Great Lakes Bioinformatics Conference 2014

ACCOMMODATIONS

updated Oct 22, 2013

Discounted rates have been secured for the GLBIO 2014 conference.

Kingsgate Marriott Conference Center at the University of Cincinnati

GLBIO rooms: Single or Double $135.00 USD plus taxes, until April 18, 2014. After this date, rooms are sold at the discretion of the hotel and may be subject to a higher rate.     

Reservations

• Online Reservations - Book your room online here.
  The group code of GLBGLBA will automatically populate the group code box.
  
  
• By Phone: If you prefer to make your hotel reservation by phone, please call 1-888-720-1299 and ask for the GLBIO 2014 - Great Lakes Bioinformatics Conference room block at Kingsgate Marriott Conference Center.

A valid credit card is required to reserve a room.

Parking Charges: Parking is available for hotel guests in the parking garage under the hotel at $10.00 per night with unlimited in and out privileges. Valet parking is $18.00 per night.

Please see the hotel website for driving directions, maps and other hotel related questions.

Great Lakes Bioinformatics Conference 2014

DETAILED AGENDA

Updated June 03, 2014 (Schedule and locations are subject to change. Please check back for updates.)

  Indicates that presentation slides or other resources are available.

...................

Program Book (pdf) - Click here



...................

Go directly to: [Saturday] [Sunday]

FRIDAY – May 16, 2014
Start Time	End Time	SESSION TYPE	LOCATION
		Breakfast on Own
08:00 AM	05:00 PM	Registration	Outside 203-204
09:00 am	10:30 am	Tutorials
		Introduction to Bioinformatics Jerek Meller	Research Auditorium
		Lincs Chemical Biology Data Analysis Workshop Mario Medvedovic	Rooms 203-204
10:30 am	11:00 am	Break
11:00 am	12:30 pm	Tutorials
		Introduction to Bioinformatics (continued) Jerek Meller	Research Auditorium
		canvasXpress: A Highly Interactive JavaScript Library for Analytic Visualization of Genomics Data Isaac Neuhaus	Rooms 203-204
12:30 pm	01:30 pm	Lunch
01:30 pm	02:15 pm	Tutorials
		Enabling Collaborative Research Through Synapse: A Cloud Environment for Data Sharing and Analysis Abhishek Pratap	Kresge Auditorium
		Stochastic Chemical Kinestics: Theory and Systems Biological Applications Presentation (pdf) Péter Érdi	Rooms 203-204
03:00 pm	03:20 pm	Break
03:20 pm	04:50 pm	Tutorials
		Methods and Approaches for the Analysis of Gene Signaling Pathways and Disease Gene Ranking and Systems Genetics Expression Mutation Sorin Draghici and Anil Jegga	Kresge Auditorium
04:50 pm	05:00 pm	Break
05:00 PM	06:00 PM	Keynote Speaker: Charles Brooks PCalign: A Method to Quantify Physicochemical Similarity of Protein-Protein Interfaces	Kresge Auditorium
06:30 pm	06:45 pm	Buses leave Marriott for Sign Museum > Click here for flyer <	Travel to Sign Museum
07:00 pm	10:00 pm	Annual Banquet Keynote Speaker: Anthony Phillipakis Critical Bioinformatics for the future of Medicine and Startup Companies	Sign Museum
[Top]
SATURDAY – May 17, 2014
Start Time	End Time	SESSION TYPE	LOCATION
		Breakfast on Own
08:00 am	05:00 pm	Registration	Outside 203-204
08:20 AM	08:40 AM	GenomOncology Tech Talk (GenomOncology.com)	Kresge Auditorium
08:45 AM	09:00 AM	Morning Welcome	Kresge Auditorium
09:00 AM	10:00 AM	Keynote Speaker: Gary Bader Pathway Analysis of Genomics Data	Kresge Auditorium
10:00 am	10:20 am	Break
10:20 AM	12:00 PM	RESEARCH
10:20 AM	10:40 AM	RESEARCH Prediction of Functionally Important Genes for Target Identification of Lung Cancer Disease & Pharmacophore Modeling and Molecular Docking for PEP inhibitor Venkatesh Arulalapperumal, Sundarapandian Thangapandian, Shalini John, Songmi Kim, Mahreen Arooj, Sugunadevi Sakkiah, Yuno Lee, Guang Ping Cao and Keun Woo Lee	Kresge Auditorium
10:40 AM	11:00 AM	RESEARCH Beegle: A Generic Tool for Disease-Gene Annotation based on Literature Mining Presentation (pdf) Sarah Elshal, Jesse Davis, Amin Ardeshirdavani and Yves Moreau	Kresge Auditorium
11:00 AM	11:20 AM	RESEARCH Evaluating the Efficiency and Scalability of End-to-End Next- Gen Sequencing Data Analysis in Hadoop Kareem Aggour, Dipen Sangurdekar, Lee Newberg, Vijay Kumar, Chinnappa Kodira and John Graf	Kresge Auditorium
		RESEARCH Classification Models for Clear CellRenal Carcinoma Stage Progression,Based on Tumor RNAseq ExpressionTrained Supervised MachineLearning Algorithms Zeenia Jagga and Dinesh Gupta	Rooms 203-204
11:20 AM	11:40 AM	RESEARCH Reconstruction of Metabolic Pathways by Combining Probabilistic Graphical Model-based and Knowledge-based Methods Qi Qi, Jilong Li and Jianlin Cheng	Kresge Auditorium
		RESEARCH Characteristics of Equipartition for RNA Structure Hengwu Li and Keith A Crandall	Rooms 203-204
11:40 AM	12:00 PM	RESEARCH Identifying Common Components Across Biological Network Graphs Using a Bipartite Data Model Erich Baker, Chase Culpepper, Charles Phillips, Jason Bubier, Michael Langston and Elissa Chesler	Kresge Auditorium
		RESEARCH Enhancing Temporo-Geospatial Epidemiological Analysis of H5N1 Influenza using Phylogeography Dhananjai Rao	Rooms 203-204
12:00 PM	01:30 PM	Posters and Lunch - SESSION A	UC MSB
01:30 PM	02:45 PM	HIGHLIGHTS
01:30 PM	01:45 PM	HIGHLIGHTS High-Performance In-memory Genome Project: A Platform for Integrated Genome Data Analysis Matthieu-P. Schapranow	Kresge Auditorium
		HIGHLIGHTS MRFalign: Protein Homology Detection through Alignment of Markov Random Fields Jianzhu Ma, Sheng Wang, Zhiyong Wang and Jinbo Xu	Rooms 203-204
01:45 PM	02:00 PM	HIGHLIGHTS A Probabilistic Approach to Learn Chromatin Architecture and Accurate Inference of the NF-κB/RelA Regulatory Network Using ChIP-Seq Maga Rowicka, Abhishek Mitra, Norbert Dojer, Jun Yang, Shuhua Fu and Allan Brasier Rational	Kresge Auditorium
		HIGHLIGHTS Rational Engineering of the Fungal P450 Monooxygenase CYP5136A3 to Improve its Oxidizing Activity Toward Polycyclic Aromatic Hydrocarbons Alexey Porollo and Jagjit Yadav	Rooms 203-204
02:00 PM	02:15 PM	HIGHLIGHTS Analysis and Reconstruction of 3D Conformation of Human Genome Zheng Wang, Renzhi Cao, Kristen Taylor, Aaron Briley, Tuan Trieu and Jianlin Cheng	Kresge Auditorium
		HIGHLIGHTS Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space Alexandra Schnoes, David Ream, Alexander Thorman, Patricia Babbitt and Iddo Friedberg	Rooms 203-204
02:15 PM	02:30 PM	HIGHLIGHTS Potential Artem for Epigenomics Integration To Be Announced	Kresge Auditorium
		HIGHLIGHTS Applying Molecular Crowding Models to Simulations of Virus Capsid Assembly In Vitro Gregory Smith, Lu Xie, Byoungkoo Lee and Russell Schwartz	Rooms 203-204
02:30 PM	02:45 PM	HIGHLIGHTS The Quantitative Systems Pharmacological Approach: Anxiolytic Drugs and Altered Hippocampal Theta Rhythms Péter Érdi, Tibin John, Tamás Kiss and Colin Lever	Kresge Auditorium
		HIGHLIGHTS Validation of Predicted mRNA Splicing Mutations Using High-throughput Transcriptome Data Presentation (pdf) Coby Viner, Stephanie N. Dorman, Ben C. Shirley and Peter K. Rogan	Rooms 203-204
02:45 PM	03:00 PM	HIGHLIGHTS Wnt Signaling in Cancer: A Mathematical Systems Biology Modeling Ju Bao and Jie Zheng	Kresge Auditorium
		HIGHLIGHTS Bermuda: Bidirectional de novo Assembly of Transcripts with Low Expression and Uneven Coverage Utilizing Alternate de Bruijn Graphs Qingming Tang, Jian Peng, Sheng Wang and Jinbo Xu	Rooms 203-204
03:00 PM	03:15 PM	Break
03:15 PM	04:15 PM	Keynote Speaker: Michael Hawrylcz Atlases of the Prenatal, Developing, and Adult Human Brain	Kresge Auditorium
04:15 PM	04:30 PM	Break
04:30 pm	05:30 pm	Bioinfomatics Career Session - Dr. Howard Adams Presentation (pdf)	Kresge Auditorium
		Educational Panel Discussion Led by Guenter Tusch Presentation (pdf)	Rooms 203-204
05:30 PM	07:00 PM	Poster and Reception - SESSION B	UC MSB
[Top]
SUNDAY – May 18, 2014
Start Time	End Time	SESSION TYPE	LOCATION
		Breakfast on Own
08:30 am	01:00 pm	Registration	Outside 203-204
09:00 AM	11:00 AM	FLASH TALKS
09:00 AM	09:12 AM	FLASH TALKS Improved Geometric Unmixing Models for Tumor Progression Theodore Roman, Brittany Fasy, Amir Nayyeri, Gary Miller and Russell Schwartz	Kresge Auditorium
09:12 AM	09:24 AM	FLASH TALKS GLAD: A Mixed-membership Model for Heterogeneous Tumor Subtype Classification Hachem Saddiki, Jon McAuliffe and Patrick Flaherty	Kresge Auditorium
		FLASH TALKS Towards a Universal model of Gene Block Evolution in Bacteria David Ream and Iddo Friedberg	Rooms 203-204
09:24 AM	09:36 AM	FLASH TALKS Network Based Approach to Identify Dysregulated Genes and Pathways associated with Tumour Migration in Stage III Colorectal Cancer Kshithija Nagulapalli, Meeta Pradhan and Mathew Palakal	Kresge Auditorium
		FLASH TALKS RVD2: An Ultra-sensitive Variant Detection Model for Low-depth Targeted Next-generation Sequencing Data Yuting He and Patrick Flaherty	Rooms 203-204
09:36 AM	09:48 AM	FLASH TALKS Integrating microRNA expressions in Pathway Analysis Diana Diaz, Michele Donato and Sorin Draghici	Kresge Auditorium
		FLASH TALKS Computing Gene-Centric DNA Methylati on from Probe-Level Methylation Arrays Brittany Baur and Serdar Bozdag	Rooms 203-204
09:48 AM	10:00 AM	FLASH TALKS Systems Pharmacology Analysis of Drug-induced Peripheral Neuropathy Junguk Hur, Abra Guo, Wei-Yin Loh, Eva Feldman and Jane Bai	Kresge Auditorium
		FLASH TALKS Robust Imputation of Classical HLA Alleles from SNP Data Using Ensemble Classifiers Jacek Biesiada and Jarek Meller	Rooms 203-204
10:00 AM	10:12 AM	FLASH TALKS DNMKB: A Web-based Analysis System for Diabetic Neuropathy Microarray Data Meeyoung Park, Junguk Hur and Eva Feldman	Kresge Auditorium
		FLASH TALKS Real-Time Comparison of 3D Electron Microscopy Density Maps and Protein Shapes with EM-SURFER and 3D-SURFER 2.0 Juan Esquivel-Rodriguez, Yi Xiong, Xusi Han, Shuomeng Guang and Daisuke Kihara	Rooms 203-204
10:12 AM	10:24 AM	FLASH TALKS WARDROBE Experiment Management System: Web-based Platform for Integrated Epigenomics Analysis Andrey Kartashov and Artem Barski	Kresge Auditorium
		FLASH TALKS Joint Sequence Variation Analysis Across Multiple Protein Families Reveals More Native Contacts Jianzhu Ma, Sheng Wang and Jinbo Xu	Rooms 203-204
10:25 AM	11:00 AM	Break
11:00 am	12:00 pm	Keynote Speaker: Tanya Berger-Wolf Computational Ecology	Kresge Auditorium
12:00 pm	12:30 pm	Awards and Closing Remarks Awards Committee	Kresge Auditorium

