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1.

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

Sade-Feldman, Moshe; Yizhak, Keren; Bjorgaard, Stacey L; Ray, John P; de Boer, Carl G; Jenkins, Russell W; Lieb, David J; Chen, Jonathan H; Frederick, Dennie T; Barzily-Rokni, Michal; Freeman, Samuel S; Reuben, Alexandre; Hoover, Paul J; Villani, Alexandra-Chloé; Ivanova, Elena; Portell, Andrew; Lizotte, Patrick H; Aref, Amir R; Eliane, Jean-Pierre; Hammond, Marc R; Vitzthum, Hans; Blackmon, Shauna M; Li, Bo; Gopalakrishnan, Vancheswaran; Reddy, Sangeetha M; Cooper, Zachary A; Paweletz, Cloud P; Barbie, David A; Stemmer-Rachamimov, Anat; Flaherty, Keith T; Wargo, Jennifer A; Boland, Genevieve M; Sullivan, Ryan J; Getz, Gad; Hacohen, Nir.

Cell ; 175(4): 998-1013.e20, 2018 11 01.

Article in English | MEDLINE | ID: mdl-30388456

2.

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.

Puram, Rishi V; Kowalczyk, Monika S; de Boer, Carl G; Schneider, Rebekka K; Miller, Peter G; McConkey, Marie; Tothova, Zuzana; Tejero, Héctor; Heckl, Dirk; Järås, Marcus; Chen, Michelle C; Li, Hubo; Tamayo, Alfred; Cowley, Glenn S; Rozenblatt-Rosen, Orit; Al-Shahrour, Fatima; Regev, Aviv; Ebert, Benjamin L.

Cell ; 165(2): 303-16, 2016 Apr 07.

Article in English | MEDLINE | ID: mdl-27058663

3.

Hold out the genome: a roadmap to solving the cis-regulatory code.

de Boer, Carl G; Taipale, Jussi.

Nature ; 625(7993): 41-50, 2024 Jan.

Article in English | MEDLINE | ID: mdl-38093018

4.

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

Sade-Feldman, Moshe; Yizhak, Keren; Bjorgaard, Stacey L; Ray, John P; de Boer, Carl G; Jenkins, Russell W; Lieb, David J; Chen, Jonathan H; Frederick, Dennie T; Barzily-Rokni, Michal; Freeman, Samuel S; Reuben, Alexandre; Hoover, Paul J; Villani, Alexandra-Chloé; Ivanova, Elena; Portell, Andrew; Lizotte, Patrick H; Aref, Amir R; Eliane, Jean-Pierre; Hammond, Marc R; Vitzthum, Hans; Blackmon, Shauna M; Li, Bo; Gopalakrishnan, Vancheswaran; Reddy, Sangeetha M; Cooper, Zachary A; Paweletz, Cloud P; Barbie, David A; Stemmer-Rachamimov, Anat; Flaherty, Keith T; Wargo, Jennifer A; Boland, Genevieve M; Sullivan, Ryan J; Getz, Gad; Hacohen, Nir.

Cell ; 176(1-2): 404, 2019 Jan 10.

Article in English | MEDLINE | ID: mdl-30633907

5.

The evolution, evolvability and engineering of gene regulatory DNA.

Vaishnav, Eeshit Dhaval; de Boer, Carl G; Molinet, Jennifer; Yassour, Moran; Fan, Lin; Adiconis, Xian; Thompson, Dawn A; Levin, Joshua Z; Cubillos, Francisco A; Regev, Aviv.

Nature ; 603(7901): 455-463, 2022 03.

Article in English | MEDLINE | ID: mdl-35264797

6.

Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput.

Kennedy, Patrick H; Alborzian Deh Sheikh, Amin; Balakar, Matthew; Jones, Alexander C; Olive, Meagan E; Hegde, Mudra; Matias, Maria I; Pirete, Natan; Burt, Rajan; Levy, Jonathan; Little, Tamia; Hogan, Patrick G; Liu, David R; Doench, John G; Newton, Alexandra C; Gottschalk, Rachel A; de Boer, Carl G; Alarcón, Suzie; Newby, Gregory A; Myers, Samuel A.

Nat Methods ; 2024 Apr 29.

Article in English | MEDLINE | ID: mdl-38684783

7.

The continuum of transcription factor affinities.

de Boer, Carl G.

Nat Rev Genet ; 25(6): 378, 2024 Jun.

Article in English | MEDLINE | ID: mdl-38413844

8.

Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease.

Dahlqvist, Johanna; Fulco, Charles P; Ray, John P; Liechti, Thomas; de Boer, Carl G; Lieb, David J; Eisenhaure, Thomas M; Engreitz, Jesse M; Roederer, Mario; Hacohen, Nir.

Hum Mol Genet ; 31(12): 1946-1961, 2022 06 22.

Article in English | MEDLINE | ID: mdl-34970970

9.

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.

de Boer, Carl G; Regev, Aviv.

BMC Bioinformatics ; 19(1): 253, 2018 07 03.

Article in English | MEDLINE | ID: mdl-29970004

10.

A unified model for yeast transcript definition.

de Boer, Carl G; van Bakel, Harm; Tsui, Kyle; Li, Joyce; Morris, Quaid D; Nislow, Corey; Greenblatt, Jack F; Hughes, Timothy R.

Genome Res ; 24(1): 154-66, 2014 Jan.

Article in English | MEDLINE | ID: mdl-24170600

11.

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.

de Boer, Carl G; Hughes, Timothy R.

Nucleic Acids Res ; 40(Database issue): D169-79, 2012 Jan.

Article in English | MEDLINE | ID: mdl-22102575

12.

Regulatory activity is the default DNA state in eukaryotes.

Luthra, Ishika; Jensen, Cassandra; Chen, Xinyi E; Salaudeen, Asfar Lathif; Rafi, Abdul Muntakim; de Boer, Carl G.

Nat Struct Mol Biol ; 31(3): 559-567, 2024 Mar.

Article in English | MEDLINE | ID: mdl-38448573

13.

Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells.

Mouri, Kousuke; Guo, Michael H; de Boer, Carl G; Lissner, Michelle M; Harten, Ingrid A; Newby, Gregory A; DeBerg, Hannah A; Platt, Winona F; Gentili, Matteo; Liu, David R; Campbell, Daniel J; Hacohen, Nir; Tewhey, Ryan; Ray, John P.

Nat Genet ; 54(5): 603-612, 2022 05.

Article in English | MEDLINE | ID: mdl-35513721

14.

Global discovery of lupus genetic risk variant allelic enhancer activity.

Lu, Xiaoming; Chen, Xiaoting; Forney, Carmy; Donmez, Omer; Miller, Daniel; Parameswaran, Sreeja; Hong, Ted; Huang, Yongbo; Pujato, Mario; Cazares, Tareian; Miraldi, Emily R; Ray, John P; de Boer, Carl G; Harley, John B; Weirauch, Matthew T; Kottyan, Leah C.

Nat Commun ; 12(1): 1611, 2021 03 12.

Article in English | MEDLINE | ID: mdl-33712590

15.

MAUDE: inferring expression changes in sorting-based CRISPR screens.

de Boer, Carl G; Ray, John P; Hacohen, Nir; Regev, Aviv.

Genome Biol ; 21(1): 134, 2020 06 03.

Article in English | MEDLINE | ID: mdl-32493396

16.

Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

de Boer, Carl G; Vaishnav, Eeshit Dhaval; Sadeh, Ronen; Abeyta, Esteban Luis; Friedman, Nir; Regev, Aviv.

Nat Biotechnol ; 38(10): 1211, 2020 Oct.

Article in English | MEDLINE | ID: mdl-32792646

17.

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

de Boer, Carl G; Vaishnav, Eeshit Dhaval; Sadeh, Ronen; Abeyta, Esteban Luis; Friedman, Nir; Regev, Aviv.

Nat Biotechnol ; 38(1): 56-65, 2020 01.

Article in English | MEDLINE | ID: mdl-31792407

18.

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.

Ray, John P; de Boer, Carl G; Fulco, Charles P; Lareau, Caleb A; Kanai, Masahiro; Ulirsch, Jacob C; Tewhey, Ryan; Ludwig, Leif S; Reilly, Steven K; Bergman, Drew T; Engreitz, Jesse M; Issner, Robbyn; Finucane, Hilary K; Lander, Eric S; Regev, Aviv; Hacohen, Nir.

Nat Commun ; 11(1): 1237, 2020 03 06.

Article in English | MEDLINE | ID: mdl-32144282

19.

Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age.

Mann, Mati; Mehta, Arnav; de Boer, Carl G; Kowalczyk, Monika S; Lee, Kevin; Haldeman, Pearce; Rogel, Noga; Knecht, Abigail R; Farouq, Daneyal; Regev, Aviv; Baltimore, David.

Cell Rep ; 25(11): 2992-3005.e5, 2018 12 11.

Article in English | MEDLINE | ID: mdl-30540934

20.

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast.

Salinas, Francisco; de Boer, Carl G; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F; Martínez, Claudio; Cubillos, Francisco A.

Sci Rep ; 6: 21849, 2016 Feb 22.

Article in English | MEDLINE | ID: mdl-26898953

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Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

Core Circadian Clock Genes Regulate Leukemia Stem Cells in AML.

Hold out the genome: a roadmap to solving the cis-regulatory code.

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.

The evolution, evolvability and engineering of gene regulatory DNA.

Post-translational modification-centric base editor screens to assess phosphorylation site functionality in high throughput.

The continuum of transcription factor affinities.

Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease.

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.

A unified model for yeast transcript definition.

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.

Regulatory activity is the default DNA state in eukaryotes.

Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells.

Global discovery of lupus genetic risk variant allelic enhancer activity.

MAUDE: inferring expression changes in sorting-based CRISPR screens.

Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features.

Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli Are Altered with Age.

Natural variation in non-coding regions underlying phenotypic diversity in budding yeast.