Piercing the dark matter: bioinformatics of long-range sequencing and map**

FJ Sedlazeck, H Lee, CA Darby, MC Schatz - Nature Reviews Genetics, 2018 - nature.com
Several new genomics technologies have become available that offer long-read sequencing
or long-range map** with higher throughput and higher resolution analysis than ever …

Towards precision medicine

EA Ashley - Nature Reviews Genetics, 2016 - nature.com
There is great potential for genome sequencing to enhance patient care through improved
diagnostic sensitivity and more precise therapeutic targeting. To maximize this potential …

Jasmine and Iris: population-scale structural variant comparison and analysis

M Kirsche, G Prabhu, R Sherman, B Ni, A Battle… - Nature …, 2023 - nature.com
The availability of long reads is revolutionizing studies of structural variants (SVs). However,
because SVs vary across individuals and are discovered through imprecise read …

Strelka2: fast and accurate calling of germline and somatic variants

S Kim, K Scheffler, AL Halpern, MA Bekritsky, E Noh… - Nature …, 2018 - nature.com
Abstract We describe Strelka2 (https://github. com/Illumina/strelka), an open-source small-
variant-calling method for research and clinical germline and somatic sequencing …

Scaling accurate genetic variant discovery to tens of thousands of samples

R Poplin, V Ruano-Rubio, MA DePristo, TJ Fennell… - BioRxiv, 2017 - biorxiv.org
Comprehensive disease gene discovery in both common and rare diseases will require the
efficient and accurate detection of all classes of genetic variation across tens to hundreds of …

Organoid profiling identifies common responders to chemotherapy in pancreatic cancer

H Tiriac, P Belleau, DD Engle, D Plenker, A Deschênes… - Cancer discovery, 2018 - AACR
Pancreatic cancer is the most lethal common solid malignancy. Systemic therapies are often
ineffective, and predictive biomarkers to guide treatment are urgently needed. We generated …

[HTML][HTML] Engineering quantitative trait variation for crop improvement by genome editing

D Rodríguez-Leal, ZH Lemmon, J Man, ME Bartlett… - Cell, 2017 - cell.com
Major advances in crop yields are needed in the coming decades. However, plant breeding
is currently limited by incremental improvements in quantitative traits that often rely on …

[HTML][HTML] The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer

WA Freed-Pastor, LJ Lambert, ZA Ely, NB Pattada… - Cancer cell, 2021 - cell.com
The CD155/TIGIT axis can be co-opted during immune evasion in chronic viral infections
and cancer. Pancreatic adenocarcinoma (PDAC) is a highly lethal malignancy, and immune …

Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer

PMK Westcott, NJ Sacks, JM Schenkel, ZA Ely, O Smith… - Nature cancer, 2021 - nature.com
Immune evasion is a hallmark of cancer and therapies that restore immune surveillance
have proven highly effective in cancers with high tumor mutation burden (TMB)(for example …

The contribution of de novo coding mutations to autism spectrum disorder

I Iossifov, BJ O'roak, SJ Sanders, M Ronemus… - Nature, 2014 - nature.com
Whole exome sequencing has proven to be a powerful tool for understanding the genetic
architecture of human disease. Here we apply it to more than 2,500 simplex families, each …