Program Schedule

Friday 22nd

8:00am

Exhibitor Registration Open

Hall 4A

2:00pm

Attendee Registration Open

Hall 4A

Saturday 23rd

7:00am

Registration Open

Hall 4A

8:00am

(SW4) Use of FFPE in Next-Generation Sequencing: Considerations from Bedside to Bench

Room 213B

Thomas McHugh, Hamid Khoja, Katie Hoadley, Bill LaFramboise

Whole Exome Sequencing analysis of Archival Formalin Fixed Paraffin Embedded Tissue (FFPE): comparison of different library preparation methods
Prashant Kumar Singh
Active organic solvent-free paraffin removal is the key to standardizing extraction of biomolecules from FFPE tissues
Hamid Khoja
Hamid Khoja
FFPE Sequencing and Bioinformatics
Katherine A. Hoadley

(SW3) Lean Tools for Enhanced Core Management

Room 213A

Jay W. Fox, Robert Carnahan, Elizabeth Sinclair, Thomas McHugh

Lean Tools for Enhanced Core Management
Jay W. Fox
Jay W Fox, Rob Carnahan, Thomas McHugh, Elizabeth Sinclair

(SW1) Data Independent Acquisition in Practice: Foundations and Resources for Implementing DIA

Room 212A

Benjamin Neely, Mukul Midha, Pratik Jagtap, Joanna Kirkpatrick, Kara West, Sira Echevarría-Zomeño, Jacob Lippincott, Susan Weintraub, Katherine Tran, Baozhen Shan

iPRG 2019 Metaproteomics Study
Darryl Davis
Darryl L. Davis, Magnus Palmblad, Susan T. Weintraub
(SW1) Data Independent Acquisition in Practice: Foundations and Resources for Implementing DIA
Benjamin Neely, Joanna Kirkpatrick, Mukul Midha, Paul Stemmer, LeRoy Martin, Yan Wang, Laura Herring, Brett Phinney, Baozhen Shan, Allis Chien, Pratik Jagtap

(SW2) Mentoring and Leadership for ABRF Membership and Corporate Sponsors

Room 212B

Bob Garvey

(SW2) Mentoring Skills for ABRF members and Corporate Partners
Luellen Fletcher (Organizer)

(SW5) Image Processing and Analysis for Core Facilities

Room 216

Mark Sanders, Jeffrey Salisbury

Serial Block Face SEM Service
Jeffrey Salisbury
Jeffrey L. Salisbury, Mark Sanders, Jon Charlesworth, Trace Christensen, Adam Jaspersen

4:00pm

New Member/First Time Attendee Welcome & Orientation Meeting

Room 209

Research Group/Committee Chairs Orientation Meeting

Room 208

5:00pm

Keynote Address - Perspectives of ABRF, A Bridge from the Past to the Future

Room 214ABC

Christopher Mason, Ron Niece

Journey to Now - The Origins of ABRF
Ronald Niece

6:30pm

Opening Reception

Hall 4A

Sunday 24th

6:30am

Renew Hatha Yoga

Room 208

7:30am

Registration Open

Hall 4A

8:00am

Plenary Session I (Genomics) - Big Data and Health

Room 214ABC

Michael Snyder, PhD Professor and Chair of Genetics

Analysis of Health Using Advanced Technologies
Michael Snyder, PhD Professor and Chair of Genetics
Michael Snyder

9:00am

Concurrent Scientific Session (Mass Spectrometry): Open Mic

Room 214D

Concurrent Scientific Session (Genomics): Open Mic

Room 214ABC

Stuart Levine, Krish Karuturi, Julie Dragon, Kristopher Kubow

GBIRG bioinformatics core survey highlights the challenges facing data analysis facilities.
Julie Dragon, John Hutchin, Alberton Riva, Matthew Lee Settles, Shannon Ho Sui, Jyothi Thimmapuram, Stuart Levine
Miniaturization of Illumina library preparation for high throughput, plate-based next generation sequencing studies
Stuart Levine
Stuart Levine
JAX survey of bioinformatics and datascience cores revealed 'collaborative and embedded' model is rare but a desirable path forward
Krishna Karuturi

Concurrent Scientific Session (Core Administration): Open Mic - Research Community Action Post FASEB Report on Maximizing the Value of Shared Research Resources

Room 212AB

Justine Karungi Kigenyi, Julie Auger, Katherine Hale , Isabelle Girard , Sheenah Mische , Susan Meyn, Tom McHugh, Heather Richards, Andrew Vinard, Mary Winn, Jeff Weiss, Paula Abercrombie, Susan Constable

Embracing Error: using a systems approach to improve workflow and workplace
Isabelle Girard
Research Community Action Post FASEB Report on Maximizing the Value of Shared Research Resources
Justine Karungi Kigenyi
Justine Karungi Kigenyi, Julie Auger, Katherine Hale Stemke, Isabelle Girard , Tom Hugh, Susan Meyn, Mary Winn, Andrew Vinard, Heather Richards, Sheenah Mische

Concurrent Scientific Session (Imaging): Open Mic

Room 213AB

Michelle Itano, Christopher Gilpin, Guillermo Marqués, Paula Montero Llopis

Serial block face imaging
Christopher Gilpin
Christopher J Gilpin Sharon A Kessler
Challenges of Establishing a new imaging facility: The floating core diaries
Paula Montero Llopis
Paula Montero-Llopis
Steps towards providing mouse behavior analysis across multiple core facilities
Michelle Itano
Michelle S. Itano

10:00am

Exhibit Hall Open

Hall 4A

Coffee Break

Hall 4A

10:30am

Concurrent Scientific Session (Mass Spectrometry): Making a Proteomics Core Nimble and Efficient

Room 214D

Benjamin Orsburn , Brett Phinney , Birgit Schilling

Can you deal with sample and experimental diversity in a Proteomics Core while being nimble and efficient? Answer= Not really
Brett Phinney
Brett S. Phinney
Implementation and application of data-independent acquisition workflows in a mass spectrometry facility.
Birgit Schilling
Birgit Schilling

Concurrent Scientific Session (Imaging): Imaging Flow

Room 213AB

Peter Lopez, Nicole Poulton, Hans Minderman

Imaging in flow in the 70’s—The “Correlation System”
Peter Lopez
Peter Lopez
Fluorescence in situ hybridization and nuclear translocation events quantified by imaging flow cytometry
Hans Minderman
Hans Minderman
Imaging Flow Cytometry for Phytoplankton Analysis: Instrumentation and Applications
Nicole Poulton
Nicole J Poulton

