Results.
Neurofibromatosis PT 2
Fall 2019
Original Case
Case Data
Imaging (MRI), Preclinical Drug Modeling, Genomics: Gene Expression and Mutation.
Selected Authors
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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
Original Case
Case Data
Long Read WGS, Medical Records, Metabolomics, Short Read WGS, Targeted Panel, Exome, Proteomics.
Selected Authors
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Authors
MedGenome Team
Combining Genotype and Medical Record Information.
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
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.
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
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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.
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.
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
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Applying an unsupervised transfer learning approach to identify novel targets.
Authors
Jo Varshney, DVM, PhD, Nandita Damaraju, Ben Hsu, Teng Gao.
Inferring NF2 Treatment Based on Similarity to Characterized Cancers.
Authors
Simas Gliskis, Natalia Antropova, Mohit Nalavadi, Avantika Lal, Joy Rimchala, Oren Schaedel.
Exploration of Novel/Off-Label Therapeutics for NF2.