Results.

Neurofibromatosis PT 2

Fall 2019

Imaging (MRI), Preclinical Drug Modeling, Genomics: Gene Expression and Mutation.

Selected Authors

Inferring regulators and pathways involved in NF1 and NF2 tumors originating from Schwann cells using gene expression data.

Read on Github

Authors

Stuart Tugendreich, Andreas Kraemer, Dan Shiffman, Jean-Noel Billaud, Jeff Green, Martin Jones

Integration of multidiscipline analysis from DNA sequencing, RNA sequencing, as well as the previous knowledge about the gene interactions, to identify new target genes for further drug discoveries.

Read on Github

Authors

Alex Cui, Saikrithika Gandhi, Xiaowei Zhu, Chang In Moon, Xiangying Sun, and Xiucheng Quek, Lu Yang

Inferring regulators and pathways involved in NF1 and NF2 tumors originating from Schwann cells using gene expression data.

Read on Github

Authors

Stuart Tugendreich, Andreas Kraemer, Dan Shiffman, Jean-Noel Billaud, Jeff Green, Martin Jones

Automated segmentation of whole body MRI using deep learning segmentation algorithms.

Read on Github

Authors

Amanda Paulson, Katarina Slama, Michael Eickenberg, Joseph Carlson

Comprehensive Research Suite for integrated Phenotyping, Genotyping and 3D Modeling for NF patients.

Read on Github

Authors

Mika Tabata, Warren Ho Chan, Rushil Srivastava, Michael Yan, Nam Nguyen, Neekon Saadat

Undiagnosed-1

Summer 2019

Long Read WGS, Medical Records, Metabolomics, Short Read WGS, Targeted Panel, Exome, Proteomics.

Selected Authors

Authors

MedGenome Team

Combining Genotype and Medical Record Information.

Read on Github

DNAnexus writeup

Authors

Arkarchai Fungtammasan, Saurabh Paliwal, Chiao-Feng Lin, Saikrithika Gandhi, Lee Yi Jie Joel, Gunjan Baid, Jason Chin

Identifying putative causal variants in the noncoding genome

Read on Github

Authors

Michael Apostolides, Orion Buske, Andrew Jung, Mariel Marshall, Matthew Moss, Shraddha Pai, Magda Price

SNPnotes: Software Pipeline for Functional Annotation of Whole Genome Single Nucleotide Variations

Read on Github

Authors

Shraddha Pai, Michael J. Apostolides, Andrew Jung, Matthew A. Moss

Evaluation of potential brain stem area related dysfunction, collagen disorder and lysosomal storage disease.

Read on Github

Authors

Vaishali Chaudhuri, Lakshmi Arbatti, Monica Javidnia, Anil Kemisetti, Xiangyi Xu, Xiaoyun Cheng.

Finding SNPs in WGS VCF's within Gene Coding Regions and 500 bp away from Gene Coding

Read on Github

Authors

Rilson Nascimento, Usman Qazi, PhD, Lei Pan, MS, Jordan Wilheim, Candace Liu, Andrew Sharo

Ehlers-Danlos Type III and Tenascin-X deficiency related Gastric Dysfunction

Read on Github

Authors

Biter Bilen, Chase Violet, Christian Clough, Dima (Dmytro) Lituiev, Holly Deremo, Jared Bennett, Julide Bilen, Kubilay Demir, Maki Ogawa, Mike D'Amour, Rena Yang, Sarah Daniels. Sree Vaddi, Steven Ganz

Analysis of Notable Gene Variants and Candidate Pathways

Read on Github

Authors

AJ Schick, Alex Li, Catherine Tcheandjieu, Deepika Gunasekaran, Matt Aguirre, Randi Paynter, Sal Palmisano

Papillary Renal-Cell Carcinoma Type 1 (p1RCC)

Summer 2018

Original Case

Data

BGI-SEQ 500 >90x Whole Genome Sequencing. Tumor and Normal. Medical Records.

New Data Available - October 2019:

WES Blood Normal 150X
WES Kidney Tumor 300X
RNA-seq Kidney Tumor - 300M reads
RNA-seq Kidney Normal – 150M reads

Selected Authors

Linking Binary Gene Relationships to Drivers of Renal Cell Carcinoma Reveals Convergent Function in Alternate tumor progression paths.

Read on Nature

Authors

William L. Poehlman, James J. Hsieh & F. Alex Feltus

Varient filtering and target pruning, including training a Deep Chem graph convolutional model searching for optimal hyperparameters.

Read on Github

Authors

Prasun Mishra, Biter Bilen, Jeff Lam, Mike D'Amour, Xiaowei Zhu, Monika Maleszewska, Andrew Mills, Tahera Zabuawala, Lei Tian.

Identification of neo-antigens by machine learning major histocompatibility, uncovering peptides with high MHC binding affinity.

Read on Github

Authors

Andrew Wallace, Christian Clough, Felix Frayman, Matt Callahan, Nandita Damaraju, Pak Yu, Sebastian Nguyen, William Wright.

Discovering candidate biomarkers for p1RCC via collaborative filtering using probability matrix factorization.

Read on Github

Authors

Sofia Medina, Amrit Virdee, Nikhil Balajil, Yuri Bendana, and Maricris Macabeo.

Training and applying genomic deep learning models using Deep Variant.

Read on Github

DNA Nexus Blog Post

Authors

Jason Chin, Andrew Carroll, Samantha Zarate, Pi-Chuan Chang.

RCC Subtype Salient Feature Discovery: Modeling time series stage and subtype using neural networks / Constructing and Identifying co-expression networks and shared gene interaction communities.

Read on Github

Authors

A. Feltus, S. Niu, K. Matusow, W. Poehlman, B. Shealy, C. Shearer, C. Targonski, E. Weill.

Neurofibromatosis Type 2

Summer 2017

Original Case

Data

Whole Genome Sequencing 60-90x with Base Pairs. Blood and Tumor.

Selected Authors

Applying an unsupervised transfer learning approach to identify novel targets.

Read on Github

Authors

Jo Varshney, DVM, PhD, Nandita Damaraju, Ben Hsu, Teng Gao.

Inferring NF2 Treatment Based on Similarity to Characterized Cancers.

Read on Github | See Poster

Authors

Simas Gliskis, Natalia Antropova, Mohit Nalavadi, Avantika Lal, Joy Rimchala, Oren Schaedel.

Exploration of Novel/Off-Label Therapeutics for NF2.

Read on Github

Results.

Neurofibromatosis PT 2​

​

Imaging (MRI), Preclinical Drug Modeling, Genomics: Gene Expression and Mutation.

Selected Authors

​

​

​

​

​

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Automated segmentation of whole body MRI using deep learning segmentation algorithms.

​

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Comprehensive Research Suite for integrated Phenotyping, Genotyping and 3D Modeling for NF patients.

​

​

Undiagnosed-1​

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Long Read WGS, Medical Records, Metabolomics, Short Read WGS, Targeted Panel, Exome, Proteomics.

Selected Authors

Authors

MedGenome Team

Authors

Arkarchai Fungtammasan, Saurabh Paliwal, Chiao-Feng Lin, Saikrithika Gandhi, Lee Yi Jie Joel, Gunjan Baid, Jason Chin

Authors

Vaishali Chaudhuri, Lakshmi Arbatti, Monica Javidnia, Anil Kemisetti, Xiangyi Xu, Xiaoyun Cheng.

Papillary Renal-Cell Carcinoma Type 1 (p1RCC)​

​

Data

BGI-SEQ 500 >90x Whole Genome Sequencing. Tumor and Normal. Medical Records.

​

New Data Available - October 2019:

Selected Authors

Authors

William L. Poehlman, James J. Hsieh & F. Alex Feltus

Authors

Prasun Mishra, Biter Bilen, Jeff Lam, Mike D'Amour, Xiaowei Zhu, Monika Maleszewska, Andrew Mills, Tahera Zabuawala, Lei Tian.

Authors

Andrew Wallace, Christian Clough, Felix Frayman, Matt Callahan, Nandita Damaraju, Pak Yu, Sebastian Nguyen, William Wright.

Read on Github

Authors

Sofia Medina, Amrit Virdee, Nikhil Balajil, Yuri Bendana, and Maricris Macabeo.

Read on Github

DNA Nexus Blog Post

​

Authors

Jason Chin, Andrew Carroll, Samantha Zarate, Pi-Chuan Chang.

Authors

A. Feltus, S. Niu, K. Matusow, W. Poehlman, B. Shealy, C. Shearer, C. Targonski, E. Weill.

Neurofibromatosis Type 2

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​

Data

Whole Genome Sequencing 60-90x with Base Pairs. Blood and Tumor.

Selected Authors

Authors

Jo Varshney, DVM, PhD, Nandita Damaraju, Ben Hsu, Teng Gao.

Authors

Simas Gliskis, Natalia Antropova, Mohit Nalavadi, Avantika Lal, Joy Rimchala, Oren Schaedel.

Authors

Neurofibromatosis PT 2

Undiagnosed-1

Papillary Renal-Cell Carcinoma Type 1 (p1RCC)