[Top]

Great Lakes Bioinformatics Conference 2014

POSTER PRESENTATIONS

as of April 25, 2014

Go directly to Session B - Click here

<--------------SESSION A-------------->

Poster 1
The Bacillus thuringiensis Information Resource (BTIR): An Online Portal for Genomic, Proteomic, and Metabolomic Data for Bt Toxins
Abraham Moller, Lin Liu and Chun Liang

Poster 2
Inter- and Intra-population Genetic Variations in Humans
Ahmed Al-Khudhair, Alexei Fedorov, Xi Cheng, Shuhao Qiu, Shilpi Chowdhury, Meghan Wyse, Dulat Bekbolsynov and Arnab Saha-Mandal

Poster 3
A Coarse Grained Investigation of Fiber Strain and Fracture
Andrew Marmaduke

Poster 4
WARDROBE Experiment Management System: Web-based Platform for Integrated Epigenomics Analysis
Andrey Kartashov and Artem Barski

Poster 5
The Evolution of the Plant Mobile Domain in Glycine Max
Athena Mascarenhas

Poster 6
Assessing the Prevalence of the CRISPR/Cas Systems in the Environment
David Baltrusaitis, Paul O'Malley and Catherine Putonti

Poster 7
Genomic Analysis of a Fitness Landscape
Ethan Knapp and Francisco Moore

Poster 8
A Population Genomics Approach to the Identification of Strain-specific Inheritance Patterns in Toxoplasma
Gondii Javi Zhang and John Parkinson

Poster 9
Predicting Genes with Lethal Mutant Phenotypes in Arabidopsis Thaliana
John Lloyd, Alex Seddon, Gaurav Moghe and Shin-Han Shiu

Poster 10
Real-Time Comparison of 3D Electron Microscopy Density Maps and Protein Shapes with EM-SURFER and 3D-SURFER 2.0
Juan Esquivel-Rodriguez, Yi Xiong, Xusi Han, Shuomeng Guang and Daisuke Kihara

Poster 11
Stochastic Kinetic Model of the Circular Gene Expression Hypothesis
László Zalányi, Judit Szente, László Négyessy and Peter Erdi

Poster 12
PLANTORDB, a Comprehensive Ortholog Database for Plant and Green Algae
Lei Li, Guoli Ji and Chun Liang

Poster 13
Spatial and Temporal Structure of Adult Survival, Breeding Effort, and Movement at a Spotted Salamander (Ambystoma Maculatum) Breeding Pond
Scott Thomas and Peter Niewiarowski

Poster 14
Integrating Genomic and Image Data Using Biological Database of Images and Genomes
Andrew Oberlin, Dominika Jurkovic, Asma Bankapur, Mitchell Balish and Iddo Friedberg

Poster 15
ToppMiR: Significance-ranking of microRNAs and their mRNA Targets Based on Biological Context and Functional Associations
Chao Wu, Eric Bardes, Anil Jegga and Bruce Aronow

Poster 16
Integrating microRNA Expressions in Pathway Analysis
Diana Diaz, Michele Donato and Sorin Draghici

Poster 17
GLAD: A Mixed-membership Model for Heterogeneous TumorSsubtype Classification
Hachem Saddiki, Jon McAuliffe and Patrick Flaherty

Poster 18
Systematic Genomic Identification of Colorectal Cancer Genes Delineating Advanced from Early Clinical Stage and Metastasis
Hojoon Lee, Patrick Flaherty and Hanlee Ji

Poster 19
Systems Pharmacology Analysis of Drug-induced Peripheral Neuropathy
Junguk Hur, Abra Guo, Wei-Yin Loh, Eva Feldman and Jane Bai

Poster 20
Cancer Screening Using Biomimetic Pattern Recognition with Hyper-dimensional Planar Structures
Leonila Lagunes and Charles Lee

Poster 21
Identification of Novel Therapeutics for Hypertension from Genome-wide Association Data
Mani P. Grover

Poster 22
DNMKB: A Web-based Analysis System for Diabetic Neuropathy Microarray Data
Meeyoung Park, Junguk Hur and Eva Feldman

Poster 23
Determining Biological Trends Using Machine Learning Techniques
Regie Felix, Nazli Dereli, Petko Bogdanov and Nick Beck

Poster 24
Improved Geometric Unmixing Models for Tumor Progression
Theodore Roman, Brittany Fasy, Amir Nayyeri, Gary Miller and Russell Schwartz

Poster 25
A Novel Systems-based Bioinformatics Platform for Metatranscriptome (RNA-seq) Analysis
Yue Jiang, Xuejian Xiong and John Parkinson

Poster 26
Cis-regulatory Code of Root and Shoot Salt Response in Arabidopsis
Alexander Seddon, Sahra Ugyun, Ming Jung Liu, Melissa Lehti-Shiu and Shin-Han Shiu

