|
Presenting Author |
Abstract Title |
Talk/Poster |
|
Aghazadeh, Amirali |
Universal microbial diagnostics using random DNA probes |
poster |
|
An, Lin |
A computational framework to predict chromatin interaction using genomic and epigenomic data |
poster |
|
Avsec, Ziga |
A convolutional neural network framework for modelling cis-regulatory elements with application to RNA stability |
poster |
|
Awan, Mohammed O |
Investigating how the transcription factor fkh-8 is expressed in BAG neurons and the dopaminergic pathway |
poster |
|
Baryshnikova, Anastasia |
Functional annotation and visualization of large-scale biological networks |
talk |
|
Boeing, Stefan |
Multiomic analysis of the UV-induced DNA damage response |
poster |
|
Bourque, Guillaume |
IHEC Data Portal—A resource for discovering, analysing and sharing epigenomics data |
talk |
|
Bradic, Martina |
Transposable element-mediated gene regulation in the parasite Trichomonas vaginalis |
poster |
|
Brown, Stuart |
Fast annotation of metagenomic shotgun sequences with a microbial gene catalog and Bowtie2 |
poster |
|
Bryan, Jordan G |
CERES—A model for inferring genetic dependencies in cancer cell lines from CRISPR knockout screens |
talk |
|
Campagne, Fabien |
MetaR—Towards an R notebook with composable languages |
talk |
|
Chilton, John M |
Planemo—A scientific workflow SDK |
poster |
|
Choudhary, Krishna |
Methods for rapid and scalable quality assessment of RNA structure probing data |
poster |
|
Chougule, Kapeel M |
Benchmarking alignment and quantification tools on plant RNA-seq data with Cyverse cyberinfrastructure |
poster |
|
Clarke, Declan |
Integrative approaches for variant interpretation in coding regions |
poster |
|
Corry, Schuyler |
Pollen counting and analysis with the Attune acoustic flow cytometer |
poster |
|
Cox, Nancy J |
Novel discovery from a gene by medical phenome catalog |
talk |
|
Cukuroglu, Engin |
Computational analysis of endogenous retroviral element expression during the development of human embryos |
poster |
|
Damani, Farhan N |
Predicting tissue-specific effects of rare genetic variants |
talk |
|
Darnell, Gregory |
Winner’s Curse in quantitative genomics studies |
talk |
|
DeFord, Peter M |
StruMs—A flexible and information-rich representation of DNA motifs |
talk |
|
Devisetty, Upendra Kumar |
Evolinc—A computational pipeline for comparative genomic and transcriptomic analyses of long non-coding RNAs from large RNA-Seq datasets |
poster |
|
Dikow, Rebecca B |
A whole-genome phylogenetic hypothesis across the three domains of life |
poster |
|
Dunn, Nathan A |
Apollo—Collaborative and scalable manual genome annotation |
talk |
|
Emad, Amin |
The KnowEnG platform for biological data analytics on the Cloud—A use case in gene prioritization for pharmacogenomics |
talk |
|
Fabregat Mundo, Antonio |
Reactome pathway analysis—A high-performance in-memory approach |
talk |
|
Fang, Han |
Scikit-ribo reveals precise codon-level translational control by dissecting ribosome pausing and codon elongation |
talk |
|
Frandsen, Paul B |
Building a biological data science infrastructure at the Smithsonian Institution |
poster |
|
Friedberg, Iddo |
Community computational challenges in biological data science—An optimistically cautionary tale |
poster |
|
Fulton, Alexander D |
Complete site saturation of Bacillus subtilis Lipase A to study the influence of single amino acids on the overall stability in surfactants |
poster |
|
Gawronski, Alexander R |
Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer |
talk |
|
Ghosh, Ambarnil |
A systematic study on the distribution and occurrence of mutations within regulatory motifs from cancer genome |
talk |
|
Giangreco, Nicholas P |
Arid1a mutations in an Apc/Pten-deficient mouse model of ovarian tumors profoundly alter DNA methylation and transcription |
poster |
|
Greenfield, Nick |
Towards "dry side" reproducibility—A technical survey of the challenges to and building blocks for reproducible, secure, and usable (microbial) genomics data infrastructure |
poster |
|
Groff, Abigail |
In vivo characterization of Linc-p21 reveals functional cis-regulatory DNA elements |
poster |
|
Hansen, Kasper D |
Choice of reference genome can introduce massive bias in bisulfite sequencing data |
talk |
|
Hansen, Kasper D |
The quantitative relationship between histone modifications and gene expression across different individuals |
poster |
|
Hansen, Nancy |
Use of low coverage short read sequence data for quality control and familial relationship identification |
poster |
|
Harmanci, Arif |
Quantification of sensitive information leakage from genomic linking attacks |
talk |
|
He, Yuan |
Distant regulatory effects of genetic variation in multiple human tissues |
talk |
|
Herrin, Steve M |
Experiences migrating large scale bioinformatics data pipelines to a cloud infrastructure |
talk |
|
Hoffman, Michael |
Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet |
talk |
|
Huang, Yifei |
Estimation of nucleotide- and allele-specific selection coefficients in the human genome using deep learning and population genetics |
talk |
|
Hutton, Elizabeth |
Prediction of essential coding and noncoding elements using CRISPR |
poster |
|
Irizarry, Rafael |
Overcoming bias and systematic error in high-throughput technologies are key for the success of data science |
talk |
|
Ishii, Kazuo |
Shell scripting-based mathematical modeling for transcriptome data with bootstrapping and parallel computing |
poster |
|
Israeli, Johnny |
How To Train Your DragoNN (Deep Regulatory Genomic Neural Network) |
talk |
|
Jacques, Pierre-Etienne |
Thousands of public epigenomic datasets can be exploited through the Galaxy-GenAP project and the GeEC tool |
talk |
|
Jain, Chirag |
Fast approximate mapping of single molecule sequences using MinHash |
talk |
|
Jin, Yumi |
Evaluating population structure for subjects in the dbGaP Database |
talk |
|
Kahles, Andre |
Metagenome annotation with distributed reference graphs |
talk |
|
Kamalakaran, Sitharthan |
Analysis Tool for Annotated Variants—A comprehensive platform for population-scale genomic analyses |
poster |
|
Kasukawa, Takeya |
FANTOM5 SSTAR—A challenge to establish a continuously extensible database for a large scale data production project |
poster |
|
Kim, Minji |
Hi-C data compression |
poster |
|
Kiwala, Susanna |
pVAC-Seq—Development of an open-source software pipeline for tumor neoantigen discovery and personalized immunotherapy |
poster |
|
Kucukural, Alper |
Dolphin—A graphical user interface for the analysis and processing of high throughput genomics |
poster |
|
Kugler, Hillel |
Analysis and synthesis of gene regulatory networks via formal reasoning—Main applications and future challenges |
poster |
|
Kumar, Vivek |
Advancing systems biology using an open, extensible and scalable KBase platform |
talk |
|
Kyle, Kathleen E |
Gtracks—A framework for creating and maintaining UCSC track databases using google spreadsheets |
poster |
|
Langmead, Ben T |
A tandem simulation framework for predicting mapping quality |
talk |
|
Leuthaeuser, Janelle B |
Comparison of protein similarity network topologies using sequence- and active site-similarity edge metrics |
poster |
|
Li, Yulong |
Optimized contigs assembly and SNP discovery by overlapping paired-end RAD sequencing in roughskin sculpin (Trachidermus fasciatus Heckel) |
poster |
|
Liang, Suh-yuen |
The TCGA data analysis for the function and regulation of the protein tyrosine phosphatase superfamily in human cancers |
poster |
|
Liu, Bingjian |
Genome-wide SNP discovery and preliminary population genetic analysis in Japanese eel (Anguilla japonica) based on RAD sequencing |
