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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: 2005 – 2008

Scientific Posters: 2005 – 2008

To view and download the following posters, go to https://publications.lbl.gov/

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

DOE JGI Project Management Office (DOE BERAC review at JGI 2008) Marcia Mcgowan

Eukaryotic Microbial Program (DOE BERAC review at JGI 2008) Igor Grigoriev, Alla Lapidus, Scott Baker

Eukaryotic Genome Annotation (DOE BERAC review at JGI 2008) Igor V. Grigoriev

PGF Computing Resources (DOE BERAC review at JGI 2008) Brian Yumae, Jeremy Brand

Metagenomic Finishing at the JGI (Metagenomics 2008) Alla Lapidus, Stephen Lowry, Alicia Clum, Eugene Goltsman, Hector Garcia Martin, Phil Hugenholtz, Susan Lucas

PyroTag: Pyrosequencing as a Powerful Tool to Study the Diversity of Microbial Community (FLX User Group Meeting 2008) Feng Chen, Anna Engelbrektson, Natasha Zvenigorodsky, Howard Ochman, Philip Hugenholt

Optimization of the 454 Production Sequencing Workflow at the DOE Joint Genome Institute (Roche GLX Users Meeting 2008) Christopher Daum, Matthew Hamilton, Nicole Shapiro, David Robinson, Christopher Hack, Megan Kennedy, Martin Pollard, David Humphries, Simon Roberts, Eli Novin, Jan-Fang Cheng, Susan Lucas

Gap Closure with Roche/ 454 Reads (Roche GLX Users Meeting 2008) Jan-Fang Cheng, Hope N. Tice, Stephanie Malfatti, Wilson Phung, Matthew Hamilton, Alla Lapidus, Susan Lucas

Metagenomic Bacterial Finshing at the JGI (Finishing in the Future 2008) Stephen Lowry, Alicia Clum, Eugene Goltsman, Hector Garcia Martin, Phil Hugenholtz, Alla Lapidus

Ligation-mediated PCR Amplification as a Tool to Finish Microbial Genomes (Finishing in the Future 2008) Hope N. Tice, Eileen M. Dalin, Ze Peng, Susan Lucas, Jan-Fang Cheng

POLISHER: a Tool for Using Ultra Short Reads in Microbial Genome Finishing (Finishing in the Future 2008) Kurt LaButti, Brian Foster, Steve Lowry, Stephan Trong, Eugene Goltsman, Alla Lapidus

Library Construction Using Trace Amount of DNA (Finishing in the Future 2008) Julianna Chow, Eileen Dalin, Tanja Woyke, Susan Lucas, Jan-Fang Cheng

Modification of the GS LT Paired-end Library Protocol for Constructing Longer Insert Size Libraries (Finishing in the Future 2008) Ze Peng, Matthew Hamilton, Sara Ting, Hank Tu, Eugene Goltsman, Alla Lapidus, Susan Lucas, Jan-Fang Cheng

Finishing of Spirochaeta aurantia M1 (Finishing in the Future 2008) Alicia Clum, Steve Lowry, Brian A. Rabkin, Hui Sun, Alla Lapidus

Enhancing Microbial Genome Finishing Through Frameshift Targeting (Finishing in the Future 2008) Brian Foster, Eugene Goltsman, Kurt LaButti, Steve Lowry, Alla L. Lapidus

Single Cell Genome Reconstruction of Two Uncultured, Proteorhodopsin-containing Flavobacteria (Finishing in the Future 2008) Tanja Woyke, Alex Copeland, Gary Xie, Cliff Han, Jan-Fang Cheng, Hajnalka Kiss, Jimmy Saw, Pavel Senin, Michael E. Sieracki, Ramunas Stepanauskas

Establishing Optimal Coverage Levels for Different Sequencing Platforms (Finishing in the Future 2008) Eugene Goltsman, Brian Foster, Alex Copeland, Mingkun Li, Kurt LaButti, Alla Lapidus

Whole-Genome gene expression and gene family analyses of Phycomyces blakesleeanus, a model photoresponsive zygomycete (European Conference on Fungal Genetics 2008) Alan Kuo, Asaf Salamov, Alex Atkins, Luis Corrochano, Igor Grogiriev

An annotation “minipipe” to rapidly assess genomic assemblies of 454 pyrosequencing reads (JGI User Meeting 2008) Alan Kuo, Igor Grigoriev, Paul Richardson, Darren Platt

Creating a Critical Mass of Data for Genome annotation and comparative Analysis (Asilomar Fungal Conference 2008) Igor Grigoriev, Andrea Aerts, Jean Challacombe, Alan Kuo, Asaf Salamov, Diego Martinez, Monica Misra, Robert Otillar, Astrid Terry, Kemin Zhou

MyJGI: Tools for Collaborators (JGI User Meeting 2008) Joni Fazo, David Pletcher, Kristen Taylor, Annette Greiner, Anthony Kosky, Rene Perrier, Arkady Voloshin

Eukaryotic Genome Annotation and Analysis @ JGI (JGI User Meeting 2008) Igor Grigoriev, Andrea Aerts, Frank Korzeniewski, Alan Kuo, Asaf Salamov, Robert Otillar, Xueling Zhao, Kemin Zhou

De Novo Genome Sequencing: Genome Annotation as a Tool to Assess Short Read Assemblies (2008) Igor Grigoriev, Alan Kuo, Edward Kirton, Erika Lindquist, Paul Richardson, Darren Platt

Rearray Manager (Finishing in the Future 2008) Alicia Clum, Eugene Goltsman, Steve Lowry, Hui Sun, Brian Foster, Stephan Trong, Paul Richardson, Alla Lapidus

Overview: The Manual Peeling Process (2008) Simon R. Roberts, Mark West, Karl Petermann, Charles Reiter, Christine Naca, Megan Kennedy, Gerald Ilog, Martin J. Pollard, Michael Pintor, Laura Sandor, Kathryn Bowser, Ira Janowitz, Debra Rosett, Roy Kaltschmidt

Production workflow tracking and QC analysis (2008) Heather Kimball, Stephan Trong, Art Kobayashi, Sam Pitluck, Yunian Lou, Matt Nolan

Coral Reef Genomics: A Genome-Wide Approach to the Study of Coral Symbiosis (2008) Jodi Schwarz, Peter Brokstein, Cindy Lewis, Chitra Manohar, Dave Nelson, Carol Tang, Alina Szmant, Mary Alice Coffroth, Monica Medina

Quality Control of JGI Microbial Sequencing Projects (2008) Kerrie W. Barry, Alla L. Lapidus, Eugene V. Goltsman, Matt P. Nolan, Joel A. Martin, Mingkun Li, Paul M. Richardson, Alex C. Copeland

The US DOE Joint Genome Institute Microbial Genome Program (2008) Alla Lapidus, Patrick Chain, Cliff Han, Thomas Brettin, Alex Copeland, Chris Detter, Samuel Pitluck, Tijana Glavina del Rio, Susan Lucas, Kerrie Barry, Miriam Land, Frank Larimer, Nikos Kyrpides, Natalia Ivanova, Jeremy Schmutz, Victor M. Markowitz, David Bruce, Paul Gilna, Jim Bristow, Eddy Rubin, Paul Richardson

Shotgun Library Utilization for Microbial Sequencing Projects at the JGI (2008) Chris Detter, Eileen Dalin, Doug Smith, Hope Tice, Mariana Anaya, Dean Ng, Victor Dorsett, Alex Copeland, Kerrie Barry, Miranda Smith-Harmon, Susan Lucas, Eddy Rubin, Paul Richardson

Integrated Microbial Genomes genomic data analysis system (2008) Nikos C. Kyrpides
Two rounds of whole genome duplication in the ancestral vertebrate (2008) Paramvir Dehal, Jeffrey L. Boore

A Phylogenomic Gene Cluster Resource: The Phylogenetically Inferred Groups (PhIGs) Database (2008) Paramvir Dehal, Wayne Huang, Jeffrey L. Boore

Metazome (2008) Bill Dirks, David Goodstein, Uffe Hellsten, Dan Rokhsar

One Million Reads of Maize (2008) Jarrod Chapman, Asaf Salamov, Uffe Hellsten, J. Chris Detter, Tijana Glavina-del Rio, Susan Lucas, Daniel Rokhsar

Soybean Rust, A Rising Star in Phytopathology (2008) Martha L. Posada-Buitrago, Jeffrey Boore, Reid D. Frederick

Automated High-Throughput Fosmid Isolation and End-Sequencing Using Magnetic Beads and Reduced Terminator Cycling Sequencing Reaction Kit (2008) Feng Chen, Joseph Alessi, Jamie Jett, Steven Wilson, Dou-Shuan Yang, Paul Richardson

Complete Mitochondrial Genome Sequences for Four Bryozoan Species (2008) Tori L. Takaoka, Kevin G. Helfenbein, Jeffrey L. Boore, Monica Medina

Over/Under-Representation of sigma-70 promoter-like signals in Different Genomic Regions (2008) Jeff Froula, Maria Pilar Francino, Araceli H. Huerta

Comparing the fine structure of promoter regions across bacterial species (2008) Araceli M. Huerta, Julio Collado-Vides, M. Pilar Francino

Genetic Elucidation of Metabolic Diversity in Dechloromonas aromatica strain RCB (2008) J.D. Coates

Microbial Finishing at JGI (2008) Alla Lapidus, Patrick Chain, Cliff Han, Eugene Goltsman, Michele Martinez, Stephanie Malfatty, Olga Chertkov, Stephan Trong, Tom Brettin, Roxanne Tapia, Alex Copeland, Paul Richardson

Quality assessment of predicted gene models in microbial genomes (2008)E. Kim, B.J. Dunham, I.W. Bogorad, L.C. Croitor, J.H. Kuo, X. Zhao, I.J. Anderson, A. Lykidis, K. Mavromatis, N. Ivanova, N.C. Kyrpides

Integrated Microbial Genomes (IMG): New Data and Functionality in Version 1.2 (2008) Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anuradha Padki, Zhao Xueling, Philip Hugenholz, Konstantinos Mavromatis, Iain Anderson, Athanasios Lykidis, Natalia Ivanova, Nikos C. Kyrpides

Implementation of a CyBio Integrated System to Aliquot Amplified DNA and Dispense DNA Sequencing Chemistry (Lab Automation 2008) Nancy Hammon

Automated High-Throughput 384-well Fosmid Isolation and End-Sequencing Using Magnetic Beads and Reduced Terminator Cycling Sequencing Reaction Kit (2008) Feng Chen, Jamie Jett, Joseph Alessi, Steven Wilson, Nancy Marie Hammon, Lisa Kegg, Duane Kubischta, Christine Naca, Paul Richardson

High Performance Magnetic Separation Technology for Microtiter Plates, Microarrays, Single Molecule Manipulation and Beyond. (2008) David Humphries, Martin Pollard

Implementing Automated 384 Well Fosmid Prep at JGI (2008) Steven Wilson, Feng Chen, Jamie Jett, Nancy Hammon, Duane Kubischta, Simon Roberts, Charles Reiter, Diana Lawrence, Paul Richardson

Automation of Fosmid Preps at the Joint Genome Institute (2008) Martin Pollard, Steven Wilson, Bruce Gray, Simon Roberts, Joseph Alessi, Dou-Shuan Yang, Jamie Jett, Danielle Mihalkanin, Christine Naca, Tijana Glavina

Creating Custom Software for the Genetix QPixII Colony Picker using the Genetix Developer’s Toolkit SDK (2008) Steven Wilson, Zach Radding, Tijana Glavina, Jennifer Hesse, Sandy Huynh, Danielle Mihalkanin, Martin Pollard

Comparison of Whole Genome Shotgun Assemblers (2008) Stephan Trong, Benjamin Horowitz, Vasanth Singan, Eugene Goltsman, Alex Copeland, Alla Lapidus

Comparison of 454 Sequencing Platform with Traditional Sanger Sequencing: a Case Study with de novo Sequencing of Prochlorococcus Marinus NATL2A Genome (2008) Feng Chen, Alessi Joseph, Edward Kirton, Vasanth Singan, Paul Richardson

Metagenomics study of Enhanced Biological Phosphorus Removal (EBPR) (2008) Hector Garcia Martin, Natalia Ivanova, Victor Kunin, Kerrie Barry, Falk Warnecke, Katherine McMahon, Philip Hugenholtz

JGI Portfolio (2008) Tijana Glavina del Rio, Susan M. Lucas, Alex Copeland, Kerrie Barry, Paul Richardson, Miranda Harmon-Smith, Eileen Dalin, Hope Tice, Harris Shapiro, Jasmyn Pangilinan, David Bruce, Alla Lapidus, Daniel Rokhsar, Darren Platt, Jim Bristow

The Joining of Competitors: The Dual Operation of the ABI 3730xl and GE MegaBACE4500 DNA Sequence Analyzers at the DOE Joint Genome Institute (2008) Christopher Daum, Damon Tighe, Lena Philip, Danielle Mihalkanin, Cailyn Spurrell, Don Miller, Alex Copeland, Susan M. Lucas

DOE Joint Genome Institute EST and cDNA Program (2008) Erika Lindquist, Peter Brokstein, Paul Richardson
The Joint Genome Institute User Facility Sequencing Programs (2008) Paul Richardson, David Bruce, Susan Lucas, Thomas Brettin, Paul Gilna, Jim Bristow, Eddy Rubin

Metagenomics of two sludge microbial communities: population structure and biogeography (2008) Victor Kunin, Hector Garcia-Martin, Falk Warnecke, Katherine McMahon, Linda Blackall, Phil Hugenholtz

Microbial Finishing at DOE Joint Genome Institute (JGI): Sequencing Difficult DNA Templates (2008) Michele Martinez, Paul Richardson, Alla Lapidus

JGI Sequencing Projects – The Process of Ensuring Efficiency and Quality from Initiation to Completion (2008) Tijana Glavina del Rio, Miranda Harmon-Smith, Susan M. Lucas, Alex Copeland, Kerrie Barry, Paul Richardson, Eileen Dalin, Hope Tice, Harris Shaprio, Jasmyn Pangilinan, David Bruce, Alla Lapidus, Daniel Rokhsar, Darren Platt, Jim Bristow

An Overview of the Sequencing Prep Process at the Joint Genome Institute’s Production Genomics Facility (2008) Arshi Khan, Megan Kennedy, Zalak Trivedi, David Robinson, Michael Philips, Terri Jackson, Michael Pintor, Tijana Glavina del Rio

Assembler Complementation Tool (2008) Vasanth Singan, Stephan Trong, Eugene Goltsman, Alla Lapidus

Statistical Methods for Troubleshooting of Genomic Shotgun Data (2008) Eugene Goltsman, Vasanth Singan, Stephan Trong, Alla Lapidus, Kerrie Barry, Alex Copeland

An Overview of the Capillary Electrophoresis Process at the DOE Joint Genome Institute Production Genomics Facility: The Dual Operation of the AB 3730xl and GE MegaBACE 4500 DNA Sequence Analyzers (2008) Christopher Daum, Lena Philip, Danielle Mihalkanin, Cailyn Spurrell, Don Miller, Susan M. Lucas, Alex Copeland, Damon Tighe, Eric Abbott, Marlon Arcaina, Nicholas Eattock, Melanie Lafrades, Albert Linkowski, Adrienne Loero-Pequignot, Andy Yuen, Mathew Zane

I. An Overview of the Library Support Process Used at the Joint Genome Institute Production Genomics Facility (2008) Catherine Adam, Karli Ikeda, Sandy Huynh, Javadevi Krishnakumar, Jim Fey, Diane Bauer, Sanna Anwar, Mansi Chovatia, Nicole Shapiro, Miranda Harmon-Smith

Selection for efficiency at the transcriptional and translational levels are correlated across bacteria (2008) Jeff Froula, M. Pilar Francino

Soybean Rust Genome Sequencing Project (2008) Martha L. Posada-Buitrago, Jeffrey L. Boore, Reid D. Frederick

Comparative analysis of expressed sequence tags (ESTs) generated from four specific-stages of Phakopsor pachyrhizi (2008) Martha L. Posada-Buitrago, Jeffrey L. Boore, Reid D. Frederick

Testing the fidelity of assembly, binning and gene calling in metagenomes (2008) Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Phil Hugenholtz, Nikos C. Kyrpides

The Genome of Amphioxus and the Ancestral Proto-chordate (2008) Nicholas Putnam, Takeshi Kawashima, Astrid Terry, Sky You, Yutaka Satou, Erika Lindquist, Igor Grigoriev, Jeremy Gibson-Brown, Marianne Bronner-Frasier, Peter Holland, Asao Fujiyama, Nori Satoh, Linda Holland, Daniel Rokhsar

Small Antisense Regulatory RNA Genes in Bacterial Genomes (2008) K. Mavromatis, N.C. Kyrpides

Genome sequence and analysis of Thermobifida fusca YX (2008) Athanasios Lykidis, Natalia Ivanova, Iain Anderson, Konstantinos Mavromatis1, Paul Richardson, Susan Lucas, Alla Lapidus, David Wilson, Nikos Kyrpides

Whole Genome Shotgun Library Approach For Microbial Sequencing Projects at the JGI (2008) Eileen M. Dalin, Doug Smith, Hope Tice, Kerrie Barry, Alla Lapidus, David Bruce, Paul M. Richardson

Integrated Microbial Genomes: From Genomes to Metagenomes (2008) N.C. Kyrpides

Comparing the fine structure of promoter regions across enteric bacteria. (2008) M. Pilar Francino

Human Computer Interface of Tier 1/2/3 Bioinformatics Tools (2008) Annette Greiner, Kristen Taylor

Characterization of CRISPR repeat sequences (2008) Philip Hugenholtz
On the fidelity of assembly, binning and gene calling of metagenom es using simulated datasets (2008) Konstantinos Mavromatis, Natalia Ivanova, Kerrie Barry, Harris Shapiro, Eugene Goltsman, Alice McHardy, Isidore Rigoutsos, Asaf Salamov, Frank Korzeniewski, Miriam Land, Alla Lapidus, Igor Grigoriev, Phil Hugenholtz, Nikos C. Kyrpides

Closed Loop Optimization of Gene Sequencing Run Times (2008) Daniel T. Casner, Jason K. Baumohl, Alex C. Copeland, Joshua V. Dillon, David C. Pletcher Isolation of Production Modi Operandi Correlated with Anomalous Behavior (2008) Joshua V. Dillon, Jason K. Baumohl, Daniel T. Casner, Alex C. Copeland, David C. Pletcher

454 Sequencing is an Effective Method for Gap Closure in Microbial Whole Genome Shotgun Sequencing (2008) Feng Chen, Jamie Jett, Edward Kirton, Eugene Goltsmna, Vasanth Singan, Christopher Hack, Douglas Smith, Paul Richardson

Strategies for Efficient Fosmid Sequencing Using 454 Sequencing Technology (2008) Feng Chen, Jamie Jett, Douglas Smith, Edward Kirton, Andy Yuen, Jennifer Kuehl, Pilar Francino, Phillip Hugenholtz, Eileen Dalin, Paul Richardson

High Quality Microbial Finishing at JGI (2008) Alla Lapidus, Eugene Goltsman, Steve Lowry, Hui Sun, Alicia Clum, Stephan Trong, Pat Kale, Alex Copeland, Patrick Chain, Cliff Han, Tom Brettin, Jeremy Schmutz, Paul Richardson

Fosmid Ditags as a New Technology Developed at JGI (2008) Ze Peng, Ilya Malinov, Douglas Smith, Feng Chen, Paul Richardson, Len A. Pennacchio, Jan-Fang Cheng

Overview: Manual Plating Process (2008) Christine Naca

JGI sequencing projects: statistics and timelines (2008) Tijana Glavina del Rio, Kerrie Barry, Lynne Goodwin, Miranda Harmon-Smith, Harris Shapiro, Susan Lucas, David Bruce

Shake ‘n plate (Applied Ergonimics Conference 2008) Christine Naca, Diane Bauer, Catherine Adam, Simon R. Roberts, Karla Ikeda, Charles Reiter, Miranda Harmon-Smith, Sanna Anwar, Ira Janowitz

Balancing Sanger and 454 Data for Microbial Sequencing (2008) Eugene Goltsman, Ed Kirton, Alla Lapidus, Paul Richardson

The Pyrosequencing Process (2008) Christopher Hack, Doug Smith, Ed Kirton, Andy Yuen, Jamie Jett, Feng Chen, Paul Richardson

DOE Joint Genome Institute Production Genomics Facility (PGF) Finishing Pipeline (2008) H. Sun, A. Clum, E. Goltsman, S. Lowry, B. Foster, S. Trong, P. Kale, P. Richardson, A.L. Lapidus

JGI Production Sequencing Process (2008) Christine Naca

JGI Sequencing Projects: Statistics and Timelines (JGI User Meeting 2007) Tijana Glavina del Rio, Kerrie Barry, Lynne Goodwin, Miranda Harmon-Smith, Harris Shapiro, Susan Lucas and David Bruce.

What’s new in project management? A Look at the JGI Project Management Office (JGI User Meeting 2007) David Bruce, Lynne Goodwin, Kerrie Barry, Susannah Tringe, Tijana Glavina del Rio

Comparison of Protocols for Isolating Large Insert Clone DNA that is Suitable for High Throughput Library Construction (JGI User Meeting 2007) Karla Ikeda, Eileen Dalin, Miranda Harmon-Smith, Jan-Fang Cheng, Susan Lucas, & JGI Production Sequencing Department

Microbial Genomics, Comparative and Functional Analyses at JGI-LLNL (JGI User Meeting 2007) Stephanie Malfatti, Lisa Vergez, Maria Shin, Mari Christensen, Jeff Elliott, Dorothy Lang and Patrick Chain

Automating the JGI’s Community Sequencing Program (JGI User Meeting 2007) Jayant Patil, Joni Fazo, Art Kobayashi, Annette Greiner, Arkady Voloshin, Pat Kale, Marsha Fenner, David Bruce, Jan-Fang Cheng, and Jim Bristow

Fosmid Ditags as a New Technology Developed at JGI (JGI User Meeting 2007) Ze Peng, Ilya Malinov, Doug Smith, Feng Chen, Paul Richardson, Len A. Pennacchio, and Jan-Fang Cheng

Life-cycle of a JGI Microbial Finishing Project – LANL (JGI User Meeting 2007) David Sims, Olga Chertkov, Chris Munk, Hajnalka Kiss, Liz Saunders, Sue Thompson, Linda Meincke and Cliff Han

Fosmid RCA Production Line at JGI (JGI User Meeting 2007) Damon Tighe, Feng Chen, Jan-Fang Chen, Nancy Hammon, James Han, Alex Copeland, Alla Lapidus, Hui Sun, David Hillman, Jamie Jett, David Robinson, Arshi Khan

An Overview of the Joint Genome Institute Production Sequencing Line (JGI User Meeting 2007) Chris Wong, Miranda Harmon-Smith, Kathleen Lail, Chris Daum, and Lena Philip

Assembler Complementation Tool (Finishing in the Future 2006); Vasanth Singan, Stephan Trong, Eugene Goltsman, Alla Lapidus

Whole Genome Shotgun Library Approach For Microbial Sequencing Projects at the JGI (Finishing in the Future 2006); Eileen M. Dalin, Doug Smith, Hope Tice, Kerrie Barry, Alla Lapidus, David Bruce, and Paul M. Richardson

Statistical Methods for Troubleshooting of Genomic Shotgun Data (Finishing in the Future 2006); Eugene Goltsman, Vasanth Singan, Stephan Trong, Alla Lapidus, Kerrie Barry, Alex Copeland

Microbial Finishing at DOE Joint Genome Institute (JGI): Sequencing Difficult DNA Templates (Finishing in the Future 2006); Michele Martinez, Paul Richardson, Alla Lapidus

An Overview of the Library Support Process Used at the Joint Genome Institute Production Genomics Facility (JGI User Meeting 2006); Catherine Adam, KarliIkeda, Sandy Huynh, Jayadevi Krishnakumar, Jim Fey, Diane Bauer, SannaAnwar, Mansi Chovatia, Nicole Shapiro, Miranda Harmon-Smith

An Overview of the Capillary Electrophoresis Process at the DOE Joint Genome Institute Production Genomics Facility: The Dual Operation of the AB 3730xl & GE MegaBACE 4500 DNA Sequence Analyzers (JGI User Meeting 2006); Christopher Daum, Lena Philip, Danielle Mihalkanin, Cailyn Spurrell, Don Miller, Susan M. Lucas, Alex Copeland, Damon Tighe, Eric Abbott, Marlon Arcaina, Nicholas Eattock, Melanie Lafrades, Albert Linkowski, Adrienne Loero-Pequignot, Andy Yuen, Mathew Zane

A Statistical Monitoring and Diagnosis System for High-Throughput DNA Sequencing (RECOMB06); Mingkun Li , Alex C. Copeland, Susan Lucas

The Joint Genome Institute User Facility Sequencing Programs (ECI2006); Paul Richardson, David Bruce, Susan Lucas, Thomas Brettin, Paul Gilna, Jim Bristow, Eddy Rubin and the JGI Sequencing Staff

The Joining of Competitors: The Dual Operation of the ABI 3730xl and GE MegaBACE4500 DNA Sequence Analyzers at the DOE Joint Genome Institute (AGBT 2006); Christopher Daum, Damon Tighe, Lena Philip, Danielle Mihalkanin, Cailyn Spurrell, Don Miller, Alex Copeland, Susan M. Lucas and the JGI Sequencing Team

JGI Portfolio (AGBT 2006); Tijana Glavina del Rio, Susan M. Lucas, Alex Copeland, Kerrie Barry, Paul Richardson, Miranda Harmon-Smith, Eileen Dalin, Hope Tice, Harris Shapiro, Jasmyn Pangilinan, David Bruce, Alla Lapidus, Daniel Rokhsar, Darren Platt, Jim Bristow and the JGI Sequencing Team

High Performance Magnetic Separation Technology for Microtiter Plates, Microarrays,
Single Molecule Manipulation and Beyond (LabAutomation 2006); David Humphries and Martin Pollard

Implementation of a CyBio Integrated System to Aliquot Amplified DNA and Dispense DNA Sequencing Chemistry (LabAutomation 2006); Simon Roberts, Martin Pollard, Bruce Gray, Kecia Duffy-Wei, Steven Wilson, and Nancy Hammon

Implementing Automated 384 well Fosmid Prep at JGI (LabAutomation 2006); Steven Wilson, Feng Chen, Jamie Jett, Nancy Hammon, Duane Kubischta, Simon Roberts, Charles Reiter, Diana Lawrence, and Paul Richardson

The US DOE Joint Genome Institute Microbial Genome Program (PAG 2006); Alla Lapidus, Patrick Chain, Cliff Han, Thomas Brettin, Alex Copeland, Chris Detter, Samuel Pitluck, Tijana Glavinadelrio, Susan Lucas, Kerrie Berry, Miriam Land, Frank Larimer, Nikos Kyrpides, Natalia Ivanova, Jeremy Schmutz, Victor M Markowitz, David Bruce, Paul Gilna, Jim Bristow, Eddy Rubin , and Paul Richardson

Comparison of 454 Sequencing Platform with Traditional Sanger Sequencing: a Case Study with de novo Sequencing of Prochlorococcus marinus NATL2A Genome (PAG 2006); Feng Chen, Joseph Alessi, Edward Kirton, Vasanth Singan, and Paul Richardson

Quality Control of JGI Microbial Sequencing Projects (ICMG 2005); Kerrie W. Barry, Alla L. Lapidus, Eugene V. Goltsman, Matt P. Nolan, Joel A. Martin, Mingkun Li, Paul M. Richardson, and Alex C. Copeland

Integrated Microbial Genomes Genomic Data Analysis System (ICMG 2005); V.M. Markowitz, K. Palanniappan, E. Szeto, F. Korzeniewski, G. Werner, A. Greiner, A. Padki, K. Taylor, P. Hugenholtz, K. Mavromatis, I. Anderson, A. Lykidis, N. Ivanova, and N.C. Kyrpides

  • Scientific Posters: 2005 - 2008

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