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Carl G. de Boer · SciRah

Researcher profile · Semantic Scholar

Carl G. de Boer

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Carl G. de Boer — researcher profile on SciRah

h-index: 21
Works: 54
Citations: 3,943

Most-cited papers

Defining T cell states associated with response to checkpoint immunotherapy in melanoma
M. Sade-Feldman, K. Yizhak, Stacey L. Bjorgaard, John P. Ray +31 more
2018Cell1,933 citations Open access
Semantic Scholar
The evolution, evolvability, and engineering of gene regulatory DNA
E. D. Vaishnav, Carl G. de Boer, Jennifer Molinet, M. Yassour +6 more
2022Nature251 citations Open access
Semantic Scholar
Core circadian clock genes regulate leukemia stem cells in AML
Rishi V. Puram, Monika S. Kowalczyk, Carl G. de Boer, R. Schneider +14 more
2016Cell246 citations Open access
Semantic Scholar
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities
Carl G. de Boer, T. Hughes
2011Nucleic Acids Res.206 citations Open access
Semantic Scholar
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
Carl G. de Boer, E. D. Vaishnav, R. Sadeh, E. Abeyta +2 more
2019Nature Biotechnology170 citations Open access
Semantic Scholar
Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age
Mati Mann, Arnav Mehta, Carl G. de Boer, Monika S. Kowalczyk +7 more
2017bioRxiv162 citations Open access
Semantic Scholar
Deciphering eukaryotic cis-regulatory logic with 100 million random promoters
Carl G. de Boer, E. D. Vaishnav, R. Sadeh, E. Abeyta +2 more
2017bioRxiv114 citations Open access
Semantic Scholar
Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma
M. Sade-Feldman, K. Yizhak, Stacey L. Bjorgaard, John P. Ray +31 more
2019Cell103 citations Open access
Semantic Scholar
Hold out the genome: a roadmap to solving the cis-regulatory code
Carl G. de Boer, J. Taipale
2023bioRxiv92 citations Open access
Semantic Scholar
Mapping Yeast Transcriptional Networks
T. Hughes, Carl G. de Boer
2013Genetics82 citations Open access
Semantic Scholar
Global discovery of lupus genetic risk variant allelic enhancer activity
Xiaoming Lu, Xiao-Ting Chen, C. Forney, O. Donmez +12 more
2021Nature Communications60 citations Open access
Semantic Scholar
Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
John P. Ray, Carl G. de Boer, Charles P. Fulco, C. Lareau +12 more
2020Nature Communications55 citations Open access
Semantic Scholar
Natural variation in non-coding regions underlying phenotypic diversity in budding yeast
F. Salinas, Carl G. de Boer, Valentina Abarca, V. García +5 more
2016Scientific Reports50 citations Open access
Semantic Scholar
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
K. Mouri, Michael H. Guo, Carl G. de Boer, Michelle M. Lissner +10 more
2022Nature Genetics48 citations Open access
Semantic Scholar
LegNet: a best-in-class deep learning model for short DNA regulatory regions
Dmitry D. Penzar, Daria S. Nogina, Elizaveta Noskova, A. Zinkevich +5 more
2023bioRxiv46 citations Open access
Semantic Scholar
BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization
Carl G. de Boer, A. Regev
2018BMC Bioinformatics44 citations Open access
Semantic Scholar
A community effort to optimize sequence-based deep learning models of gene regulation
Abdul Muntakim Rafi, Daria S. Nogina, Dmitry D. Penzar, Dohoon Lee +95 more
2024Nature Biotechnology40 citations Open access
Semantic Scholar
MAUDE: inferring expression changes in sorting-based CRISPR screens
Carl G. de Boer, John P. Ray, N. Hacohen, A. Regev
2019Genome Biology35 citations Open access
Semantic Scholar
Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high-throughput
Patrick H. Kennedy, A. Sheikh, Matthew Balakar, Alexander C. Jones +16 more
2024Nature Methods25 citations
Semantic Scholar
Regulatory activity is the default DNA state in eukaryotes
Ishika Luthra, Cassandra Jensen, Xinyi E. Chen, Asfar Lathif Salaudeen +2 more
2024Nature Structural & Molecular Biology24 citations Open access
Semantic Scholar
Deciphering variance in epigenomic regulators by k-mer factorization
Carl G. de Boer, A. Regev
2017bioRxiv22 citations Open access
Semantic Scholar
A unified model for yeast transcript definition
Carl G. de Boer, H. van Bakel, Kyle Tsui, Joyce Li +4 more
2014Genome Research21 citations Open access
Semantic Scholar
Poly-dA:dT Tracts Form an In Vivo Nucleosomal Turnstile
Carl G. de Boer, T. Hughes
2014PLoS ONE21 citations Open access
Semantic Scholar
Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae
Zimo Jin, Yueming Dong, Abdul Muntakim Rafi, M. M. Patwary +4 more
2025Nucleic Acids Research12 citations Open access
Semantic Scholar
Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease.
J. Dahlqvist, Charles P. Fulco, John P. Ray, T. Liechti +6 more
2021Human Molecular Genetics11 citations Open access
Semantic Scholar
Characterizing homology-induced data leakage and memorization in genome-trained sequence models