poster |
|
Luo, Ruibang |
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model |
poster |
|
Mah, Nancy |
The CellFinder on-line data resource and its applications for stem cell research |
poster |
|
Malik, Laraib I |
GRASS—Graph regularized annotation via semi-supervised learning |
poster |
|
McKerrow, Wilson H |
Improved repeat alignment by simultaneous estimation of variation and alignment |
poster |
|
Milosavljevic, Aleksandar |
The exRNA Atlas—Linking data, tools, and computable pathway knowledge to interpret the first 1000 uniformly processed profiles of extracellular RNA from human bodily fluids |
talk |
|
Molik, David |
Deployment of a bioinformatics analytics platform in the cloud |
poster |
|
Montgomery, Philip G |
Conseq—A metadata-driven tool for executing bioinformatic pipelines |
poster |
|
Morgan, Martin |
Traditional approaches and contemporary challenges to production of useful scientific software—Lessons from Bioconductor |
talk |
|
Nattestad, Maria |
Interactive genomic visualization tools for long read sequencing, assembly, and cancer |
poster |
|
Nekrutenko, Anton |
Enhancing pre-defined workflows with ad hoc analytics in a single environment—Unlocking Jupyter and RStudio for biologists |
poster |
|
Nellore, Abhinav |
Gpeg—Lossy and lossless compression of sequencing read alignments across many samples |
poster |
|
Nellore, Abhinav |
Recount—A large-scale resource of analysis-ready RNA-seq expression data |
poster |
|
Niknafs, Yashar S |
TACO—Multi-sample transcriptome assembly for RNA-seq |
poster |
|
Nothaft, Frank A |
Processing terabyte-scale genomics datasets with ADAM and Toil |
talk |
|
Oguz, Cihan |
Integrative and predictive modeling of severe controlled and severe resistant hypertension among African-Americans in the MH-GRID Network |
poster |
|
Olson, Andrew |
Searching and exploring Gramene’s comparative genomics datasets on the web |
poster |
|
Onami, Shuichi |
Analysis of quantitative data of nuclear division dynamics from single gene knockdown embryos for all essential embryonic genes in C. elegans |
poster |
|
Park, YoSon |
Cell type specific gene expression variation in differentiated induced pluripotent stem cells |
talk |
|
Paten, Benedict J |
Reproducible, portable, scalable and open genomics with Toil, ADAM and Dockstore |
talk |
|
Phan, Lon |
dbSNP in the era of next-generation sequencing and big data |
poster |
|
Piccolo, Stephen R |
A comprehensive benchmark comparison of machine-learning algorithms for classification of biomedical outcomes using gene-expression data |
poster |
|
Piccolo, Stephen R |
How to quantify expression for thousands of RNA-Sequencing samples in a day for a minimal cost |
talk |
|
Piccolo, Stephen R |
ShinyLearner—Enabling biologists to perform robust machine-learning classification |
poster |
|
Pritt, Mark J |
Let the right ones in—The cost and benefit of including alternate alleles in the reference genome |
talk |
|
Pulman, Jane A |
EuPathDB—Integrating eukaryotic pathogen genomics data with advanced search capabilities |
poster |
|
Ramakrishnan, Srividya |
RNA-seq expression analysis made easy in KBase |
poster |
|
Ravanmehr, Vida |
A state-of-the-art compression method for ChIP-seq data |
poster |
|
Razaviyayn, Meisam |
CONVEX—Fast and accurate de novo transcriptome recovery from long reads |
talk |
|
Rosenfeld, Jeffrey A |
Computational determination of tumor type for cancers of unknown primary using mutation data |
poster |
|
Rubanova, Yulia |
Reconstructing changes in mutational processes during tumour evolution |
talk |
|
Saha, Ashis |
Transcriptome-wide networks reveal candidate splicing regulatory relationships |
poster |
|
Sahinalp, Cenk |
SCENA—Secure compressed gENomic data analysis in a cloud environment |
poster |
|
