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Events
MorPhiC: Decoding Human Protein-Coding Gene Function at Scale in hiPSC-Derived Multicellular Systems
The 106th Meeting of the National Advisory Council for Human Genome Research
MorPhiC presentation starts at 1 hour 51 minutes.
Watch Video →
Publications
Protocol to rapidly verify silent gene reporter in human pluripotent stem cells using CRISPR activation
STAR protocols, 2025 Dec 19;6(4).
Wu Y, Zhong A, Ramirez B, Wai SS, