Personal information

Websites & social links

https://daklab.github.io/

Countries

United States

Activities

Collapse all

Employment (2)

New York Genome Center: New York, NY, US

2019 to present | Core Faculty Member
Employment
Source: Self-asserted source
David A Knowles

Columbia University: New York, NY, US

2019 to present | Assistant Professor (Computer Science)
Employment
Source: Self-asserted source
David A Knowles

Works (50 of 72)

Items per page:
Page 1 of 2

Integration of Deep Learning Annotations with Functional Genomics Improves Identification of Causal Alzheimer's Disease Variants

2025-03-10 | Preprint
DOI: 10.1101/2025.03.07.25323578
Contributors: Chirag M Lakhani; Jui-Shan T Lin; Anjali Das; Tatsuhiko Naito; Towfique Raj; David A Knowles
Source: check_circle
Crossref

Multi-sample, multi-platform isoform quantification using empirical Bayes

2025-02-08 | Preprint
DOI: 10.1101/2025.02.08.637184
Contributors: Arghamitra Talukder; Shree Thavarekere; Madison Mehlferber; Gloria M Sheynkman; David A. Knowles
Source: check_circle
Crossref

Leveraging functional annotations to map rare variants associated with Alzheimer’s disease with gruyere

2024-12-08 | Preprint
DOI: 10.1101/2024.12.06.24318577
Contributors: Anjali Das; Chirag Lakhani; Chloé Terwagne; Jui-Shan T. Lin; Tatsuhiko Naito; Towfique Raj; David A. Knowles
Source: check_circle
Crossref

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

Nature Biotechnology
2024-04 | Journal article
DOI: 10.1038/s41587-023-01830-8
Contributors: Hans-Hermann Wessels; Andrew Stirn; Alejandro Méndez-Mancilla; Eric J. Kim; Sydney K. Hart; David A. Knowles; Neville E. Sanjana
Source: check_circle
Crossref

Investigating RNA splicing as a source of cellular diversity using a binomial mixture model

2023-10-20 | Preprint
DOI: 10.1101/2023.10.17.562774
Contributors: Keren Isaev; David A Knowles
Source: check_circle
Crossref

Large-scale causal discovery using interventional data sheds light on the regulatory network architecture of blood traits

2023-10-17 | Preprint
DOI: 10.1101/2023.10.13.562293
Contributors: Brielin C. Brown; John A. Morris; Tuuli Lappalainen; David A. Knowles
Source: check_circle
Crossref

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

2023-09-13 | Preprint
DOI: 10.1101/2023.09.12.557474
Contributors: 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
Source: check_circle
Crossref

Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths.

Cell stem cell
2023-08 | Journal article
DOI: 10.1016/j.stem.2023.07.012
PMID: 37582363
Contributors: Cortés-López M; Chamely P; Hawkins AG; Stanley RF; Swett AD; Ganesan S; Mouhieddine TH; Dai X; Kluegel L; Chen C et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

Cell genomics
2023-07 | Journal article
DOI: 10.1016/j.xgen.2023.100359
PMID: 37601969
PMC: PMC10435377
Contributors: Brown BC; Wang C; Kasela S; Aguet F; Nachun DC; Taylor KD; Tracy RP; Durda P; Liu Y; Johnson WC et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Computational models of dopamine release measured by fast scan cyclic voltammetry in vivo

PNAS Nexus
2023-03-03 | Journal article
DOI: 10.1093/pnasnexus/pgad044
Contributors: N Shashaank; Mahalakshmi Somayaji; Mattia Miotto; Eugene V Mosharov; Emily A Makowicz; David A Knowles; Giancarlo Ruocco; David L Sulzer; Rui Reis
Source: check_circle
Crossref

LDmat: efficiently queryable compression of linkage disequilibrium matrices

Bioinformatics
2023-02-03 | Journal article
DOI: 10.1093/bioinformatics/btad092
Contributors: Rockwell J Weiner; Chirag Lakhani; David A Knowles; Gamze Gürsoy; Christina Kendziorski
Source: check_circle
Crossref

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

PLoS genetics
2023-01 | Journal article
DOI: 10.1371/journal.pgen.1010567
PMID: 36656803
PMC: PMC9851565
Contributors: Wattacheril JJ; Raj S; Knowles DA; Greally JM
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

Nature neuroscience
2022-12 | Journal article
DOI: 10.1038/s41593-022-01205-3
PMID: 36482247
Contributors: Humphrey J; Venkatesh S; Hasan R; Herb JT; de Paiva Lopes K; Küçükali F; Byrska-Bishop M; Evani US; Narzisi G; Fagegaltier D et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Smoother: A Unified and Modular Framework for Incorporating Structural Dependency in Spatial Omics Data

2022-10 | Preprint
DOI: 10.1101/2022.10.25.513785
PPR: PPR563054
Contributors: Su J; Reynier J; Fu X; Zhong G; Jiang J; Escalante RS; Wang Y; Aparicio L; Izar B; Knowles DA et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

PLOS Computational Biology
2022-10-20 | Journal article
DOI: 10.1371/journal.pcbi.1009880
Contributors: Stephen Malina; Luca Pinello; Daniel Cizin; David A. Knowles
Source: check_circle
Crossref

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

2022-07 | Preprint
DOI: 10.1101/2022.07.18.500246
PPR: PPR521350
Contributors: Brown BC; Wang C; Kasela S; Aguet F; Nachun DC; Taylor KD; Tracy RP; Durda P; Liu Y; Johnson WC et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Single-cell multi-omics defines the cell-type specific impact of splicing aberrations in human hematopoietic clonal outgrowths

2022-06 | Preprint
DOI: 10.1101/2022.06.08.495292
PPR: PPR504124
Contributors: Gaiti F; Chamely P; Hawkins AG; Cortés-López M; Swett AD; Ganesan S; Mouhieddine TH; Dai X; Kluegel L; Chen C et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Novel Computational Models of Evoked Dopamine Release In Vivo Measured by Fast Scan Cyclic Voltammetry Quantify the Regulation of Presynaptic Kinetics by Synucleins

2022-05-05 | Preprint
DOI: 10.1101/2022.05.04.490695
Contributors: N Shashaank; Mahalakshmi Somayaji; Mattia Miotto; Eugene V. Mosharov; David A. Knowles; Giancarlo Ruocco; David L. Sulzer
Source: check_circle
Crossref

Deep Mendelian Randomization: Investigating the Causal Knowledge of Genomic Deep Learning Models

2022-02 | Preprint
DOI: 10.1101/2022.02.01.478608
PPR: PPR449630
Contributors: Malina S; Cizin D; Knowles DA
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

American journal of human genetics
2021-12 | Journal article
DOI: 10.1016/j.ajhg.2021.10.006
PMID: 34861175
PMC: PMC8715134
Contributors: Brown BC; Knowles DA
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

The American Journal of Human Genetics
2021-10 | Journal article
DOI: 10.1016/j.ajhg.2021.08.014
Contributors: Brunilda Balliu; Ivan Carcamo-Orive; Michael J. Gloudemans; Daniel C. Nachun; Matthew G. Durrant; Steven Gazal; Chong Y. Park; David A. Knowles; Martin Wabitsch; Thomas Quertermous et al.
Source: check_circle
Crossref

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

2021-09 | Preprint
DOI: 10.1101/2021.08.31.21262682
PPR: PPR390032
Contributors: Humphrey J; Venkatesh S; Hasan R; Herb JT; de Paiva Lopes K; Küçükali F; Byrska-Bishop M; Evani US; Narzisi G; Fagegaltier D et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

2021-04 | Preprint
DOI: 10.1101/2021.04.09.439229
PPR: PPR309724
Contributors: Brown BC; Knowles DA
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

2021-02-25 | Preprint
DOI: 10.1101/2021.02.23.432608
Contributors: Brunilda Balliu; Ivan Carcamo -Orive; Michael J. Gloudemans; Daniel C. Nachun; Matthew G. Durrant; Steven Gazal; Chong Y. Park; David A. Knowles; Martin Wabitsch; Thomas Quertermous et al.
Source: check_circle
Crossref

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

Cell
2020-10 | Journal article
DOI: 10.1016/j.cell.2020.08.006
PMID: 33007263
PMC: PMC7912537
Contributors: Hadi K; Yao X; Behr JM; Deshpande A; Xanthopoulakis C; Tian H; Kudman S; Rosiene J; Darmofal M; DeRose J et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Phenome-scale causal network discovery with bidirectional mediated Mendelian randomization

2020-06-20 | Preprint
DOI: 10.1101/2020.06.18.160176
Contributors: Brielin C. Brown; David A. Knowles
Source: check_circle
Crossref

A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk.