Sajnani, Manisha R |
In silico analysis of viral diversity obtained through viral metagenomics of chicken respiratory tract |
poster |
|
Sajnani, Manisha R |
Optimizing de novo assembly for Meloidogyne indica transcriptome—A root-knot nematode |
poster |
|
Sarkar, Hirak |
Joint probabilistic model for multiple steps of gene regulation |
poster |
|
Sayed, Khaled |
Explaining cancer microenvironments via automated literature exploration |
poster |
|
Schneider, Valerie |
The evolving human reference genome assembly drives changes in data management and representation |
talk |
|
Sedlazeck, Fritz J. |
Accurate and fast detection of complex and nested structural variations using long read technologies |
talk |
|
Severin, Jessica |
Interactive visualization and analysis of large-scale sequencing datasets with the ZENBU genome browser system |
poster |
|
Sharma, Surbhi |
C-terminome—An application to investigate C-terminal minimotifs in human proteins |
poster |
|
Shcherbina, Anna |
Deep learning regulatory sequence drivers of chromatin accessibility dynamics during cellular reprogramming |
poster |
|
Shrikumar, Avanti |
Not just a black box—Interpretable deep learning for genomics |
talk |
|
Simi, Manuele |
NextflowWorkbench—Composable languages for reproducible and reusable workflows |
poster |
|
Stewart, Paul A |
Multi-Omic Network Analysis (MONA), a new tool for integrative analysis |
poster |
|
Stricker, Georg |
GenoGAM—Genome-wide generalized additive models for ChIP-seq analysis |
poster |
|
Sun, Chen |
VarMatch—Robust matching of small variant datasets using flexible scoring schemes |
talk |
|
Tan, Jie |
Compendium-wide analysis of public data with eADAGE reveals novel regulatory mechanisms |
poster |
|
Tang, Yin |
Novel roles for RNA revealed from in vivo RNA structuromes |
poster |
|
Taschuk, Morgan |
Making research software more robust |
poster |
|
Tello-Ruiz, Marcela K |
Plant Reactome—A resource for comparative plant pathway analysis |
poster |
|
Thistlethwaite, William A |
Infrastructure and development of the exRNA virtual biorepository |
poster |
|
Timbers, Tiffany A |
Combining phenome and genome to uncover the genetic basis for naturally occurring differences in development and behavior |
talk |
|
Torracinta, Remi C |
Training a somatic mutations caller with deep learning and semi-simulated data |
poster |
|
Ueda, Hiroki |
Volt—Cloud base pure java NGS Mapping software and analysis pipeline |
poster |
|
Verzotto, Davide |
Super-scaffolding of large eukaryotic genomes with single molecule maps |
poster |
|
Wainberg, Michael |
kmer2vec—Unsupervised embedding of regulatory DNA sequences |
poster |
|
Wang, Liya |
SciApps—A distributed CyVerse system for cloud computing |
poster |
|
Wilks, Christopher |
Snaptron—Enabling flexible querying and exploratory analysis of human RNA splicing |
poster |
|
Williams, Jason |
Required parameters—What does it take to bring bioinformatics into the classroom at the national level? |
poster |
|
Yan, Tingfen |
Characterization of regulatory roles of CtBP in breast cancer using integrated genomic and proteomic analysis |
poster |
|
Yazdani, Azam M |
Identification of robust metabolomics causal networks in observational study using data integration |
poster |
|
Yi, Song |
Functionalizing human disease variants through systems modeling and network analysis |
talk |
|
Yin, Wen-Chi |
Tumor-suppressive and -promoting functions of Sufu in the SHH subgroup of medulloblastoma |
poster |
|
Zhou, Naihui |
The critical assessment of protein function annotation—Improving on the “state-of-the-art” |
poster |
|
Zhou, Weizhuang |
Using a top-down approach to understand the human transcriptome |
poster |
|
Ziegler, John S |
MSKCC Paperless Lab Initiative (MSK-PLI)—Software for analysis of fragment and qualitative PCR assays |
poster |