Publications

13 Results (Filters Applied)

Knowles Lab x

Nature Biotechnology. 2023 July 3.

Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning.

Hans-Hermann Wessels, Andrew Stirn, Alejandro Méndez-Mancilla, Eric J. Kim, Sydney K. Hart, David A. Knowles & Neville E. Sanjana

Bioinformatics. 2023 Feb. 16.

LDmat: Efficiently Queryable Compression of Linkage Disequilibrium Matrices.

Rockwell J Weiner, Chirag Lakhani, David A Knowles, Gamze Gürsoy

PLOS Genetics. 2023 Jan. 19.

Using epigenomics to understand cellular responses to environmental influences in diseases.

Julia J. Wattacheril, Srilakshmi Raj, David A. Knowles, John M. Greally

Nature Neuroscience. 2022 Dec. 8.

Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes.

Jack Humphrey, Sanan Venkatesh, Rahat Hasan, Jake T. Herb, Katia de Paiva Lopes, Fahri Küçükali, Marta Byrska-Bishop, Uday S. Evani, Giuseppe Narzisi, Delphine Fagegaltier, NYGC ALS Consortium, Kristel Sleegers, Hemali Phatnani, David A. Knowles, Pietro Fratta & Towfique Raj

PLOS Computational Biology. 2022 Oct. 20.

Deep mendelian randomization: Investigating the causal knowledge of genomic deep learning models.

Stephen Malina, Daniel Cizin, David A. Knowles

American Journal of Human Genetics. 2021 Dec. 2.

Welch-weighted Egger regression reduces false positives due to correlated pleiotropy in Mendelian randomization.

Brielin C Brown, David A Knowles

American Journal of Human Genetics. 2021 Sept. 27.

An integrated approach to identify environmental modulators of genetic risk factors for complex traits.

Balliu B, Carcamo-Orive I, Gloudemans MJ, Nachun DC, Durrant MG, Gazal S, Park CY, Knowles DA, Wabitsch M, Quertermous T, Knowles JW, Montgomery SB.

Cell. 2020 October 1.

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.

Kevin Hadi, Xiaotong Yao, Julie M. Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Huasong Tian,Sarah Kudman, Joel Rosiene, Madison Darmofal, Joseph DeRose, Rick Mortensen, Emily M. Adney, Alon Shaiber, Zoran Gajic, Michael Sigouros, Kenneth Eng, Jeremiah A. Wala, Kazimierz O. Wrzeszczynski Kanika Arora, Minita Shah, Anne-Katrin Emde, Vanessa Felice, Mayu O. Frank, Robert B. Darnell, Mahmoud Ghandi, Franklin Huang, Sally Dewhurst, John Maciejowski,Titia de Lange, Jeremy Setton, Nadeem Riaz, Jorge S. Reis-Filho, Simon Powell, David A. Knowles, Ed Reznik, Bud Mishra, Rameen Beroukhim, Michael C. Zody, Nicolas Robine, Kenji M. Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid, Xiaohong Li, David Wilkes, Andrea Sboner,Juan Miguel Mosquera, Olivier Elemento, and Marcin Imielinski

Genome Biology. 2019 Nov. 4.

Genetic regulation of gene expression and splicing during a 10-year period of human aging.

Balliu B, Durrant M, Goede O, Abell N, Li X, Liu B, Gloudemans MJ, Cook NL, Smith KS, Knowles DA, Pala M, Cucca F, Schlessinger D, Jaiswal S, Sabatti C, Lind L, Ingelsson E, Montgomery SB.

Nat Genet. 2019 2019 Mar 29.

Opportunities and challenges for transcriptome-wide association studies.

Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren JLM, Im HK, Pasaniuc B, Rivas MA, Kundaje A.

Nature Genetics. 2017 December 11.

Annotation-free quantification of RNA splicing using LeafCutter.

Li YI, Knowles DA, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK.

Nature Methods. 2017 May 22.

Allele-specific expression reveals interactions between genetic variation and environment.

Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A.

Elife. 2018 May 8.

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes.

Knowles DA, Burrows CK, Blischak JD, Patterson KM, Serie DJ, Norton N, Ober C, Pritchard JK, Gilad Y.

PRE-PRINT PUBLICATIONS

bioRxiv. 2023 Sept. 12.

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox.

Megan D Schertzer, Andrew Stirn, Keren Isaev, Laura Pereira, Anjali Das, Claire Harbison, Stella H Park, Hans-Hermann Wessels, Neville E Sanjana, David A Knowles

bioRxiv. 2022 July 20.

Multiset correlation and factor analysis enables exploration of multi-omic data.

Brielin C Brown, Collin L. Wang, Silva Kasela, Francois Aguet, Daniel C. Nachun, Kent D. Taylor, Russel P. Tracy, Peter Durda, Yongmei Lui, W Craig Johnson, David Van Den Berg, Namrata Gupta, Stacy Gabriel, Joshua D. Smith, Robert Gerzten, Clary Clish, Quenna Wong, George Papanicolau, Thomas W. Blackwell, Jerome I. Rotter, Stephen S. Rich, Kristen G Ardlie, David A. Knowles, Tuuli Lappalainen

medRxiv. 2021 Sept. 2.

Integrative genetic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes.

Jack Humphrey, , Rahat Hasan, Jake T Herb, , Fahri Kucukali, Marta Byrska-Bishop, Uday S Evani, Giuseppe Narzisi, Delphine Fagegaltier, NYGC ALS Consortium, Kristel Sleegers, Hemali Phatnani, David A Knowles, Pietro Fratta, Towfique Raj

bioRxiv. 2020 June 20.

Phenome-scale causal network discovery with bidirectional mediated Mendelian randomization.