Poster 27
Global Metabolomic Profiling of Cuprizone-induced Oligodendrocyte Degeneration
Alexandra Taraboletti and Leah Shriver

Poster 28
PredβTM: An Algorithm to Predict Transmembrane Beta-Barrels
Amrita Roy Choudhury and Marjana Novič

Poster 29
Bilitranslocase – Towards Structural Elucidation and Functional Mechanism
Amrita Roy Choudhury, Marjana Novič and Igor Zhukov

Poster 30
Computing Gene-centric DNA Methylation from Probe-level Methylation Arrays
Brittany Baur and Serdar Bozdag

Poster 31
A Novel Algorithm for Detecting Inverted Repeats Based on Vector Calculation
Congting Ye, Guoli Ji and Chun Liang

Poster 32
Towards a Universal Model of Gene Block Evolution in Bacteria
David Ream and Iddo Friedberg

Poster 33
Extended Analysis of Class I Methyltransferases
Dorothy McAfee and John Perozich

Poster 34
Robust Imputation of Classical HLA Alleles from SNP Data Using Ensemble Classifiers
Jacek Biesiada and Jarek Meller

Poster 35
Joint Sequence Variation Analysis Across Multiple Protein Families Reveals More Native Contacts
Jianzhu Ma, Sheng Wang and Jinbo Xu

Poster 36
Detection of Short Circularized DNA from Short-read DNA Sequencing
Mark Maienschein-Cline, Zhengdeng Lei, Pinal Kanabar, Oleksiy Karpenko, Morris Chukhman, Robert Johnson, Neil Bahroos, Stefan Green and Chunxiang Zhang

Poster 37
findAdapter: A Fast, Lightweight Adapter Trimming Program for Next Generation Sequencing Data
Min Dong, Guoli Ji and Chun Liang

Poster 38

Poster 39
Tracing Genes Origins with Fast Scanning of Biological Databases on GPU
Mohamed Issa, Ahmed Alzohairy and Julie Thompson

Poster 40
Extended Analysis of Nucleotide-Sugar Dehydrogenases
Nicholas Freas and John Perozich

Poster 41
Function and Evolution of Cyclic Gene Expression in Chlamydomonas
Reinhardtii Nicholas Panchy, Guangxi Wu, Jin Chen, Eva Farre and Shinhan Shiu

Poster 42
Impact of Sequencing Conditions on RNA-Seq Accuracy
Phillip Dexheimer, Satwica Yerneni, Bruce Aronow and Mehdi Keddache

Poster 43
Bermuda -- A New RNA-Seq de Novo Assembler
Qingming Tang and Jinbo Xu

Poster 44
Detecting Evolutionary Strata on the Human X Chromosome in the Absence of Gametologous Y-linked Sequences
Rajeev Azad, Ravi Shanker Pandey and Melissa Wilson Sayres

Poster 45
GIST - An Ensemble Approach to the Taxonomic Classification of Metatranscriptomic Reads
Samantha Halliday and John Parkinson

Poster 46
Sequence Analysis Pipeline for Complex Microbial Communities/em>
SShareef Dabdoub, Matthew Mason and Purnima Kumar

Poster 47
Protein Visualization with Sacks Spiral Method: A 2-D Application in Genomic Engineering to Enhance Search Algorithms' Performance and Compare Proteins at Various Structural Levels
Susan Nachawati

Poster 48
RVD2: An Ultra-sensitive Variant Detection Model for Low-depth Targeted Next-generation Sequencing Data
YuYuting He and Patrick Flaherty

[top]

<--------------SESSION B-------------->

Poster 1
Multi-compartment Biochemical Metabolic Network for the Malaria Parasite, Plasmodium Falciparum
Abolaji Famuyiwa, Adebiyi Ezekiel and Adebiyi Marion

Poster 2
A Hybrid System Based Approach of Mitochondria-Gastrointestinal System in Autism
Adam Gaynor and Krishnendu Ghosh

Poster 3
A Genomics-based Approach for Identifying the Sex-determining Region of the Clam Shrimp (Eulimnadia Texana) Genome
Adam Reese and Donald Gasper

Poster 4
Structural Divergence of the Calcium Antiporter ChaA
Alex Tegland and Hazel Barton

Poster 5
Whole Exome Analysis of Individuals and Families with Chronic Recurrent Multifocal Osteomyelitis (CRMO)
Allison Cox, Benjamin Darbro, Xinyu Bing, Alexander Bassuk and Polly Ferguson

