DOE Joint Genome Institute

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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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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