Concurrent Scientific Session (Genomics): Epitranscriptomics

Room 214ABC

Roham Razaghi, Christopher Mason, Fiona Stewart

Signal analysis of nanopore RNA sequencing to interrogate poly(A) tails and post-transcriptional modifications
Roham Razaghi
Roham Razaghi
Signal analysis of nanopore RNA sequencing to interrogate poly(A) tails and post-transcriptional modifications
Roham Razaghi
Roham Razaghi
Platinum Sponsor Talk: New Options for Methylome Analysis and RNA Depletion
Fiona Stewart
Fiona Stewart
Methods and Tools for MeRIP-seq and nanopore detection of m6A(m) changes
Christopher E. Mason; Alexa B.R. McIntyre; Nandan S. Gokhale; Leandro Cerchietti; Stacy M. Horner

Concurrent Scientific Session(Core Administration): Multi-Institutional Core Collaborations

Room 212AB

Tom Colella, Nicholas Ambulos, Eric Chow, William Russell, Michael Zwick

Multi-Institutional Core Collaborations
Tom Colella
Tom Colella, Nicholas P. Ambulos, Eric Chow, William Russell, Michael E. Zwick

12:00pm

Lunch

Hall 4A

1:00pm

Plenary Session II (Core Administration) - Understanding the Science of Branding when Branding for Science

Room 214ABC

Chris Dillon

Understanding the Science of Branding When Branding for Science
Chris Dillon
Chris Dillon

2:00pm

Coffee Break

Hall 4A

2:30pm

Concurrent Workshop (Core Administration): The Future of ABRF: Strategic Planning and Branding

Room 212AB

Andrew Chitty , Chris Dillon, Ken Schoppmann

The Future of ABRF: Strategic Planning and Branding
Andrew Chitty
Andrew Chitty

Concurrent Workshop (Imaging): Light Microscopy and Flow Cytometry Research Groups

Room 213AB

Kristopher Kubow , Nicolas Loof

FCRG - Fixation and Sorting for RNA
Nicolas Loof
Nicolas Loof, Abshari Mehrnoosh, Alan Bergeron, Alan Saluk, Andrew Box, Kathleen Brundage, Dave Adams, Karen Dwyer, Ernest Meyer, Matthew Cochran, Laura Holmes, Nancy Fisher, Zachary Niziolek, Peter Lopez, Regina Harley, Roxana Del Rio Guerra, Sherry Thornton
Accuracy and reproducibility of image segmentation by microscopist end-users using widely accessible programs
Kristopher Kubow
Kristopher E. Kubow

Concurrent Workshop (Genomics): GRG (Genomics Research Group) / DSRG (DNA Sequencing Research Group)

Room 214ABC

John Aston, Jessica Podnar

Cross Site Evaluation of Sanger Sequencing Dye Chemistries
Jessica Podnar
Jessica W. Podnar, Fred W. Kolling, Molly J. Zeller, Yanping Zhang, Jyothi Thimmapuram, Yuriy O. Alekseyev, Alex Deiulio, Jeremy Niece, Heather Deiderick, Jun Fan, Xiaoling Xuei, Lorena Pantano, Stuart S. Levine, Zachary T. Herbert, Marie Adams, Jan Kieleczawa, Jan Kieleczawa
Single-cell Genomics: Best practices and new insights.
John M. Ashton

Concurrent Workshop (Mass Spectrometry): Proteomics Research Groups: PRG, iPRG, WIN

Room 214D

Joanna Kirkpatrick, Yan Wang, Darryl Davis, Benjamin Orsburn , Alex Campos, Lindsay Lozeau, Rachel Friedman Ohana

Chemical Proteomic Strategy Utilizing a Chloroalkane Capture Tag for Target Discovery
Rachel Ohana

3:45pm

Concurrent Workshop (Imaging): Spectroscopic Imaging

Room 213AB

Alex Valm, Cynthia McMurray, Meredith Calvert

Spectral Phenotyping
Cynthia McMurray
Cynthia McMurray
Systems imaging to reveal the eukaryotic organelle interactome and oral microbiome structure and assembly
Alex Valm

Concurrent Workshop (Genomics): GERG (Genome Editing Research Group/GBIRG (Genome Bioinformatics Research Group)

Room 214ABC

Daniela Bezdan , Kym Delventhal, Stephen Jackson

Platinum Sponsor Talk: Genetic Analysis Tools for Genome Editing Workflows
Stephen Jackson
Stephen Jackson
Reproducibility of indel formation rates by comparing guideRNA format and delivery method
Kym Delventhal
Kym Delventhal
Distribution of microbial communities and antimicrobial resistances in urban environments and on the ISS space station
Daniela Bezdan, David Danko, Christopher E. Mason

Concurrent Workshop (Core Administration): Publication Tracking/Acknowledgement

Room 212AB

Amanda (Nicole) White, Caleb Smith, Vaughn Hinrichs, Jeanne Hunter, Kelsey Rosell, Katherine Hale