Abdul Muntakim Rafi, Brett Kiyota, Nozomu Yachie, Carl G. de Boer
2026bioRxiv10 citations Open access
Semantic Scholar
Genetic and epigenetic screens in primary human T cells link candidate causal autoimmune variants to T cell networks
Ching-Huang Ho, Maxwell A. Dippel, Meghan S. McQuade, LeAnn P. Nguyen +13 more
2025Nature Genetics10 citations Open access
Semantic Scholar
Culture wars: Empirically determining the best approach for plasmid library amplification
Nicholas Mateyko, Carl G. de Boer
2024bioRxiv8 citations Open access
Semantic Scholar
Evaluation and optimization of sequence-based gene regulatory deep learning models
Abdul Muntakim Rafi, Daria S. Nogina, Dmitry D. Penzar, Dohoon Lee +21 more
2024bioRxiv6 citations Open access
Semantic Scholar
The continuum of transcription factor affinities
Carl G. de Boer
2024Nature reviews genetics6 citations
Semantic Scholar
Biochemical activity is the default DNA state in eukaryotes
Ishika Luthra, Xin-Yi Chen, C. Jensen, Abdul Muntakim Rafi +2 more
2022bioRxiv6 citations Open access
Semantic Scholar
A comprehensive fitness landscape model reveals the evolutionary history and future evolvability of eukaryotic cis-regulatory DNA sequences
E. D. Vaishnav, Carl G. de Boer, M. Yassour, Jennifer Molinet +6 more
2021bioRxiv6 citations Open access
Semantic Scholar
Polygenic backgrounds influence phenotypic consequences of variants in cells, individuals, and populations
Madison Chapel, J. Dennis, Carl G. de Boer
2025bioRxiv4 citations Open access
Semantic Scholar
Genome-wide discovery of SLE genetic risk variant allelic enhancer activity
Xiaoming Lu, Xiao-Ting Chen, C. Forney, O. Donmez +12 more
2020bioRxiv4 citations Open access
Semantic Scholar
Yorzoi: Predicting RNA-seq coverage from DNA sequence in yeast
T. Schneider, Abdul Muntakim Rafi, Cassandra Jensen, Daniella Liao +3 more
2025bioRxiv3 citations Open access
Semantic Scholar
LegNet: resetting the bar in deep learning for accurate prediction of promoter activity and variant effects from massive parallel reporter assays
Dmitry D. Penzar, Daria S. Nogina, G. Meshcheryakov, A. Lando +4 more
20223 citations
Semantic Scholar
Evaluation of Active Learning Selection Strategies and Characterization of Informative Sequences for Sequence-to-Expression Models
Justin Qian, Abdul Muntakim Rafi, Emmanuel Cazottes, Carl G. de Boer
2026bioRxiv2 citations Open access
Semantic Scholar
GAME: Genomic API for Model Evaluation
Ishika Luthra, Satyam Priyadarshi, Rui Guo, Lukas Mahieu +29 more
2025bioRxiv2 citations
Semantic Scholar
Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput
Patrick H. Kennedy, Amin Alborzian Deh Sheikh, Matthew Balakar, Alexander C. Jones +16 more
2023bioRxiv2 citations Open access
Semantic Scholar
Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
Carl G. de Boer, E. D. Vaishnav, R. Sadeh, E. Abeyta +2 more
2020Nature Biotechnology2 citations Open access
Semantic Scholar
Mechanisms of Yeast Gene Definition
Carl G. de Boer
20142 citations
Semantic Scholar
How to build the regulatory genome: a constructionist guide to the cis-regulatory code.
Charles C. Bell, Carl G. de Boer, Brendan R. Camellato, M. Delás +2 more
2026Development1 citations
Semantic Scholar
RAPID-DASH: fast and efficient assembly of guide RNA arrays for multiplexed CRISPR-Cas9 applications
Asfar Lathif Salaudeen, Nicholas Mateyko, Carl G. de Boer
2025bioRxiv1 citations Open access
Semantic Scholar
GIL: a python package for designing custom indexing primers
Nicholas Mateyko, Omar Tariq, Xin-Yi Chen, W. Cheney +7 more
2022bioRxiv1 citations Open access
Semantic Scholar
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
K. Mouri, Michael H. Guo, Carl G. de Boer, Gregory A. Newby +5 more
2021bioRxiv1 citations Open access
Semantic Scholar
MAUDE v1.0
Carl G. de Boer
20201 citations
Semantic Scholar
Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age
Mati Mann, Arnav Mehta, Carl G. de Boer, Monika S. Kowalczyk +4 more
20171 citations
Semantic Scholar
Virus-like particle-delivered base editor collection to expand the genome engineering toolbox
Asfar Lathif Salaudeen, Trevor Shyiak, Carl G. de Boer
2026bioRxiv0 citations Open access
Semantic Scholar
Position-dependent variant effects reveal importance of context in genomic regulation
Sambina Islam Aninta, R. Tewhey, Carl G. de Boer
2026bioRxiv0 citations Open access
Semantic Scholar
Evolutionary Simulations Reveal Role for Genomic Recombination in the Evolution of Gene Regulatory Network Complexity and Robustness
Madison Chapel, Carl G. de Boer
2025bioRxiv0 citations Open access
Semantic Scholar

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Abdul Muntakim Rafi×11
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John P. Ray×9
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Dmitry D. Penzar×5

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