Scientific Posters
Note: neither these posters nor their contents may be reproduced except by permission of JGI.
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
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
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
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
Archives (2007 posters and earlier)