Publications Tracking/Acknowledgement
Katherine Hale
Katherine Stemke

5:30pm

Poster Session I and Wine & Cheese Reception

Hall 4A

(313) LipidQuan–A Plug and Play Solution for Targeted Lipid Profiling
Suraj Dhungana, Giorgis Isaac, Nyasha Munjoma, Lee A. Gethings, Robert S. Plumb
(143) MagMax DNA Multi-Sample Ultra 2.0 genomic DNA purification from DBS cards on the KingFisher instrument
Charmaine San Jose Hinahon, Luming Qu He, Xingwang Fang, Natalie Supunpong Hernandez, Angie Cheng, Emily Zeringer, Marie Gonzalez
(161) Streamlining DNA Sequencing and Bioinformatics Analysis Using Software Containers
Alberto Riva, J. Lucas Boatwright, Tongjun Gu, Fahong Yu, W. Brad Barbazuk
(167) Design, Analysis, and Validation of Error-Correcting Internal Spike-In Controls for Metagenomics
Nick Greenfield
(151) QIAseq FastSelect: One-step, rapid removal of rRNA during whole transcriptome NGS library prep
Jonathan Shaffer, Daniel Kim, Melanie Hussong, Christopher Howard, Niels Tolstrup, Samuel Rulli, Eric Lader
(401) Data Portal: Experiences Managing and Delivering Data to End Users at the University of Illinois at Chicago
George E. Chlipala, Sai Shravith Reddy Marri, Amogh Venkatesh, Tim Johnson, Pinal Kanabar, Zhengdeng Lei, Kevin Kunstman, Stefan J. Green, Sonika Anand, Mark Maienschein-Cline
(329) Quantitative Profiling of Post-Translational Modifications in E. coli
Charles L. Farnsworth, Jian Min Ren, Kimberly Lee, Wayne Gatlin, Justin Topp, Matthew P. Stokes
(205) Validation of antibody panels for high-plex immunohistochemistry applications
Douglas Hinerfeld, Kristi Barker, Chris Merritt, Joseph Beechem
(305) Evaluation of different sample preparation workflows for reproducible, quantitative, and in-depth analysis of urine proteomics
Hua Ding, Hossein Fazelinia, Lynn A. Spruce, Dana A. Weiss, Stephen A. Zderic, Steven H. Seeholzer
(201) Imaging in Developmental Biology: An Essential Tool with No Instructions
Guillermo Marqués, Thomas Pengo, Mark A. Sanders
(323) SysMet: A Tool for Integrative Systems Metabolomics
Mohammad R. Nezami Ranjbar, Ziling Fan, Yan Gao, Habtom Ressom
(107) MULTI-seq: Scalable Single-Cell RNA-seq Multiplexing Using Lipid-Tagged Indices
Eric Chow, Christopher S McGinnis, David M Patterson, Juliane Winkler, Marco Y Hein, Vasudha Srivastava, Daniel N Conrad, Lyndsay M Murrow, Jonathan S Weissman, Zena Werb, Zev J Gartner
(303) Absolute Quantitation of the N-Linked Glycans from Biotheraputic IgGs
Ron Orlando, Marla Popov, Ben Libert, Barry Boyes
(503) Leveraging the versatility of the chicken embryo chorioallantoic membrane (CAM) model as a tool in the fight against cancer.
Hugo Villanueva, Mariana Villanueva, Sandra Francisco, Hsuan-Chen Liu, Andrew G. Sikora
(157) Sample quality control of cell-free DNA
Elisa Viering
(121) Comprehensive structural analysis of cancer genomes by genome mapping
Ernest T Lam
(203) Molecular-targeted optical coherent microscopy as an optical biopsy tool for early detection of cancer
Will Xia, Chao Zhou
(173) SMART-Seq® Stranded Kit performance with ovarian cancer cells
Luke Sherlin, Anastasia Potts, Nathalie Bolduc, Simon Lee, Magnolia Bostick, Andrew Farmer
(325) Maximize the output of routine proteome analyses by using micro pillar array column technology
Geert Van Raemdonck
(139) Infectious Disease Metagenomics – Error Mitigation And Best Practices For The Clinical Routine Use Of Metagenomic Sequencing
Nur A. Hasan, Huai Li, Brian Fanelli, Arne Materna, Manoj Dadlani, Rita R. Colwell
(309) Impact of enrichment strategy on observed expression in fresh frozen tissues
Kratika Singhal, Rowan Matney, Fang Liu, Allis Chien, Ryan Leib
(177) Cross Site Evaluation of Sanger Sequencing Dye Chemistries
Jessica W. Podnar
(111) A metagenomic analysis of environmental and clinical samples using a secure hybrid cloud solution
Rachid Ounit, Chris Mason, Stefano Lonardi, Niamh O'Hara
(133) High throughput, reduction transcriptomics using Ultraplex RNA sequencing
Samuel Rulli, Martin Kreutz, Qiong Jiang1, Raed Samara, Jonathan Shaffer, Eric Lader
(129) Evaluation of Cell Fixations for Downstream RNA Isolation
Kathy Brundage, Mike Meyers, Dave Adams, Roxana Del Rio Guerra, Laura Holmes, Matthew Cochran, Al Saluk, Alan Bergeron, Peter Lopez, Andrew Box, Nancy Fisher, Nicolas Loof, Mehrnoosh Abshari, Sherry Thornton, Zachary Niziolek, Regina Harley
(179) Hierarchical model for integrative analysis of mRNA-seq and miRNA-seq data
Rency S. Varghese, Yuan Zhou, Megan E. Barefoot, Md Islam, Mahlet G. Tadesse, Habtom Ressom
(315) MetaboQuan-R: A Series of Rapid, Targeted UPLC-MS/MS Methods for Metabolomics Research in a Core Laboratory
Suraj Dhungana, Billy J. Molloy, Robert S. Plumb
(155) RipTide™ High Throughput NGS Library Prep for Genotyping in Populations
Azeem Siddique, Gaia Suckow, Phillip Ordoukhanian, Steve Head, Nils Homer, Alvaro Hernandez, Keith Brown, Lior Glick, Kobi Baruch, Paul Doran
(301) Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling
Uma Aryal, Katelyn E. Connelly, Victoria Hedrick, Tiago Jose Paschoal Sobreira, Emily C. Dykhuizen
(327) Preliminary Study on Protein Profiling from Raw Honey
Umaima Akhtar, Basir Syed, Ishtiaq Ahmad Khan, Aftab Ahmed
(123) Deconstructed PCR: A novel method for reducing PCR bias
Stefan J. Green, Ankur Naqib
(501) Evaluation of a New Gradient Elution Protein Sequencer
Joshua Emory
(169) Automated Co-extraction of High-quality DNA and RNA from Single Clinical FFPE Samples
Hamid Khoja, Sean T. Glenn, Martina Werner, Patrick McCarthy, Jon Andreas, Jeffrey Conroy, Jim Laugharn
(153) Raw Signal Analysis of Low Coverage Oxford Nanopore Reads Produces Highly Accurate Clinically Relevant Genotypes
Jeffrey Rosenfeld, Marcus Stoiber, Melissa delaBastide, Tim Massingham, Sara Goodwin, Shridar Ganesan
(159) Simple and scalable genome analysis with Transposase Enzyme Linked Long-read Sequencing (TELL-Seq): from haplotype phasing to de novo assembly in a tube
Ming Lei1, Long Pham1, Donna Wu1, Qingpeng Zhang1, Yu Xia1, Tan Phan2, Tuan Tran2, Son Pham2, Yong Wang1, Tom Chen1
(105) Genotyping by sequencing of Canis familiaris using iGenomX RipTide DNA library preparation
Azeem Siddique, Gaia Suckow, Nils Homer, Alvaro Hernandez, Phillip Ordoukhanian, Steve Head, Keith Brown, Joe Pickrell, Matt Huentelman
(165) Genomic and RNA Profiling Core (GARP)
Rene Stalnaker, Sukhinder Sandhu, Ornella Pavel Tuekam, Md Habibul Islam, Lisa D. White, Daniel C. Kraushaar
(117) Automation of IDT probe-based targeted enrichment workflow using xGen® Lockdown Probes in a high-throughput lab
Jessica Gearhart, Beth Marosy, Brian Craig, Kim Doheny
(119) Comparison of three libraries for 10x Genomics single cell immune TCR repertoire profiling
Yunxin Chen, David P. Pollock, Yuan Qi, Jin Seon lm, Xiaoping Su, Erika J. Thompson
(145) Multiplex miRNA Profiling for Biomarker Discovery and Verification Studies Using the FirePlex® Platform
M. Tackett, B. Heinrich, I. Diwan, G. Tejada, C. Rafferty, E. Atabakhsh, and D. Pregibon
(149) New Developments in Nucleic Acid Sample Quality Control
Susanne Etteldorf
(137) Immuno-biotechnology and bioinformatics in Community Colleges
Todd Smith, Sandra Porter, Dina Kovarik
(403) Exploring Core Facility Employee Job Satisfaction: Influence of Institutional Support and Career Development.
A. Nicole White
(175) Elucidating acrylamide adverse effects on zebrafish using a multi-omics approach
Natalia Vinas, Demetrio Raldúa, Eva Prats, Melissa Faria, Chuan-Yu Hsu, Mark A. Arick, Tamar Ziv, Arie Admon, Benjamin Piña
(113) ampPD – An Automated Primer Design Tool for Highly Multiplexed, Single-tube Tiled Amplicon PCR for Resequencing of Tumor Samples
Martin Zillmann, Yue Ke, Nicholas Lodato, Melanie Prasol, Zhaohui Wang
(163) The Complete Microbiome Workflow: Deciphering the Secrets of the Human Microbiome for Future Diagnostic Solutions
MADHURI JASTI, Vlassov, Alexander V
(307) High Sensitivity PTM Characterization in Complex Cell Lysates Using Trapped Ion Mobility
Matthew Willetts, Shourjo Ghose, Gary Kruppa, Matthew Stokes, Charles Farnsworth, Kimberly Lee
(115) Analysis of Complex Microbial Samples Using High Definition Mapping
John S. Oliver, Barrett Bready, Anthony P. Catalano, Jennifer R. Davis, Michael D. Kaiser, Jay M. Sage
(141) Liquid biopsy quality control – the importance of plasma quality, sample preparation, and library input for next generation sequencing analysis
Hannah Elizabeth Saunders
(109) A Fluorescence-based Method for Accurate Quantification of NGS libraries in Minutes
Ashesh A. Saraiya, Chaitali Parikh, Bin Li, Joe Don Heath
(171) Automating Genomic DNA Extraction from Whole Blood and Serum with GenFind V3 on the Biomek i7 Hybrid Liquid Handling System
Randy Pares, Li Liu, Han Wei, Mary Blair
(317) Purification, Characterization and Cytotoxic Activity of Peptides and Proteins from Bitter Melon (Momordica charantia) Seeds
Yamna Khurshid, Basir Syed, Jerika Lam , Shabana U Simjee, Aftab Ahmed
(131) Exploring the benefits of using commercially available pre-plated DNA-seq reagents for high throughput NGS library prep
Shannon Piehl, Matt Carter, Josh Kinman, Kyoko Kushiro, Arvind Kothandaraman
(127) Enzymatic Methyl-Seq: Next Generation Methylomes
Fiona J. Stewart, Louise Williams, V K Chaithanya Ponnaluri, Brittany Sexton, Lana Saleh, Katherine Marks, Mala Samaranayake, Laurence Ettwiller, Shengxi Guan, Heidi E. Church, Nan Dai, Esta Tamanaha, Erbay Yigit, Bradley W. Langhorst, Zhiyi Sun, Thomas C. Evans, Jr., Romualdas Vaisvila, Eileen T. Dimalanta, Theodore B. Davis
(211) Meta-Max:An easy to use calibration tool to maximize the value of fluorescence microscopy data
David Grunwald, Maximiliaan Huisman, Carlas Smith
(311) Integrating database search and de novo sequencing for immunopeptidomics with DIA approach
Paul Shan, Hieu Tran
(101) Accelerating high-throughput screening with FirePlex®-HT
A. Perea, B. Heinrich, W. Austin, C. Rafferty, M. Camilleri, L. To, E. Atabakhsh, and D. Pregibon
(207) Whole organ vascular imaging with cellular resolution
Thomas Pingel, Uwe Schröer, Friedemann Kiefer

