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