Functional Genomics Publications

Acknowledging ICCB-L in Publications

Researchers using the services of ICCB-L staff or equipment agree to acknowledge the support of 'ICCB-Longwood Screening Facility at Harvard Medical School' in publications arising from your use of the facility. If an ICCB-L member has made an important intellectual contribution to the project, as determined by generally accepted criteria for academic collaborations, then that person should be considered for authorship on the publication. If your project was supported by a grant that also directly supports the ICCB-L, please consult the ICCB-L Director regarding the appropriate grant citation. Please notify Jen Smith upon public release of your publication.

Below is a list of publications that have resulted from RNAi screening efforts at ICCB-Longwood. Please notify us of your publications that involve use of the ICCB-Longwood Screening Facility.

2025

Li W, Sparks RP, Sun C, Yang Y, Pantano L, Kirchner R, Arghiani N, Weilheimer A, Toles BJ, Chen JY, Moran SP, Barrera V, Li Z, Zhou P, Brassil ML, Wrobel D, Sui SJH, Aspnes G, Schuler M, Smith J, Medoff BD, Zhou C, Boustany-Kari CM, Rippmann JF, Santos DM, Doerner JF, Mullen AC. Screening the human druggable genome identifies ABHD17B as an anti-fibrotic target in hepatic stellate cells.
Nature communications. 2025;16(1):2109. PMID: 40025044
Li W, Sparks RP, Sun C, Yang Y, Pantano L, Kirchner R, Arghiani N, Weilheimer A, Toles BJ, Chen JY, Moran SP, Barrera V, Li Z, Zhou P, Brassil ML, Wrobel D, Sui SJH, Aspnes G, Schuler M, Smith J, Medoff BD, Zhou C, Boustany-Kari CM, Rippmann JF, Santos DM, Doerner JF, Mullen AC. Screening the human druggable genome identifies ABHD17B as an anti-fibrotic target in hepatic stellate cells.
Nature communications. 2025;16(1):2109. PMID: 40025044
Chong SJF, Lu J, Valentin R, Lehmberg TZ, Eu JQ, Wang J, Zhu F, Kong LR, Fernandes SM, Zhang J, Herbaux C, Goh BC, Brown JR, Niemann CU, Huber W, Zenz T, Davids MS. BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia.
Molecular cancer. 2025;24(1):62. PMID: 40025512
Chong SJF, Lu J, Valentin R, Lehmberg TZ, Eu JQ, Wang J, Zhu F, Kong LR, Fernandes SM, Zhang J, Herbaux C, Goh BC, Brown JR, Niemann CU, Huber W, Zenz T, Davids MS. BCL-2 dependence is a favorable predictive marker of response to therapy for chronic lymphocytic leukemia.
Molecular cancer. 2025;24(1):62. PMID: 40025512

2024

Chang KC, Silvestri F, Oliphant MUJ, Martinez-Gakidis A, Orgill DP, Garber JE, Dillon DD, Brugge JS. Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness.
NPJ breast cancer. 2024;10(1):107. PMID: 39702422
Chang KC, Silvestri F, Oliphant MUJ, Martinez-Gakidis A, Orgill DP, Garber JE, Dillon DD, Brugge JS. Breast organoid suspension cultures maintain long-term estrogen receptor expression and responsiveness.
NPJ breast cancer. 2024;10(1):107. PMID: 39702422
Kilgas S, Syed A, Toolan-Kerr P, Swift ML, Roychoudhury S, Sarkar A, Wilkins S, Quigley M, Poetsch AR, Botuyan MV, Cui G, Mer G, Ule J, Drané P, Chowdhury D. NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity.
Nature communications. 2024;15(1):8438. PMID: 39349456
Kilgas S, Syed A, Toolan-Kerr P, Swift ML, Roychoudhury S, Sarkar A, Wilkins S, Quigley M, Poetsch AR, Botuyan MV, Cui G, Mer G, Ule J, Drané P, Chowdhury D. NEAT1 modulates the TIRR/53BP1 complex to maintain genome integrity.
Nature communications. 2024;15(1):8438. PMID: 39349456
Chidley C, Darnell A, Gaudio B, Lien E, Barbeau A, Vander-Heiden M, Sorger P. A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments.
Nat Cell Biol. 2024;(11 April).
Chidley C, Darnell A, Gaudio B, Lien E, Barbeau A, Vander-Heiden M, Sorger P. A CRISPRi/a screening platform to study cellular nutrient transport in diverse microenvironments.
Nat Cell Biol. 2024;(11 April).

2023

Park D, Nguyen S, Isenhart R, Shah P, Kim W, Barnett R, Chandra A, Luppino J, Harke J, Wai M, Walsh P, Abdill R, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki M, Vahedi G, Phillips-Cremins J, Jain R, Joyce E. High-throughput Oligopaint screen identifies druggable 3D genome regulators.
Nature. 2023;620:209–217.
Park D, Nguyen S, Isenhart R, Shah P, Kim W, Barnett R, Chandra A, Luppino J, Harke J, Wai M, Walsh P, Abdill R, Yang R, Lan Y, Yoon S, Yunker R, Kanemaki M, Vahedi G, Phillips-Cremins J, Jain R, Joyce E. High-throughput Oligopaint screen identifies druggable 3D genome regulators.
Nature. 2023;620:209–217.
Durall R, Huang J, Wojenski L, Huang Y, Gokhale P, Leeper B, Nash J, Ballester P, Davidson S, Shlien A, Sotirakis E, Bertaux F, Dubus V, Luo J, Wu C, Keskin D, Eagen K, Shapiro G, French C. The BRD4-NUT fusion alone drives malignant transformation of NUT carcinoma.
Cancer Res. 2023;(Oct 11).
Durall R, Huang J, Wojenski L, Huang Y, Gokhale P, Leeper B, Nash J, Ballester P, Davidson S, Shlien A, Sotirakis E, Bertaux F, Dubus V, Luo J, Wu C, Keskin D, Eagen K, Shapiro G, French C. The BRD4-NUT fusion alone drives malignant transformation of NUT carcinoma.
Cancer Res. 2023;(Oct 11).
Chen DY, Chin C, Kenney D, Tavares A, Khan N, Conway H, Liu G, Choudhary M, Gertje H, O’Connell A, Adams S, Kotton D, Herrmann A, Ensser A, Connor J, Bosmann M, Li J, Gack M, Baker S, Kirchdoerfer R, Kataria Y, Crossland N, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation.
Nature. 2023;615:143–150.
Chen DY, Chin C, Kenney D, Tavares A, Khan N, Conway H, Liu G, Choudhary M, Gertje H, O’Connell A, Adams S, Kotton D, Herrmann A, Ensser A, Connor J, Bosmann M, Li J, Gack M, Baker S, Kirchdoerfer R, Kataria Y, Crossland N, Douam F, Saeed M. Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation.
Nature. 2023;615:143–150.
Schmaier A, Anderson P, Chen S, El-Darzi E, Aivasovsky I, Kaushik M, Sack K, Hartzell H, Parikh S, Flaumenhaft, Schulman S. TMEM16E regulates endothelial cell procoagulant activity and thrombosis.
J Clin Invest. 2023;133(11):e163808.
Schmaier A, Anderson P, Chen S, El-Darzi E, Aivasovsky I, Kaushik M, Sack K, Hartzell H, Parikh S, Flaumenhaft, Schulman S. TMEM16E regulates endothelial cell procoagulant activity and thrombosis.
J Clin Invest. 2023;133(11):e163808.
Jovanović B, Temko D, Stevens L, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper N, Daniels V, Xiao-Yun H, Ge J, Alečković M, Pyrdol J, Hinohara K, Egri S, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram M, Subedee A, Herbert Z, Wucherpfennig K, Letai A, Jaffe J, Sicinski P, Brown M, Dillon D, Long H, Michor, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer.
Cell Rep. 2023;42(12):113564.
Jovanović B, Temko D, Stevens L, Seehawer M, Fassl A, Murphy K, Anand J, Garza K, Gulvady A, Qiu X, Harper N, Daniels V, Xiao-Yun H, Ge J, Alečković M, Pyrdol J, Hinohara K, Egri S, Papanastasiou M, Vadhi R, Font-Tello A, Witwicki R, Peluffo G, Trinh A, Shu S, Diciaccio B, Ekram M, Subedee A, Herbert Z, Wucherpfennig K, Letai A, Jaffe J, Sicinski P, Brown M, Dillon D, Long H, Michor, Polyak K. Heterogeneity and transcriptional drivers of triple-negative breast cancer.
Cell Rep. 2023;42(12):113564.

2022

Martínez-Noël, Szajner, Kramer R, Boyland K, Sheikh, Smith J, Howley P. Identification of MicroRNAs That Stabilize p53 in Human Papillomavirus-Positive Cancer Cells.
J Virol. 2022;96(4).
Martínez-Noël, Szajner, Kramer R, Boyland K, Sheikh, Smith J, Howley P. Identification of MicroRNAs That Stabilize p53 in Human Papillomavirus-Positive Cancer Cells.
J Virol. 2022;96(4).
Vora S, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman, Gehrke L, Shi M, Wang L, Iwasaki A, Wu. Targeting stem-loop 1 of the SARS-CoV-2 5’ UTR to suppress viral translation and Nsp1 evasion.
Proc Natl Acad Sci U S A. 2022;119(9):e2117198119.
Vora S, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman, Gehrke L, Shi M, Wang L, Iwasaki A, Wu. Targeting stem-loop 1 of the SARS-CoV-2 5’ UTR to suppress viral translation and Nsp1 evasion.
Proc Natl Acad Sci U S A. 2022;119(9):e2117198119.
Jutzi J, Marneth A, Ciboddo M, Guerra-Moreno A, Jiménez-Santos M, Kosmidou A, Dressman J, Liang H, Hamel R, Lozano P, Rumi E, Doench J, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs.
Blood. 2022;140(11):1291–1304.
Jutzi J, Marneth A, Ciboddo M, Guerra-Moreno A, Jiménez-Santos M, Kosmidou A, Dressman J, Liang H, Hamel R, Lozano P, Rumi E, Doench J, Gotlib J, Krishnan A, Elf S, Al-Shahrour F, Mullally A. Whole-genome CRISPR screening identifies N-glycosylation as a genetic and therapeutic vulnerability in CALR-mutant MPNs.
Blood. 2022;140(11):1291–1304.
Coverdell T, Abraham-Fan RJ, Wu C, Abbott S, Campbell J. Genetic encoding of an esophageal motor circuit.
Cell Rep. 2022;39(11):110962.
Coverdell T, Abraham-Fan RJ, Wu C, Abbott S, Campbell J. Genetic encoding of an esophageal motor circuit.
Cell Rep. 2022;39(11):110962.
Boekell K, Brown B, Talbot B, Schlondorff J. Trpc6 gain-of-function disease mutation enhances phosphatidylserine exposure in murine platelets.
PLoS One. 2022;17(6):e0270431.
Boekell K, Brown B, Talbot B, Schlondorff J. Trpc6 gain-of-function disease mutation enhances phosphatidylserine exposure in murine platelets.
PLoS One. 2022;17(6):e0270431.

2021

Chu V, Feng Q, Lim Y, Shao S. Selective destabilization of polypeptides synthesized from NMD-targeted transcripts.
Mol Biol Cell. 2021;32(22):ar38.
Chu V, Feng Q, Lim Y, Shao S. Selective destabilization of polypeptides synthesized from NMD-targeted transcripts.
Mol Biol Cell. 2021;32(22):ar38.
Tasdemir-Yilmaz O, Druckenbrod N, Olukoya O, Dong W, Yung A, Bastille I, Pazyra-Murphy M, Sitko A, Hale E, Vigneau S, Gimelbrant A, Kharchenko P, Goodrich L, Segal R. Diversity of developing peripheral glia revealed by single-cell RNA sequencing.
Dev Cell. 2021;56(17):2516–2535.
Tasdemir-Yilmaz O, Druckenbrod N, Olukoya O, Dong W, Yung A, Bastille I, Pazyra-Murphy M, Sitko A, Hale E, Vigneau S, Gimelbrant A, Kharchenko P, Goodrich L, Segal R. Diversity of developing peripheral glia revealed by single-cell RNA sequencing.
Dev Cell. 2021;56(17):2516–2535.

2020

Tattikota S, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh M, Yoon SH, Comjean A, Li F, Dervis F, Hung RJ, Nam JW, Sui S, Shim, Perrimon. A single-cell survey of Drosophila blood.
eLife. 2020;9:e54818.
Tattikota S, Cho B, Liu Y, Hu Y, Barrera V, Steinbaugh M, Yoon SH, Comjean A, Li F, Dervis F, Hung RJ, Nam JW, Sui S, Shim, Perrimon. A single-cell survey of Drosophila blood.
eLife. 2020;9:e54818.
Cruz F, Colbert J, Rock K. The GTPase Rab39a promotes phagosome maturation into MHC-I antigen-presenting compartments.
EMBO J. 2020;39:e102020.
Cruz F, Colbert J, Rock K. The GTPase Rab39a promotes phagosome maturation into MHC-I antigen-presenting compartments.
EMBO J. 2020;39:e102020.
Egusquiaguirre S, Liu S, Tošić I, Jiang K, Walker S, Nicolais M, Saw T, Xiang M, Bartel K, Nelson E, Frank D. CDK5RAP3 is a co-factor for the oncogenic transcription factor STAT3.
Neoplasia. 2020;22(1):47–59.
Egusquiaguirre S, Liu S, Tošić I, Jiang K, Walker S, Nicolais M, Saw T, Xiang M, Bartel K, Nelson E, Frank D. CDK5RAP3 is a co-factor for the oncogenic transcription factor STAT3.
Neoplasia. 2020;22(1):47–59.
Takahashi, Cho P, Selfors L, Kuiken H, Kaul R, Fujiwara T, Harris I, Zhang T, Gygi S, Brugge J. 3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis.
Mol Cell. 2020;80(5):828–844.
Takahashi, Cho P, Selfors L, Kuiken H, Kaul R, Fujiwara T, Harris I, Zhang T, Gygi S, Brugge J. 3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis.
Mol Cell. 2020;80(5):828–844.
Todd W, Venner A, Anaclet C, Broadhurst R, Luca R, Bandaru S, Issokson L, Hablitz L, Cravetchi O, Arrigoni E, Campbell J, Allen C, Olson D, Fuller P. Suprachiasmatic VIP neurons are required for normal circadian rhythmicity and comprised of molecularly distinct subpopulations.
Nat Commun. 2020;11:4410.
Todd W, Venner A, Anaclet C, Broadhurst R, Luca R, Bandaru S, Issokson L, Hablitz L, Cravetchi O, Arrigoni E, Campbell J, Allen C, Olson D, Fuller P. Suprachiasmatic VIP neurons are required for normal circadian rhythmicity and comprised of molecularly distinct subpopulations.
Nat Commun. 2020;11:4410.

2019

Iuchi S, Paulo J. Lysine-specific demethylase 2A enhances binding of various nuclear factors to CpG-rich genomic DNAs by action of its CXXC-PHD domain.
Sci Rep. 2019;9:5496.
Iuchi S, Paulo J. Lysine-specific demethylase 2A enhances binding of various nuclear factors to CpG-rich genomic DNAs by action of its CXXC-PHD domain.
Sci Rep. 2019;9:5496.

2018

Zeid, Lawlor M, Poon, Reyes J, Fulciniti, Lopez M, Scott T, Nabet, Erb M, Winter G, Jacobson, Polaski D, Karlin K, Hirsch R, Munshi N, Westbrook T, Chesler, Lin C, Bradner J. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma.
Nat Genet. . 2018;Jan 29 doi: 10.1038/s41588-018-0044-9.
Zeid, Lawlor M, Poon, Reyes J, Fulciniti, Lopez M, Scott T, Nabet, Erb M, Winter G, Jacobson, Polaski D, Karlin K, Hirsch R, Munshi N, Westbrook T, Chesler, Lin C, Bradner J. Enhancer invasion shapes MYCN-dependent transcriptional amplification in neuroblastoma.
Nat Genet. . 2018;Jan 29 doi: 10.1038/s41588-018-0044-9.
Amin, Florez, Najafov, Pan, Geng, Ofengeim, Dziedzic S, Wang H, Barrett V, Ito, LaVoie M, Yuan. Regulation of a distinct activated RIPK1 intermediatebridging complex I and complex II inTNFα-mediated apoptosis.
PNAS. 2018;115(26):E5944-E5953.
Amin, Florez, Najafov, Pan, Geng, Ofengeim, Dziedzic S, Wang H, Barrett V, Ito, LaVoie M, Yuan. Regulation of a distinct activated RIPK1 intermediatebridging complex I and complex II inTNFα-mediated apoptosis.
PNAS. 2018;115(26):E5944-E5953.
Takahashi, Chen HY, Harris I, Stover D, Selfors L, Bronson R, Deraedt T, Cichowski K, Welm A, Mori, Mills G, Brugge J. Cancer Cells Co-opt the Neuronal Redox-Sensing Channel TRPA1 to Promote Oxidative-Stress Tolerance.
Cancer Cell. 2018;33(6):985–1003.
Takahashi, Chen HY, Harris I, Stover D, Selfors L, Bronson R, Deraedt T, Cichowski K, Welm A, Mori, Mills G, Brugge J. Cancer Cells Co-opt the Neuronal Redox-Sensing Channel TRPA1 to Promote Oxidative-Stress Tolerance.
Cancer Cell. 2018;33(6):985–1003.
Bodnar N, Kim K, Ji Z, Wales T, Svetlov V, Nudler E, Engen J, Walz T, Rapoport T. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Nat Struct Mol Biol. 2018;25(7):616–622.
Bodnar N, Kim K, Ji Z, Wales T, Svetlov V, Nudler E, Engen J, Walz T, Rapoport T. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.
Nat Struct Mol Biol. 2018;25(7):616–622.

2017

Nelms, Dalomba N, Lencer. A targeted RNAi screen identifies factors affecting diverse stages of receptor-mediated transcytosis.
J Cell Biol. 2017;216(2):511–525.
Nelms, Dalomba N, Lencer. A targeted RNAi screen identifies factors affecting diverse stages of receptor-mediated transcytosis.
J Cell Biol. 2017;216(2):511–525.
Simpson K, Smith J. Knocking down the obstacles to functional genomics data sharing.
Sci Data. 2017;4:170019 doi:10.1038/sdata.2017.19.
Simpson K, Smith J. Knocking down the obstacles to functional genomics data sharing.
Sci Data. 2017;4:170019 doi:10.1038/sdata.2017.19.
Fu, Zhao, Wang, Patil, Smith J, Juncadella I, Zuvela-Jelaska, Dorf, Li. RNAi Screen and Proteomics Reveal NXF1 as a Novel Regulator of IRF5 Signaling.
Sci Rep. 2017;Jun 2; 7(1):2683.
Fu, Zhao, Wang, Patil, Smith J, Juncadella I, Zuvela-Jelaska, Dorf, Li. RNAi Screen and Proteomics Reveal NXF1 as a Novel Regulator of IRF5 Signaling.
Sci Rep. 2017;Jun 2; 7(1):2683.