6:30pm

Technology Showcase - Argolight: Ensure the Performance of Your Fluorescence Microscope

Room 212AB

Technology Showcase - Agilent Technologies: New Developments in NGS sample Quality Control – from FFPE RNA to cell-free DNA

Room 213AB

Technology Showcase - Nanostring Technologies: Morphology-Driven High-Plex Spatial Analysis of Tissue Microenviroments

Room 210AB

Technology Showcase - Pillar Biosciences: Making Precision Medicine Accessible with SLIMamp™ Robust, Rapid, Single-Tube Multiplex NGS Panels

Room 209

Technology Showcase - Bionano Genomics: Strengthening the Core with Bionano Genome Mapping – An Easily Integrated, Cost-Effective Tool to Super-Charge Genome Assembly and Fully Reveal Whole-Genome Structural Variants in Human Genetics and Cancer Research

Room 216

Technology Showcase- BenchSci: The Antibody Crisis: Leveraging Machine Learning for Evidence-Based Antibody Search

Room 214D

Monday 25th

7:30am

Registration Open

Hall 4A

8:00am

The ABRF Annual Award for Outstanding Contributions to Biomolecular Technologies Presentation

Room 214ABC

Richard M. Caprioli

9:00am

Plenary Session III (Imaging) – Light Microscopy

Room 214ABC

Erika Holzbaur, PhD

Dynamic actin cycling regulates mitochondrial dynamics
Erika Holzbaur, PhD
Erika Holzbaur

10:00am

Coffee Break

Hall 4A

Exhibit Hall Open

Hall 4A

10:30am

Concurrent Scientific Session (Genomics): Metagenomics

Room 214ABC

Kasthuri Venkateswaran, Josh Quick, Robyn A. Barbato, Ken Mcgrath, John Oliver

Ultra-long read nanopore sequencing methods for metagenomics
Josh Quick
Josh Quick
Finding NEMO: discovering Novel Endemic Micro-Organisms in the gut microbiome using a genome-centric metagenomics analysis
Ken Mcgrath
Ken McGrath
Combining high resolution whole genome mapping with long read DNA sequencing for microbial genome assembly
John Oliver
John Oliver
Understanding Permafrost Dynamics Using Metagenomics and Systems Biology
Robyn A. Barbato
Robyn A. Barbato
Microbes in Space
Kasthuri Venkateswaran
Kasthuri Venkateswaran

Concurrent Scientific Session (Imaging and Mass Spectrometry): Imaging and Spatially Explicit Mass Spectrometry

Room 214D

Ryan Kelly, Christina Ferreira, Jared Burks, Christopher Anderton

Mass Cytometry Why Multiplex
Jared Burks
Jared K. Burks
Desorption Electrospray Ionization – Mass Spectrometry Imaging: Recent Developments and Perspectives
Christina Ferreira
Christina Ferreira, Clint M. Alfaro, Valentina Pirro, R. Graham Cooks
Single cell proteome mapping of tissue heterogeneity using microfluidic nanodroplet sample processing and ultrasensitive LC-MS
Ryan Kelly
Ryan Kelly, Ying Zhu, Yiran Liang, Yongzheng Cong, Paul Piehowski, Maowei Dou, Rui Zhao, Wei-Jun Qian, Kristin Burnum-Johnson, Charles Ansong

Concurrent Scientific Session (Core Administration): Mentoring Approaches in Varied Professional Environments

Room 212AB

Laura Lewis-Tuffin, Robert Burgoyne, Heather Brewer, Paul Schwartz, Todd Smith

Mentoring approaches in varied professional environments
Laura Lewis-Tuffin
Laura Lewis-Tuffin

12:00pm

Lunch

Hall 4A

1:00pm

Concurrent Scientific Session (Imaging): Analysis of Super-Resolution Microscopy Image Data

Room 213AB

Rusty Nicovich, Marcel Müller

Single molecule localization microscopy for quantitative biology
Rusty Nicovich
SIM data acquisition and processing for fast live-cell imaging
Marcel Müller

Concurrent Scientific Session (Genomics): CRISPR/Cas Technology

Room 214ABC

Michael Collingwood, C.B. Gurumuthy, Shondra Miller

Genome Editing Session: Trends and core functions for CRISPR-directed gene editing
Michael Collingwood
Eric B. Kmiec
Engineered AsCas12a variants with enhanced activity and broadened PAM compatibility
Michael Collingwood
Michael A. Collingwood, Christopher A. Vakulskas, Liyang Zhang, Rolf Turk, Nicole M. Bode, Ashley M. Jacobi, Matthew S. McNeill, Kyle McQuisten, Bernice Thommandru, and Mark A. Behlke

Concurrent Scientific Session (Mass Spectrometry): Emerging Technologies to Bring Glycoproteomics within Reach

Room 214D

Parastoo Azadi , Nicola L. Pohl, Nathan Edwards

Emerging Technologies to Bring Glycoproteomics Within Reach
Douglas M. Sheeley
Douglas M. Sheeley, Parastoo Azadi, Nicola L. Pohl

Concurrent Scientific Session (Core Administration): Pathways to Sustainability: Green Lab Program, International Institute for Sustainable Laboratories (I2SL) and BETR Grants

Room 212AB

Sheenah Mische, Kathryn Ramirez-Aguilar, Phil Wirdzek

Pathways to Laboratory Sustainability: Green Lab Program, International Institute for Sustainable Laboratories (I2SL) and BETR Grants
Kathryn Ramirez-Aguilar
Kathryn Ramirez-Aguilar(1), Phil Wridzek (2), Sheenah Mische (3)

2:30pm

Poster Session II and Coffee Break

Hall 4A

(164) Whole Genome Sequencing of Microbial Communities for Scaling Microbiome and Metagenomic Studies
Jefferson Lai, Scott Hutto, John Lesnick
(124) Depletion of Abundant RNAs in Eukaryote, Blood Samples, and Bacteria Increases Sensitivity of Next Generation Sequencing-Based Transcriptome Profiling
Melissa Arn, Deyra N. Rodríguez, Keerthana Krishnan, Daniela B. Munafó, Bradley W. Langhorst, Jian Sun, Brittany Sexton, Anetta Nowosielska-Vecchietti, Timur Shtatland, Christine J. Sumner, Fiona J. Stewart, Eileen T. Dimalanta and Theodore B. Davis
(138) Impact of fecal microbiome extraction technique on relative abundance of genera within expected and unexpected communities
Samantha Chill, Emily Vogtman, Christian Abnet, Rashmi Sinha, Belynda Hicks, Kristine Jones, Amy Hutchinson, Casey Dagnall
(142) Long fragments achieve lower base quality in Illumina paired-end sequencing
Lennart Opitz, Ge Tan, Catharine Aquino, Ralph Schlapbach, Hubert Rehrauer
(116) Automated genomic DNA extraction from large volume whole blood
Han Wei, Randy Pares, Li Liu, Mary Blair
(108) A 12 minute, single tube, nanogram input library prep
Joseph Dunham PhD, Christopher Angermayer, Timothy Harkins PhD
(174) Keanu: a novel visualization tool to explore biodiversity in metagenomes
Natàlia Vinas, Adam Thrash, Mark Arick II, Robert Jones, Thomas Douglas, Edward Perkins
(110) A Low DNA Input Protocol for High-quality PacBio De Novo Genome Assemblies
Turner Duncan, Sarah B. Kingan, Christine C. Lambert, Primo Baybayan, Jonas Korlach
(158) Sequencing complex genomes with PromethION technology in a core setting
Sara Goodwin , W. Richard McCombie
(402) Delivering greater value by operating core facilities under a quality management system.
Julie Rothacker, Mahyar Nasabi, Shane Reeve, Ian Smith
(304) Characterization and cytotoxic activity of Non-Specific Lipid Transfer Protein (NsLTP) from Fennel (Foeniculum vulgare) seeds
Mekdes Megeressa, Yamna Khurshid, and Aftab Ahmed.
(152) QIAseq multimodal analytical technology: Single workflow DNA/RNA NGS library prep and analysis
Qiong Jiang, Quan Peng, Daniel Kim, Geoff Wilt, Mohammad Ranjbar, John DiCarlo, Krishna Amin, Raed Samara, Yexun Wang, Jonathan Shaffer, Eric Lader
(106) High-Throughput, High MW DNA Extraction and Size Selection for Long-Read Sequencing
Kelvin Liu, Jeffrey Burke, Duncan Kilburn, Renee Fedak, Michelle Kim, Heather Ferrao, Brendan Galvin, Keith Bjornson, Rachael Workman, Norah Hilger, Winston Timp
(170) Automated Unbiased Metagenomic DNA Extraction for Long-Read Sequencing
Joshua Tjokrosurjo, Angel Gonzalez, Kevin Lin, Shuiquan Tang, Xi Yu Jia
(312) Let it brie: Using the non-destructive SepQuant dropletProbe sampling system to analyze the free amino acid content of various cheeses
Sloane Tilley, Vilmos Kertez
(128) Evaluating Next Generation Sequencing library quantification methods
Ryan Lynch (1), Heidi Munger (1), Chia-Lin Wei (2)
(122) Core Analysis Viewer: Simplifying Omics Data Delivery, Training, and Interpretation
Shawn W. Polson, Longqian Zheng, Jaysheel D. Bhavsar
(206) Integration and validation of RNA ISH, multispectral imaging and analysis protocols into a Core environment
Shanmugapriya Selvaraj, Valeria Mezzano, Branka Dabovic, Cindy Loomis
(400) Adoption of Evaluation and Assessment Data Management Tools for a Growing Core Facility with Program Grants
Diane B. Smith, Barbara J. Jibben, Tracy L. Yarnell, Julia T. Oxford
(104) End-to-end next-generation sequencing for strain sub-typing and epidemiological analysis: an exploration of relatedness and virulence in Streptococcus pyogenes and SDSE
Nur A. Hasan, Huai Li, Brian Fanelli, Manoj Dadlani, Arne Materna, Kelly Moffat, Rita R. Colwell
(310) Incorporating In-Source Fragments Improves Metabolite Identification Accuracy in Untargeted LC−MS and LC−MS/MS Datasets.
Brian C. Searle, Jacob C. Lippincott, Phillip M. Seitzer
(168) NEXT-GEN SEQUENCING OLIGOS (NGSO) FOR CONSISTENT AND EFFICIENT SEQUENCE ASSEMBLY
Christopher Lemke, M. Zulfiquer Hossain, Joseph Frangipane, Karen Juntunen, Tom Russell
(316) Purification and Characterization of Proteins and Peptides from Marshmallow (Althaea officinalis) Seeds
Mahshid Amini, Yamna Khurshid, Mekdes Megeressa, Sherif Elshahawi, and Aftab Ahmed
(114) An Unbiased Comparison of BigDye Terminator and BrilliantDye Terminator
Petros, C.M., Walls, D.M., Munger, H.J., Wei, C-L
(112) A Robust, Streamlined, Enzyme-based DNA Library Preparation Method Amenable to a Wide Range of DNA Inputs
Amanda Hoppers, Lynne Apone, Vaishnavi Panchapakesa, Karen McKay, Pingfang Liu, Chen Song, Christine Sumner, Christine Rozzi, Melissa Arn, Jonathan Sanford, Bradley W. Langhorst, Timur Shtatland, Fiona J. Stewart, Daniela Munafo, Eileen T. Dimalanta, Theodore B. Davis
(208) Neuroprotective roles of fractalkine in multiple sclerosis: Characterization of novel humanized animal model
Sandra M. Cardona, Sangwon V. Kim, Kaira A. Church, Vanessa O. Torres, Ian A. Cleary, Andrew S. Mendiola, Stephen P. Saville, Stephanie S. Watowich, Jan Parker-Thornburg, Alejandro Soto- Ospina, Pedronel Araque, Richard M. Ransohoff, Astrid E. Cardona
(140) Linking the Resistome to the Microbiome: A Culture-Free Method Links Plasmid, Virus, and Antimicrobial Resistance Genes to their Hosts in Complex Microbial Populations
Ivan Liachko, Maximilian Press, Thibault Stalder, Derek Bickhart, Sergey Koren, Eva Top, Adam Phillippy, Timothy Smith, Shawn Sullivan
(308) High throughput profiling of glycans released from therapeutic glycoproteins via micro-permethylation.
Asif Shajahan, Nitin T Supekar, Christian Heiss, Parastoo Azadi
(162) Supporting Single Cell RNA-seq Analysis at Harvard - A Community Approach
Shannan Ho Sui, Rory Kirchner, Michael Steinbaugh, Sarah Boswell, Mary Piper, Victor Barrera, Lorena Pantano, Radhika Khetani, Meeta Mistry, Kayleigh Rutherford, John Hutchinson
(160) Streamlined SMRTbell® library generation using addition-only, single tube strategy for all library types reduces time to results.
Jenny Ekholm
(306) Flash Oxidation (FOX): A New and Improved Platform for Biopharmaceutical Hydroxyl Radical Protein Foot-printing Higher Order Structural Analysis
Ron Orlando, Scot Weinberger, Josh Sharp
(300) ABRF-sPRG 2018-2019: Development and Characterization of a Stable-Isotope Labeled Phosphopeptide Standard
Anthony Herren, Brian Searle, David Hawke, Kimberly Lee, Antonius Koller, Ryan Leib, Brett Phinney, Allis Chien, Bhavin Patel
(166) Simultaneously DNA and RNA extraction from formalin-fixed paraffin embedded (FFPE) tissue
Han Wei, Zach Smith, Jung Doh , Jimmy Adediran
(126) Echo® System-Enhanced SMART-Seq v2 for RNASeq Applications
Jefferson Lai, Scott Hutto, John Lesnick
(154) Reproducibility of indel formation rates by comparing guideRNA format and delivery method
Kym Delventhal, Brandon Miller, Shondra M. Pruett-Miller, Shirin Modarai, Shaina N. Porter, Maureen R. Regan, Elizabeth Sergison
(318) Total Solubilization of FFPE Samples for High-Throughput Clinical Proteomics in One Step
John P. Wilson, Ilyana Ilieva, Darryl J. Pappin, John B. Wojcik
(202) K-means Spectral Unmixing for Multi-channel Imaging and Image Analysis Platform at a Core Facility
Yurong Gao, Tristan McRae
(132) Generating Standards for Epigenetics Research: The FDA’s Working Group on Epigenome Quality Control (EpiQC)
Claudia Lalancette, Jonathan Foox, Bradley W. Langhorst, Louise Williams, Chaithanya Ponnaluri, Daniel Butler, John M. Greally, Masako Suzuki, Michelle Lacey, Ting Gong, Youping Deng, Mark Menor, Masaki Nasu, Altuna Akalin, Andreas Scherer, Stephen Bruinsma, Gosia Golda, Pawel Labaj, Frank Wos, Jessica Nordlund, Amanda Raine, Ulrika Liljedahl, Tomas Axelsson, Charles Wang, Agata Muszynska, Inmaculada Ibáñez de Cáceres, Carlos Rodriguez-Antolin, Rocio Rosas, John (Zhong) Chen, Justin Wade Davis, Jennifer Ishii, Dalila B. Megherbi, Wenming Xiao, Zhaowei Yang, Jing Li, Will Liao, Christopher E. Mason
(118) Bead-Linked Transposome Technology: Ushers a Next Era in library prep enabling a normalization-free workflow for whole genome and flexible targeted resequencing
Anu Khanna, Steve Bruinsma, Joshua Burgess, Agata Czyz, Natalie Morrell, Daniel Schlingman, Katie Ballenger, Heather Meinholz, Lindsay Freeberg, Haiying Grunenwald, Niall Gormley, Gourab Bhattacharjee, Gary P Schroth
(172) Next Generation Whole-Genome Amplification Methods
Luke Sherlin, Greyson King, Julie Laliberte, Emmanuel Kamberov, Andrew Farmer
(120) Comprehensive Detection of Germline and Somatic Structural Mutation in Cancer Genomes by Bionano Genomics Optical Mapping
A.W.C. Pang, J. Lee, T. Anantharaman, E.T. Lam, A. Hastie, M. Borodkin
(136) High-Throughput, Low Volume gDNA Extraction from Whole Blood Enabled by Covaris Adaptive Focused Acoustics (AFA) and oneTUBE-10
Lauren Jansen , Vanessa Process, Kristopher Amirault, Sean Gerrin, Ulrich Thomann
(200) Automated single cell tracking of in vitro multi-cellular morphogenesis predicts pluripotent stem cell fate decisions
David Joy, Ashley Libby, Todd McDevitt
(404) Research Resource Identifiers (RRID) for Core Facilities and Research Equipment
Claudius Mundoma, Nicholas Ruhs, Michael Meth, Annie Glerum, Mark Lopez, Renaine Julian
(204) QUALITY CONTROL OF MODERN FLUORESCENCE MICROSCOPES
Arnaud ROYON
(134) High-throughput and automated procedures for microbiome analysis of stool and soil
Dominic O'Neil, Helena Block, Doerte Lehmann, Silvia Magyar, Nicola Scholle, Stefanie Schroeer, Markus Spreger-Haussels
(302) A Rapid and Simple Proteomics Digestion Protocol
Shreya Ahuja, Zhiyun Cao, Amber Henry, Judy Boland, Nicolas Caffarelli, Jeffrey Turner, and Kevin Ray
(324) Spatial Mapping of Lipids and Neurotransmitters in Rat Brain Section Using DESI Ion Mobility Mass Spectrometry
Roy Martin, Anthony Midey, Hernando Olivos, Bindesh Shrestha, Emmanuelle Claude
(144) Miniaturized automated PCR setup
Issa Isaac, Chris A Waddling, David J Onley, David M Lathlean
(150) NGS DreamPrepTM: A fully automated NGS library preparation solution from sample to quantified, pooled, and sequence-ready libraries
Joe Don Heath, Michael Benway, Enrique Neumann, KD Modi
(148) Multi-site Evaluation of Next-Generation Sequencing Methods for Small RNA Quantification
Zachary T. Herbert, Jyothi Thimmapuram, Shaojun Xie, Jamie P. Kershner, Fred W. Kolling, Yuriy O. Alekseyev, Jessica W. Podnar, Yanping Zhang, Xiaoling Xue, Marie Adams, Stuart S. Levine
(176) Automated library preparation for the MCI Advantage Cancer Panel at Miami Cancer Institute utilizing the Beckman Coulter Biomek i5 Span-8 liquid handler
Q. Wei, W. Shen, A. Medellin, Zach Smith
(156) RipTide™ Ultra High-Throughput Rapid DNA Library Preparation for Next Generation Sequencing
Azeem Siddique, Gaia Suckow, Jorge Bahena, Nils Homer, Phillip Ordoukhanian, Steve Head, Keith Brown
(102) Detecting Genomic DNA Contamination in RNA Samples Using the Bio-Rad Droplet Digital PCR System
Yanping Zhang, Alex Deiulio, Masum Akond and Steve Madore
(210) cellPhoresis: A dielectrophoresis based technique for rapid, nondestructive cell separation and analysis.
Aytug Gencoglu, Shannon Huey, Claire Crowther, Mark Hayes, David Charlot
(178) MULTI-seq: Scalable Sample Multiplexing for Single-Cell RNA Sequencing using Lipid-Tagged Indices
Eric Chow
(314) Mass spectral Analysis of acetylated peptides: Implications in proteomics
Medicharla V. Jagannadham, Deepika Chandra, Pratapa Gayathri, R. Nagaraj
(130) Evaluation of commercially available 16S metagenomics kits
David Moraga Amador, Yanping Zhang, Fahong Yu, Nedka Panayotova, Wayra Navia, Xiao Hui Zhou, Masum Akond, Alex Deiulio and Eric Triplet
(322) MetaboQuest: Tool for Metabolite Identification
Mohammad R. Nezami Ranjbar, Linge Yan, Yan Gao, Habtom W. Ressom

3:30pm

Concurrent Scientific Session (Imaging): Technical Considerations in Object/Particle Tracking

Room 213AB

Teng-Leong Chew

Concurrent Scientific Session (Genomics): MGRG (Metagenomics) and ABRF-NGS (The NGS Study Consortium)

Room 214ABC

Scott Tighe, Scott Jackson, Jonathan Foox, Olivia Koues

The MOSAIC Standards Challenge: Capturing the extent and sources of variability in NGS-based microbiome profiling protocols and analyses
Scott Jackson
Scott Jackson
Metagenomics Research Group Study: Characterizing The Whole Cell Microbial Reference Standard using RNA and DNA-Sequencing
Scott Tighe
A Multi-Platform Assessment of DNA Sequencing Reproducibility using Human and Bacterial Genomes
Jonathan Foox
Jonathan Foox

Concurrent Scientific Session (Mass Spectrometry): From Precision Proteomics to Precision Medicine

Room 214D

Emily Chen, Ian Lienert, Andre Leblanc

From Precision Proteomics To Precision Medicine
Emily Chen
Emily I. Chen, Ian Lienert, Nicolai Bache , André LeBlanc

Concurrent Scientific Session (Core Administration): Leadership in Science

Room 212AB

Mary Winn, Amanda (Nicole) White, Sheenah Mische

Leadership in Science
A. Nicole White, Sheenah Mische, Mary WInn

4:30pm

Concurrent Scientific Session (Core Administration): Rigor and Reproducibility Practices in a Core Setting

Room 214ABC

Susan Meyn, Stephan Uebel, Ian Sullivan

Developing an action plan using results from the Committee on Core Rigor and Reproducibility (CCoRRe) Survey
Susan M. Meyn
Susan Meyn
Quality control of purified proteins to improve research data reproducibility
Stephan Uebel
Stephan Uebel (1), Ario de Marco (2), Nick Berrow (3), Mario Lebendiker (4), Maria Garcia-Alai (5), Stefan H. Knauer (6), Blanca Lopez-Mendez (7), André Matagne (8), Annabel Parret (9), Kim Remans (10), Bertrand Raynal (11)
Reproducibility as a value-add
Ian Sullivan
Ian Sullivan

6:00pm

Technology Showcase - Carl Zeiss Microscopy: ZEISS Elyra 7 with Lattice SIM, a New Platform for Fast and Gentle 3D Superresolution Microscopy

Room 213AB

Technology Showcase - PacBio: Sequence with Confidence: The Next Evolution of SMRT Sequencing

Room 212AB

Technology Showcase - 10x Genomics: Biology at True Resolution with 10x Genomics Solutions

Room 214D

Technology Showcase - PharmaFluidics: Game Changing LC Technology

Room 216

Technology Showcase - Advaita Bioinformatics: Next-Gen Analysis of Genomic Variants, Differential Gene Expression and Proteomics Data

Room 210AB

Technology Showcase - QIAGEN: Novel RNAseq Workflows for rRNA Removal, Ultraplexing and Simultaneous Targeted RNA/DNA Library Construction

Room 209

7:00pm

Deep Stretch/Yin Yoga Class

Room 208

Tuesday 26th

7:30am

Registration Open

Hall 4A

8:00am

Plenary Session IV (Mass Spectrometry) - HDX and Imaging in the Core

Room 214ABC

Kevin Schey

HDX and Imaging in the Core
Kevin Schey
Kevin Schey

9:30am

Open Technical Meeting: Oxford Nanopore Methods, Metagenomics, and Beyond

Room 210AB

Scott Tighe

9:00am

Concurrent Scientific Session (Genomics, Imaging, Spectrometry, Core Administration): ABRF AND FASEB – A VALUED PARTNERSHIP

Room 214ABC

Jim Musser, Sheenah Mische

FASEB 2019: Current Topics in Science Advocacy and Policy
Jim Musser
James M. Musser

10:00am

Coffee Break

Hall 4A

Exhibit Hall Open

Hall 4A

10:30am

Concurrent Scientific Session (Core Administration): Community Colleges: the New Frontier for Advanced Biotechnology Education and Laboratory Services

Room 212AB

Linnea Fletcher, Tyler Drake, Abbe Kesterson, Todd Smith, Thomas C Tubon

Community colleges: the new frontier for advanced biotechnology education and laboratory services.
Todd Smith
Todd Smith, Linnea Fletcher , Abbe Kesterson, Tyler Drake, Thomas Tubon

Concurrent Scientific Session (Mass Spectrometry): Mass Spectrometry Guided Structural Biology

Room 214D

Sheena D'Arcy, Sophie Harvey, Michael Marty

Navigating the strait between efficiency and quality in a mass spectrometry facility
Benjamin Orsburn
Ben Orsburn, Conor Jenkins
Measuring the stoichiometry of antimicrobial peptides in nanodiscs with native mass spectrometry
Michael Marty
Michael Marty, Lawrence Walker, Elaine Marzluff
Quantifying the Dynamics of L-Kynureninase Orthologs during Catalysis using HDX-MS
Sheena D'Arcy
Sheena D'Arcy, Christos S. Karamitros, Everett Stone, George Georgiou, Kyle Murray
Native mass spectrometry for the study of membrane proteins
Sophie Harvey
Sophie R Harvey, Wendy White, Kevin L Schey, Vicki H Wysocki

Concurrent Scientific Session (Imaging): Super-Resolution Alternatives

Room 213AB

Reto Fiolka

Light-sheet microscopy with isotropic, subcellular 3D resolution
Reto Fiolka
Reto Fiolka

Concurrent Scientific Session (Genomics): Single Cell Genomics Applications

Room 214ABC

Emilio Yángüez, Fernando Biase, Fan Gao, Luke Sherlin

Combination of scRNA-seq strategies to untangle complex cell populations
Emilio Yángüez
Emilio Yángüez
Transcriptome profiling of cell lineage at single cell resolution with Rainbow-Seq
Fernando Biase
Fernando Biase
The BUS format for single-cell RNA-seq processing and analysis
Fan Gao
Fan Gao, Eduardo da Veiga Beltrame, Jase A. Gehring, Kristján E. Edljarn Hjoerleifsson, Lambda Lu, Páll Melsted , Vasilis Ntranos, Lior Pachter, Valentine Svensson