (unknown 2011) Alan Kuo, Igor V. Grigoriev

Illumina Production Sequencing at the DOE Joint Genome Institute – Workflow and Optimizations (Bay Area Illumina User Meeting 2011) Angela Tarver, Alison Fern, Matthew San Diego, Megan Kennedy, Matthew Zane, Christopher Daum, Christopher Hack, Eric Tang, Shweta Deshpande, Jan-Fang Cheng, Simon Roberts, Melanie Alexandre, Miranda Harmon-Smith, Susan Lucas

Phylogeny and comparative genome analysis of a Basidiomycete fungi (DOE JGI User Meeting 2011) Robert W. Riley, Asaf Salamov, Igor Grigoriev, David Hibbett

Portal 6.0 Released (DOE JGI User Meeting 2011) Michael Cantor, Tatyana Smirnova

UV Decontamination of MDA Reagents for Single Cell Genomics (DOE JGI User Meeting 2011) Janey Lee, Damon Tighe, Alexander Sczyrba, Rex Malmstrom, Scott Clingenpeel, Stephanie Malfatti, Christian Rinke, Zhong Wang, Ramunas Stepanauskas, Jan-Fang Cheng, Tanja Woyke

Illumina Unamplified Indexed Library Construction: An Automated Approach (DOE JGI User Meeting 2011) Christopher A. Hack, Alexander Sczyrba, Jan-Fang Cheng

DUK – A Fast and Efficient Kmer Based Sequence Matching Tool (DOE JGI User Meeting 2011) Mingkun Li, Alex Copeland, James Han

Ancient nature of alternative splicing and functions of introns (DOE JGI User Meeting 2011) Kemin Zhou, Asaf Salamov, Alan Kuo, Andrea Aerts, Igor Grigoriev

Expansion of the Genomic Encyclopedia of Bacteria and Archaea  (DOE JGI User Meeting 2011) Christian Rinke, Alex Sczyrba, Stephanie Malfatti, Janye Lee, Jan-Fang Cheng, Ramunas Stepanauskas, Jonathan A. Eisen, Steven Hallam, William P. Inskeep, Brian P. Hedlund, Stefan M. Sievert, Wen-Tso Liu, George Tsiamis, Philip Hugenholtz, Tanja Woyke

Efficient Graph Based Assembly of Short-Read Sequences on Hybrid Core Architecture (DOE JGI User Meeting 2011) Alex Sczyrba, Abhishek Pratap, Shane Canon, James Han, Alex Copeland, Zhong Wang, Tony Brewer, David Soper, Mike D’Jamoos, Kirby Collins, George Vacek

Limitations and Improvement of Constructing Long Paired-end Libraries (DOE JGI User Meeting 2011) Ze Peng, Matthew Hamilton, Jeff Froula, Aren Ewing, Jan-Fang Cheng

JGI Fungal Genomics Program (26th Annual Fungal Genetics Conference 2011) Igor V. Grigoriev

Comparative analysis of twelve Dothideomycete plant pathogens (26th Annual Fungal Genetics Conference 2011) Robin Ohm, Andrea Aerts, Asaf Salamov, Stephen B. Goodwin, Igor Grigoriev

Sequencing the Black Aspergilli species complex (26th Annual Fungal Genetics Conference 2011) Alan Kuo, Asaf Salamov, Kemin Zhou, Robert Otillar, Scott Baker, Igor Grigoriev

Illumina GA IIx & HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute (Advances of Genome Biology and Technology Meeting 2011) Christopher Daum, Matthew Zane, James Han, Megan Kennedy, Matthew San Diego, Alex Copeland, Mingkun Li, Susan Lucas

Illumina GA IIx & HiSeq 2000 Production Sequencing and QC Analysis Pipelines at the DOE Joint Genome Institute (AGBT 2011) Chris Daum, James Han, Matt Zane, Angela Tarver, Megan Kennedy, Matthew San Diego, Alex Copeland, Jarrod Chapman, Joel Martin2, Mingkun Li, JGI Production Illumina Sequencing & Rolling QC Teams, and Susan Lucas

DNA Production Sequencing at the Joint Genome Institute: A Multi-Process Operating System (Sequencing, Finishing and Analysis in the Future 2010) Miranda Harmon-Smith, Simon Roberts, Christopher Daum, Mathew Zane, Susan Lucas and the JGI Sequencing Team

It’s so easy being green (Applied Ergonomics Conference 2010) Nicole Shapiro, Angela Tarver, Megan Kennedy, Eric Tang, Natasha Zvenigorodsky, Matthew San Diego, Christine Naca, Melanie Alexandre

Robotic Enrichment Processing of Roche 454 Titanium Emulsion PCR at the DOE Joint Genome Institute (Sequencing, Finishing and Analysis in the Future Meeting 2010) Matthew Hamilton, Steven Wilson, Diane Bauer, Don Miller, Kecia Duffy-Wei, Nancy Hammon, Susan Lucas, Martin Pollard, Jan-Fang Cheng

Gap Closing/Finishing by Targeted Genomic Region Enrichment and Sequencing (Sequencing, Finishing and Analysis in the Future Meeting 2010) Kanwar Singh, Jeff Froula, Hope Trice, Len A. Pennacchio, Feng Chen

Large Gap Size Paired-end Library Construction for Second Generation Sequencing (Sequencing, Finishing and Analysis in the Future Meeting 2010) Ze Peng, Matthew Hamilton, Jeff Froula, Aren Ewing, Brian Foster, Jan-Fang Cheng

Analysis of Illumina Microbial Assemblies (Sequencing, Finishing and Analysis in the Future Meeting 2010) Alicia Clum, Brian Foster, Jeff Froula, Kurt LaButti, Alex Sczyrba, Alla Lapidus, Tanja Woyke

Development of High Throughput Process for Constructing 454 Titanium and Illumina Libraries (Sequencing, Finishing and Analysis in the Future Meeting 2010) Shweta Deshpande, Christopher Hack, Eric Tang, Stephanie Malfatti, Aren Ewing, Susan Lucas, Jan-Fang Cheng

Development of High Throughput Process for Constructing 454 Titanium Libraries (DOE JGI User Meeting 2010) Shweta Deshpande, Chris Hack, Eric Tang, Stephanie Malfatti, Susan Lucas, Jan-Fang Cheng

Development of High Throughput Processes for Constructing Illumina Libraries (JGI User Meeting 2010) Eric Tang, Christopher Hack, Aren Ewing, Jeff Froula, Susan Lucas, Shweta Deshpande, Jan-Fang Cheng

Overcoming some of the challenges to single cell genomics (JGI User Meeting 2010) Janey Lee, Damon Tighe, Mei Wang, Stephanie Malfatti, Erika Lindquist, Feng Chen, Jan-Fang Cheng, Tanja Woyke

The pan-genome of Emiliania huxleyi (JGI User Meeting 2010) Alan Kuo, Igor Grigoriev, Betsy Read

Comparative Analysis of Thermophillic Fungal Genomes (JGI User Meeting 2010) Robert Otillar, Asaf Salamov, Alex Atkins, Frank Korzeniewski, Jeremy Schmutz, Erika Lindquist, Adrian Tsang, Randy Berka, Igor Grigoriev

High EST Coverage Revealed Abundant Alternatively Spliced Transcripts (JGI User Meeting 2010) Kemin Zhou, Asaf Salamov, Alan Kuo, Andrea Aerts, Igor Grigoriev

Innovative Seed Program (JGI User Meeting 2010) Kristen Taylor, Henrik Nordberg, Tatyana Smirnova, David Gilbert

Flip Your Lid (Applied Ergonomics 2010) Angela Tarver, Bridget Swift, Megan Kennedy, Nicole Shapiro, Melanie Alexandre, Christine Naca, David Gilbert, Massie Ballon, Martin Pollard, Greg Mannino, David Humphries

Limitations and Improvement of Constructing Long Paired-end Libraries (Advances in Genome Biology and Technology (AGBT) 2010) Jan-Fang Cheng, Jeff Froula, Aren Ewing, Ze Peng

Optimization of the Roche 454-Titanium GAIIx Production Sequencing Pipelines at the DOE Joint Genome Institute (Advances in Genome Biology and Technology (AGBT) 2010) Christopher Daum, Nicole Shapiro, Angela Tarver, Diane Bauer, Bridget Swift, Megan Kennedy, Miranda Harmon-Smith, Matthew Zane, Matthew Hamilton, David Robinson, Jan-Fang Cheng, Susan Lucas

Comparative Analysis of the Complete Pichia stipitis Genome (Fungal Genetics Conference 2009) Andrea Aerts, Alan Kuo, Asaf Salamov, Paramvir Dehal, Robert P. Otillar, Jane Grimwood, Thomas W. Jeffries, Paul Richardson, Igor Grigoriev

The VISTA Synteny Viewer: Navigating Whole Genome Alignments at Multiple Levels of Resolution (Genome Informatics 2009)

POLISHER: A tool for using ultra short reads in genome sequence improvement (Illumina User Meeting) Brian Foster, Kurt LaButti, Stephan Trong, Cliff Han, Tom Brettin, Alla Lapidus

Illumina Production Sequencing at the DOE Joint Genome Institute – Workflow and Optimizations (Northern California Sequencing User Meeting 2009) Angela Tarver, Matthew Zane, Christopher Daum, Mansi Chovatia, David Robinson, Christopher Hack, Febg Chen, Cindy Choi, Jan-Fang Cheng, Greg Mannino, Marty Pollard, Simon Roberts, Christine Naca, Melanie Alexandre, Susan Lucas

Finishing of New Technology Only Microbes and Fungi (Sequencing, Analysis and Finishing in the Future 2009) Alicia Clum, Hui Sun, Kurt LaButti, Brian Foster, Steve Lowry, Stephan Trong, Alla Lapidus

Gap Resolution: A Software Package for Improving Newbler Genome Assemblies (Sequencing, Finishing and Analysis in the Future 2009) Stephan Trong, Kurt LaButti, Brian Foster, Cliff Han, Tom Brettin, Alla Lapidus

JGI Microbial Sequencing Process (Sequencing, Finishing and Analysis in the Future 2009) Tijana Glavina del Rio, Chris Daum, Shweta Deshpande, Alla Lapidus, Matt Nolan, Nicole Shapiro, Hope Tice, Lynne Goodwin, David Bruce, Susan Lucas

Cloning and Sequencing with Trace Amount of DNA on Roche/454 and Illumina Platforms (Sequencing, Finishing and Analysis in the Future 2009) Mansi Chovatia, Hope N. Tice, Jeff Froula, Jan-Fang Cheng

Genome Improvement with Bubble-PCR and Roche/ 454 Reads (Sequencing, Finishing and Analysis in the Future 2009)  Hope N. Tice, Janey Lee, Matt Hamilton, Brian Foster, Stephanie Malfatti, Patrick Chain, Alla Lapidus, Susan Lucas, Jan-Fang Cheng

Decontamination of MDA Reagents for Single Cell Genomics (Sequencing, Finishing and Analysis in the Future 2009) Damon Tighe, Tanja Woyke, Janey Lee, Jan-Fang Cheng, James Han

Modification of the Roche/ 454 Titanium Paired-end Protocol for a Scale Up Library Production (JGI User Meeting 2009) Ze Peng, Matthew Hamilton, Jan-Fang Cheng

Assembly Improvement on Data from New Sequencing Technologies (JGI User Meeting 2009) Kurt LaButti, Brian Foster, Stephan Trong, Steve Lowry, Cliff Han, Thomas Brettin, Matt Nolan, Susan Lucas, Alla Lapidus

Discovery of substrate-targeted enzymes for the degradation of biomass by Metatranscriptomics (JGI User Meeting 2009) Matthias Hess, Tao Zhang, Susanna Tringe, R. Mackie, Eddy Rubin

Fungal Genome Size Driven by Duplication and Reverse Transcriptase (JGI User Meeting 2009) Kemin Zhou

Whole Genome Annotation and Comparative Analysis of whiterot fungus Pleurotus ostreatus (JGI User Meeting 2009) Robert Otillar, Andrea Aerts, Asaf Salamov, Jeremy Schmutz, Erika Lindquist, Antonio Pisabarro, Igor Grigoriev

DOE JGI PROJECT MANAGEMENT OFFICE (JGI User Meeting 2009) Christa Pennacchio, Ed Allen, Kerrie Barry, Joni Fazo, Lynne Goodwin, Marcia McGowan, Rene Perrier, Lin Peters, Sam Pitluck, Susannah Tringe, David Bruce

THE JGI METAGENOME PROGRAM (JGI User Meeting 2009) Susannah Tringe, Martin Allgaier, Phil Hugenholtz

Annotation of Eukaryotic Genomes (JGI User Meeting 2009) Igor V. Grigoriev, Andrea Aerts, Frank Korzeniewski, Alan Kuo, Robert Otillar, Asaf Salamov, Xueling Zhao, Kemin Zhou

Improvements to the Illumina Sequencing System and New Applications (JGI User Meeting 2009) David Hillman, Mary Ann Pedraza, Sirisha Sunkara, Maria Shin, Jeff Froula, Feng Chen, Len Pennacchio

Assessment, optimization and Applications of 454 FLX Titanium Sequencing Systems (JGI User Meeting 2009) Kanwar Singh, Zhiying Jean Zhao, Natasha Zvenigorodsky, Jeff Froula, Len Pennacchio, Feng Chen

Fungal Intron Evolution: Why a small genome has many introns? (Fungal Genetics Conference at Asilomar 2009) Alan Kuo, Asaf Salamov, Igor Grigoriev, K. Zhou

Comparative Genomics Tools for analysis of Six Dothideomycete Genomes (Fungal Genetics Conference at Asilomar 2009) Andrea Aerts, Simon Minovitsky, Michael Cantor, Inna Dubchak, Igor Shabalov, Igor Grigoriev, Igor Ratnere

Exploring Variation Detection Within a Wide Range of Bioenergy-Relevant Species Via Short Read Technology (Advances in Genome Biology and Technology (AGBT) 2009) Wendy Schackwitz, Joel Martin, Sirisha Sunkara, Mary Ann Pedraza, Maria Shin, David Hillman, Anna Lipzen, Crystal Wright, Feng Chen, Len Pennacchio

PyroTag: Pyrosequencing as a Powerful Tool to Study the Diversity of microbial Community (Advances in Genome Biology and Technology (AGBT) 2009) Feng Chen, Anna Engelbrekston, Natasha Zvenigorodsky, Victor Kunin, Phil Hugenholt, Howard Ochman

Process Optimization in Production (DOE BERAC Review at JGI 2009) J.-F. Cheng, D. Tighe, D. Robinson, C. Hack, M. Hamilton, J. Chow, H. Tice, Z. Peng, S. Lucas

Supporting the Sanger, 454 and Illumina Production Lines (DOE BERAC review at JGI 2009) A. Copeland, T. Glavina del Rio, G. Pang, M. Pollard, A. Lapidus, S. Lucas

Sanger, 454 and Illumina Production Lines (DOE BERAC review at JGI 2009) C. Daum, S. Roberts, J.-F. Cheng, M. Zane, A. Tarver, N. Shapiro, M. Kennedy, K. Lail, M. Harmon-Smith, H. Tice, S. Lucas

Safety Culture at the Joint Genome Institute (DOE BERAC review a JGI 2009) Steven Wilson

Assembly and Sequence Analysis of the Single Cell Genome of an Uncultured, Marine Flavobacterium (Advances in Genome Biology and Technology 2009) A. Copeland, T. Woyke, G. Xie, C. Han, J.-F. Cheng, H. Kiss, M.E. Sierachi, R. Stepanauskas

Progress Towards a High Throughput 454 Titanium Library Construction (Advances in Genome Biology and Technology 2009) J.-F. Cheng, W. Phung, Z. Peng, C. Hack, H. Shapiro, C. Daum, S. Lucas

Optimization of the Roche/ 454 and Illumina Production Sequencing Pipelines at the DOE Joint Genome Institute (Advances in Genome Biology and Technology 2009) C. Daum, N. Shapiro, M. Zane, A. Tarver, M. Hamilton, N. Hammon, S. Wilson, K. Singh, M. Pollard, F. Chen, J.-F. Cheng, S. Lucas

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