Poster 6
Crowdsourcing Innovation to Boost Pathway Discovery from Literature
Andrew Schriner, Mayur Sarangdhar, Anil Jegga and Bruce Aronow

Poster 7
User Friendly Gene Expression Software
Anthony Deeter

Poster 8
An Integrated View of Metazoan Evolution
Ashley Wain

Poster 9
Protein Sequence Simulation for Testing Game-Theoretic Protein Clustering
Brittney Hinds, Bo Deng and Etsuko Moriyama

Poster 10
Iron-reducing Bacterial Species Contribute to Iron Ore Cave Formation
Ceth Parker, John Senko, Ira Sasowsky, Augusto Auler, Hazel Barton

Poster 11
Effects of Melanopsin Knockout on Retinal Wave Activity
Daniel Vicarel and Jordan Renna

Poster 12
Search of Genetic Signaling Pathway with the Traveling Salesman Problem
Enery Lorenzo, Mauricio Cabrera-Rios, Alexander Ropelewski, Calra Isaza

Poster 13
Regulatory Analysis of Differentially Expressed Genes Associated with Cmi-knockout in Drosophila Melanogaster
Faizah Siddiqua, Catherine Putonti and Andrew Dingwall

Poster 14
Supporting Omics Research, Finding Gene Expression Changes Over Time
Guenter Tusch, Olvi Tole, Mary Ellen Hoinski, Santhosh Dharmapuri and Shahrzad Eslamian

Poster 15
Towards a Map for Bacteriocin Hunters
James Morton, Shaun Lee and Iddo Friedberg

Poster 16
Fingerprinting and an Application of Relative Compression to Sequence Comparison
Jeff Chapman

Poster 17
Unearthing Genomic Fossils: Designing a Novel Tool for the Detection of Horizontal Gene Transference
Jonathon Brenner

Poster 18
Meta-analysis of Genetic Signaling Paths: First Ideas and Results
Juan Rosas, Mauricio Cabrera and Clara Isaza

Poster 19
Lung Cancer - New Information from Old Data: Preliminary Results
Katia I Camacho Caceres, Juan I. Irizarry Nieves, Juan C. Acebedo Díaz, Valery M Gonzales Pérez, Clara E. Isaza and Mauricio Cabrera Rios

Poster 20
Cell Nucleus Extraction and Local Feature Descriptors for Computational Analysis of Brain Images
Kazuhiko Tamaki, Hiroharu Kawanaka, Shikha Chiganti, Lili Miles, Bruce Aronow, Haruhiko Takase and Shinji Tsuruoka

Poster 21
Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs)
Kun Sun, Yu Zhao, Huating Wang and Hao Sun

Poster 22
Modeling Genetic Influences on Asthma and Pulmonary Tuberculosis
Lada A Koneva, Maxim B Freidin, Elena Bragina, Valery Puzyrev and Richard C McEachin

Poster 23
Computational Analysis of Mutational effects on substrate mobility in the ADP-glucose pyrophosphorylase from Escherichia coli
Ligin Solamen, Angela Mahaffey, Miguel Ballicora and Kenneth Olsen

Poster 24
Behavioral Neuroinformatics: A Pilot-Study in Developing a Prototype Neurobehavioral Database
Lucas Stetzik and Jeffrey Chapman

Poster 25
Co-evolutionary Analysis of Functional Domains of Proteins that are Known to be Interacting in HIV-1
Madara Hetti Arachchilage, Yi Wei, Ajay Dakappagari, Vindya Perera and Helen Piontkivska

Poster 26
Transcriptomic Profiling and Functional Analyses of the Leptin-A Knockdown in the Developing Zebrafish (D. rerio)
Mark Dalman, Anthony Deeter, Alicja Sochaka, Qin Liu, Zhong-Hui Duan and Richard Londraville

Poster 27
Bias in Evolutionary Parameter Estimates Due to Sequence Resampling in Influenza A: Too Few Countries, Too Many Sequences?
Mary Halpin and Helen Piontkivska

Poster 28
AERSMine: A High-resolution Multiple Cohort Analyzer Based on the FDA’s Adverse Events Reporting System Data
Mayur Sarangdhar, Scott Tabar, Akash Kushwaha, Anil Jegga and Bruce Aronow

Poster 29
Automated Feature Selection and Classification of Genomics Datasets at the Gene and Isoform-level
Meenakshi Venkatasubramanian, Nathan Salomonis

Poster 30
Integration of Transcriptomic Data in Genome-scale Metabolic Models Predicts in Vitro Intracellular Central Carbon Metabolic Fluxes with High Correlation in Escherichia Coli and Saccharomyces Cerevisiae Min Kyung Kim and Desmond Lun

Poster 31
Gene Fusion Detection Benchmarking
Morris Chukhman, Mark Maienschein-Cline, Pinal Kanabar, Zhengdeng Lei, Oleksiy Karpenko, Neil Bahroos, Hui Lu, Georgi Genchev and Cong Liu

Poster 32
Characterizing Viral Species in Complex Samples
Neil Kuehnle, C. Anthony Ruggeri, Zachary Romer, Kema Malki, Siobhan Watkins and Catherine Putonti

Poster 33
Benchmarking Variant Callers for Ion Torrent Data
Pinal Kanabar, Zhengdeng Lei, Mark Maienschein-Cline, Oleksiy Karpenko, Morris Chukhman, Robert Johnson, Stefan Green and Neil Bahroos

Poster 34
Transcriptome-wide Bioinformatics Analysis Reveals Human Oncogenic RNA Switches
Qiuqing Wang and Peng Yao

Poster 35
Evolutionary Trajectories of CTL Epitopes in HIV-1
Reeba Paul, Vindya Perera, Yanyi Zang and Olena Piontkivska

Poster 36
A Concurrent Next Generation Sequencing Simulator – CONGEST
Richard Tillquist and Eric Ho

Poster 37
In Silico Discovery of Tissue-specific Cis-regulatory Elements
Richard Wolfe

Poster 38
Elucidating the Catalytic Mechanism of the Glutathione Peroxidase-like Thioredoxin Peroxidase (TPxGl) of the Malaria Parasite Plasmodium Using Site Directed Mutagenesis
Shannon Mcguire

Poster 39
Apply Genome Evolution by Matrix Algorithms (GEMA) for Population Genetics Problems
Shuhao Qiu and Alexei Fedorov

Poster 40
Applications of Genome Evolution by Matrix Algorithms (GEMA) for Population Genetics Problems
Shuhao Qui, Alexei Fedorov

Poster 41
microRNA Analysis and Prediction
Sushma Reddy and Jonathan Lo

Poster 42
A Polyglot Approach to Bioinformatics Data Integration: Phylogenetic Analysis of HIV-1
Thomas Hatzopoulos, Steven Reisman, George Thiruvathukal and Catherine Putonti

Poster 43
Discovery of Early Biomarkers of Alzheimer's Disease: Connecting Biochemical Events to Oscillatory Electrical Signal Changes Using Computational Modeling
Tibin John, Tamás Kiss and Peter Erdi

Poster 44
Pathway Comparision and Target Identification of Glucocorticoid Receptor Activation Effect (GRAE) on Human Cancer Cells by Differential Gene Expression Analysis & Survival Analysis
Venkatesh Arulalapperumal, Sugunadevi Sakkiah, Shalini John, Yuno Lee, Mahreen Arooj and Keun Woo Lee

Poster 45
Homology Modeling of Protein Structure Pipeline
Wen Dong, Yichao Li, Lonnie Welch and Michael Held

Poster 46
Inferring Protein Interaction Networks through Time-lagged Correlation Analysis from Time-Series Data
Xiaoyu Liang, Rami Al-Ouran, Yichao Li, Razvan Bunescu and Lonnie Welch

Poster 47
Comparison of Methods for Estimates of Tissue Components in Mix-tissue Samples
Xuerong Liu, Xiaoqin Xia, Sujay Datta and Zhenyu Jia

Poster 48
Identification of Three Common Molecular Subtypes Between Gastric Cancer and Pancreatic Cancer
Zhengdeng Lei, Pinal Kanabar, Mark Maienschein-Cline, Oleksiy Karpenko, Morris Chukhman, Robert Johnson and Neil Bahroos

 [top]

Great Lakes Bioinformatics Conference 2014

JOBS BOARD

Updated April 21, 2014

GenomOncology
26202 Detroit Road, Suite 300,
Westlake, OH 44145
www.genomoncology.com/

BIOINFORMATICIST

COMPANY DESCRIPTION
GenomOncology is enabling precision medicine by translating next generation sequencing data into actionable information for clinicians and researchers. As the bottleneck of cancer molecular diagnostics has moved from data acquisition to data interpretation, GenomOncology has developed a proprietary technology platform to streamline the use of next generation sequencing in medicine and research.  

GenomOncology’s proprietary software and analytical tools can rapidly and interactively analyze and interpret sequenced genomic data. This approach enables GenomOncology to capture critical findings for the cancer researcher or clinical oncologist and produce a robust analysis report in less than a day. The company expects its technology will reduce the time necessary for researchers to make new discoveries, which will ultimately provide clinicians with the information necessary to prescribe “personalized” medical treatment.

We are an equal opportunity employer providing a competitive compensation and benefits package…and most importantly offer a fun, energetic and highly collaborative environment!

ROLE DESCRIPTION
Our cancer genomic analyses focus on three distinct professional fields: cancer research, clinical application, and drug discovery.  Due to our rapid growth and new client acquisition we are actively seeking Bioinformaticians to join our team.  We offer a highly collaborative, flexible and fun working environment.

QUALIFICATIONS

• Demonstrated research and working experience in bioinformatics, next-generation sequencing, and database tools/technologies.

• Must have strong analytical and quantitative skills, strong oral and written communication skills, and accustomed to working both independently and collaboratively.

• Masters/PhD (with 3+ years of experience) in Computer Science with Molecular Biology/Microbiology concentration, Molecular Biology/Microbiology with Computer Science/Bioinformatics concentration, Bioinformatics, and/or Medical Informatics.

• Demonstrated ability to develop software tools to generate useful genomic information and analyze genomic sequencing data.

• Proficiency in using build, test, version control, and documentation tools preferred.

• Demonstrated proficiency in Java, Python, and R; able to read and use PERL libraries.  Experience working with databases is a plus (SQL / NoSQL).  Proficiency working in a Linux environment and with Unix shell scripting.  Proficiency with the SGE cluster environment.

• Familiarity with the ecosystem of standard tools for primary sequence analysis (e.g. BWA, samtools, vcftools, bedtools, tabix, Picard tools, GATK, CASAVA, Bowtie, Tophat, Cufflinks), their APIs and standard file formats (SAM/BAM, VCF, BED, etc.).

• Must be able to work in a fast-paced, start-up like environment.

Please send resume/inquiries to: This email address is being protected from spambots. You need JavaScript enabled to view it.

GenomOncology
26202 Detroit Road, Suite 300,
Westlake, OH 44145
www.genomoncology.com/

GENOMIC ANALYST

COMPANY DESCRIPTION
GenomOncology is enabling precision medicine by translating next generation sequencing data into actionable information for clinicians and researchers. As the bottleneck of cancer molecular diagnostics has moved from data acquisition to data interpretation, GenomOncology has developed a proprietary technology platform to streamline the use of next generation sequencing in medicine and research.  

GenomOncology’s proprietary software and analytical tools can rapidly and interactively analyze and interpret sequenced genomic data. This approach enables GenomOncology to capture critical findings for the cancer researcher or clinical oncologist and produce a robust analysis report in less than a day. The company expects its technology will reduce the time necessary for researchers to make new discoveries, which will ultimately provide clinicians with the information necessary to prescribe “personalized” medical treatment.

We are an equal opportunity employer providing a competitive compensation and benefits package…and most importantly offer a fun, energetic and highly collaborative environment!

ROLE DESCRIPTION
GenomOncology has challenging opportunities for scientists of all experience levels who want to take their careers to a new level. We are actively pursuing candidates for our Genomic Analyst role to work onsite with our clients and assist in the analysis of both clinical and research sequencing data. The role would also involve assisting GenomOncology’s bioinformatics team in maintaining and developing capabilities for our clients.

QUALIFICATIONS

• Knowledge of human genetics and genomics; specifically cancer genomics would be most beneficial.
• Experience working in a research environment either through an internship, academic research project or as part of current job.
• Experience using bioinformatics tools to analyze genomic data.
• Experience analyzing Next Generation Sequencing data and writing analysis scripts a huge plus.
• Experience conducting literature reviews utilizing public databases such as Pubmed either for class or as part of a research project.
• Experience working in a team based environment and proven productivity when working remotely or unsupervised.
• Excellent verbal and written communicator, with strong technical documentation capabilities.
• Demonstrated analytical and problem-solving skills.
• Strong computer skills including familiarity with Mac/Linux environments and ability to independently acquire working knowledge of new software and analysis techniques.

Please send resume/inquiries to: This email address is being protected from spambots. You need JavaScript enabled to view it.

[TOP]