Ilya Chorny

mAbs are increasingly being used for treatment of chronic diseases wherein the subcutaneous delivery route is preferred to enable self-administration and at-home use. To deliver high doses (several hundred milligrams) through a small volume (∼1 mL) into the subcutaneous space, mAb solutions need to have low viscosity. Concomitantly, acceptable chemical stability is required for adequate shelf life, and normal in vivo clearance is needed for less frequent dosing. We propose in silico tools that… Show more

mAbs are increasingly being used for treatment of chronic diseases wherein the subcutaneous delivery route is preferred to enable self-administration and at-home use. To deliver high doses (several hundred milligrams) through a small volume (∼1 mL) into the subcutaneous space, mAb solutions need to have low viscosity. Concomitantly, acceptable chemical stability is required for adequate shelf life, and normal in vivo clearance is needed for less frequent dosing. We propose in silico tools that provide rapid assessment of atypical behavior of mAbs (high viscosity, chemical degradation, and fast plasma clearance), which are simply predicted from sequence and/or structure-derived parameters. Such analysis will greatly improve the probability of success to move mAb-based therapeutics efficiently into clinical development and ultimately benefit patients. Show less

An ultrafast DNA sequence aligner (Isaac Genome Alignment
Software) that takes advantage of high memory hardware (>48GB)
and variant caller (Isaac Variant Caller) have been developed. We
demonstrate that our combined pipeline (Isaac) is 4-5 times faster
than BWA+GATK on equivalent hardware, with comparable accu-
racy as measured by trio conflict rates and sensitivity. We further
show that Isaac is effective in the detection of disease-causing
variants and can… Show more

An ultrafast DNA sequence aligner (Isaac Genome Alignment
Software) that takes advantage of high memory hardware (>48GB)
and variant caller (Isaac Variant Caller) have been developed. We
demonstrate that our combined pipeline (Isaac) is 4-5 times faster
than BWA+GATK on equivalent hardware, with comparable accu-
racy as measured by trio conflict rates and sensitivity. We further
show that Isaac is effective in the detection of disease-causing
variants and can easily/economically be run on commodity hard-
ware. Show less

Peptoid molecules are biomimetic oligomers that can fold into unique three-dimensional structures. As part of an effort to advance computational design of folded oligomers, we present the first example of blind structure predictions for three peptide sequences, using a combination of Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement.