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joseph k aicher joseph k aicher about publications joseph k aicher about i am an md phd student at university of pennsylvania i am currently completing my phd in genomics and computational biology co advised by drs yoseph barash and elizabeth bhoj scientifically i am interested in machine learning statistical modeling genomics and biomedical informatics especially as they relate to human health my current research focuses on developing and applying new computational tools and frameworks to improve diagnostic rates for people with suspected mendelian disorders i am developing new approaches to detect defects in rna splicing from patient rna seq or to predict such changes directly from patient exome or genome sequencing during my phd i interned at amazon and was awarded a ruth l kirschstein national research service award f30 by the nih for my research and training prior to starting my md phd i studied at university of alabama for four years receiving an m a in mathematics and a b s in mathematics and physics my master s thesis investigated the application of probabilistic graphical models to metabolomics data i also spent two summers at university of north carolina chapel hill creating computational physics simulations of the yeast mitotic spindle email cv google scholar linkedin publications vaquero garcia j aicher j jewell p gazzara mr radens cm jha a green cj norton ss lahens nf grant gr barash y rna splicing analysis using heterogeneous and large rna seq datasets preprint biorxiv 2021 under review at nature communications paper website lubin e bryant l aicher j li d bhoj e analysis of histone variant constraint and tissue expression suggests five potential novel human disease genes h2afy2 h2afz h2afy h2afv h1f0 human genetics 2022 paper aicher jk jewell p vaquero garcia j barash y bhoj ej mapping rna splicing variations in clinically accessible and nonaccessible tissues to facilitate mendelian disease diagnosis using rna seq genetics in medicine 2020 paper website zenodo jha a aicher jk gazzara mr singh d barash y enhanced integrated gradients improving interpretability of deep learning models using splicing codes as a case study genome biology 2020 paper python package zenodo oza vh aicher jk reed lk random forest analysis of untargeted metabolomics data suggests increased use of omega fatty acid oxidation pathway in drosophila melanogaster larvae fed a medium chain fatty acid rich high fat diet metabolites 2019 paper lawrimore j aicher jk hahn p fulp a kompa b vicci l falvo m taylor rm bloom k chromoshake a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin molecular biology of the cell 2016 paper code videos baker pr friederich mw swanson ma shaikh t bhattacharya k scharer gh aicher j creadon swindell g geiger e maclean kn lee w t deshpande c freckmann m l shih l y wasserstein m rasmussen mb lund am procopis p cameron jm robinson bh brown gk brown rm compton ag dieckmann cl collard r coughlin cr spector e wempe mf van hove jlk variant non ketotic hyperglycinemia is caused by mutations in lias bola3 and the novel gene glrx5 brain 2014 paper an inspirational website