Genome biology
2020-05 | Journal article
DOI: 10.1186/s13059-020-02019-x
PMID: 32381040
PMC: PMC7206807
Contributors: Gentles AJ; Hui AB; Feng W; Azizi A; Nair RV; Bouchard G; Knowles DA; Yu A; Jeong Y; Bejnood A et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Molecular Choreography of Acute Exercise.

Cell
2020-05 | Journal article
DOI: 10.1016/j.cell.2020.04.043
PMID: 32470399
PMC: PMC7299174
Contributors: Contrepois K; Wu S; Moneghetti KJ; Hornburg D; Ahadi S; Tsai MS; Metwally AA; Wei E; Lee-McMullen B; Quijada JV et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Molecular Choreography of Acute Exercise

2020-01 | Preprint
DOI: 10.1101/2020.01.13.905349
PPR: PPR108771
Contributors: Contrepois K; Wu S; Moneghetti KJ; Hornburg D; Ahadi S; Tsai M; Metwally AA; Wei E; Lee-McMullen B; Quijada JV et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

Genome biology
2019-11 | Journal article
DOI: 10.1186/s13059-019-1840-y
PMID: 31684996
PMC: PMC6827221
Contributors: Balliu B; Durrant M; Goede O; Abell N; Li X; Liu B; Gloudemans MJ; Cook NL; Smith KS; Knowles DA et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

2019-11 | Preprint
DOI: 10.1101/836296
PPR: PPR101594
Contributors: Hadi K; Yao X; Behr JM; Deshpande A; Xanthopoulakis C; Rosiene J; Darmofal M; Tian H; DeRose J; Mortensen R et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Landscape of stimulation-responsive chromatin across diverse human immune cells.

Nature genetics
2019-09 | Journal article
DOI: 10.1038/s41588-019-0505-9
PMID: 31570894
PMC: PMC6858557
Contributors: Calderon D; Nguyen MLT; Mezger A; Kathiria A; Müller F; Nguyen V; Lescano N; Wu B; Trombetta J; Ribado JV et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Clinically-relevant cell type cross-talk identified from a human lung tumor microenvironment interactome

2019-05 | Preprint
DOI: 10.1101/637306
PPR: PPR80869
Contributors: Gentles AJ; Hui AB; Feng W; Azizi A; Nair RV; Knowles DA; Yu A; Jeong Y; Bejnood A; Forgó E et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features

PLOS Computational Biology
2019-05-28 | Journal article
DOI: 10.1371/journal.pcbi.1006743
Contributors: David A. Knowles; Florian Markowetz; Gina Bouchard; Sylvia Plevritis
Source: check_circle
Crossref

Opportunities and challenges for transcriptome-wide association studies

Nature Genetics
2019-04 | Journal article
DOI: 10.1038/s41588-019-0385-z
Contributors: Michael Wainberg; Nasa Sinnott-Armstrong; Nicholas Mancuso; Alvaro N. Barbeira; David A. Knowles; David Golan; Raili Ermel; Arno Ruusalepp; Thomas Quertermous; Ke Hao et al.
Source: check_circle
Crossref

Predicting Splicing from Primary Sequence with Deep Learning.

Cell
2019-01 | Journal article
DOI: 10.1016/j.cell.2018.12.015
PMID: 30661751
Contributors: Jaganathan K; Kyriazopoulou Panagiotopoulou S; McRae JF; Darbandi SF; Knowles D; Li YI; Kosmicki JA; Arbelaez J; Cui W; Schwartz GB et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Landscape of stimulation-responsive chromatin across diverse human immune cells

2018-09 | Preprint
DOI: 10.1101/409722
PPR: PPR54951
Contributors: Calderon D; Nguyen MLT; Mezger A; Kathiria A; Nguyen V; Lescano N; Wu B; Trombetta J; Ribado JV; Knowles DA et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

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

eLife
2018-05-08 | Journal article
DOI: 10.7554/eLife.33480
Contributors: David A Knowles; Courtney K Burrows; John D Blischak; Kristen M Patterson; Daniel J Serie; Nadine Norton; Carole Ober; Jonathan K Pritchard; Yoav Gilad
Source: check_circle
Crossref

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

PloS one
2018-04 | Journal article
DOI: 10.1371/journal.pone.0195788
PMID: 29659628
PMC: PMC5901994
Contributors: Taylor DL; Knowles DA; Scott LJ; Ramirez AH; Casale FP; Wolford BN; Guan L; Varshney A; Albanus RD; Parker SCJ et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Annotation-free quantification of RNA splicing using LeafCutter

Nature Genetics
2018-01-11 | Journal article
DOI: 10.1038/s41588-017-0004-9
Contributors: Yang I. Li; David A. Knowles; Jack Humphrey; Alvaro N. Barbeira; Scott P. Dickinson; Hae Kyung Im; Jonathan K. Pritchard
Source: check_circle
Crossref

Vulnerabilities of transcriptome-wide association studies

bioRxiv
2017 | Working paper
DOI: 10.1101/206961
Source: Self-asserted source
David A Knowles

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

2017-11-01 | Other
DOI: 10.1101/212381
Contributors: David A Knowles; Courtney K Burrows; John D Blischak; Kristen M Patterson; Carole Ober; Jonathan K Pritchard; Yoav Gilad
Source: check_circle
Crossref

Inferring Relevant Cell Types for Complex Traits by Using Single-Cell Gene Expression.

American journal of human genetics
2017-10 | Journal article
DOI: 10.1016/j.ajhg.2017.09.009
PMID: 29106824
PMC: PMC5673624
Contributors: Calderon D; Bhaskar A; Knowles DA; Golan D; Raj T; Fu AQ; Pritchard JK
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Allele-specific expression reveals interactions between genetic variation and environment

Nature Methods
2017-07-22 | Journal article
DOI: 10.1038/nmeth.4298
Contributors: David A Knowles; Joe R Davis; Hilary Edgington; Anil Raj; Marie-Julie Favé; Xiaowei Zhu; James B Potash; Myrna M Weissman; Jianxin Shi; Douglas F Levinson et al.
Source: check_circle
Crossref

Inferring relevant cell types for complex traits using single-cell gene expression

2017-05-10 | Preprint
DOI: 10.1101/136283
Contributors: Diego Calderon; Anand Bhaskar; David A. Knowles; David Golan; Towfique Raj; Audrey Q. Fu; Jonathan K. Pritchard
Source: check_circle
Crossref

Therapeutic reduction of ataxin-2 extends lifespan and reduces pathology in TDP-43 mice.

Nature
2017-04 | Journal article
DOI: 10.1038/nature22038
PMID: 28405022
PMC: PMC5642042
Contributors: Becker LA; Huang B; Bieri G; Ma R; Knowles DA; Jafar-Nejad P; Messing J; Kim HJ; Soriano A; Auburger G et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

2017-02 | Preprint
DOI: 10.1101/105429
PPR: PPR7100
Contributors: Taylor DL; Knowles DA; Scott LJ; Ramirez AH; Paolo Casale F; Wolford BN; Guan L; Varshney A; Oliveira Albanus R; Parker SC et al.
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Batch effects and the effective design of single-cell gene expression studies.

Scientific reports
2017-01 | Journal article
DOI: 10.1038/srep39921
PMID: 28045081
PMC: PMC5206706
Contributors: Tung PY; Blischak JD; Hsiao CJ; Knowles DA; Burnett JE; Pritchard JK; Gilad Y
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export.

G3 (Bethesda, Md.)
2017-01 | Journal article
DOI: 10.1534/g3.116.036137
PMID: 27799337
PMC: PMC5217120
Contributors: Tsang EK; Abell NS; Li X; Anaya V; Karczewski KJ; Knowles DA; Sierra RG; Smith KS; Montgomery SB
Source: Self-asserted source
David A Knowles via Europe PubMed Central

Batch effects and the effective design of single-cell gene expression studies

2016-07-08 | Preprint
DOI: 10.1101/062919
Contributors: Po-Yuan Tung; John D. Blischak; Chiaowen Joyce Hsiao; David A. Knowles; Jonathan E. Burnett; Jonathan K. Pritchard; Yoav Gilad
Source: check_circle
Crossref
Items per page:
Page 1 of 2

Peer review (28 reviews for 13 publications/grants)

Review activity for American journal of human genetics. (3)
Review activity for BMC bioinformatics (1)
Review activity for Genome biology. (3)
Review activity for Nature (1)
Review activity for Nature biomedical engineering. (1)
Review activity for Nature communications (7)
Review activity for Nature genetics. (4)
Review activity for Nature machine intelligence. (2)
Review activity for Nature methods. (1)
Review activity for npj genomic medicine. (1)
Review activity for PLoS computational biology. (2)
Review activity for PLOS genetics. (1)
Review activity for Science. (1)
How many people are using ORCID?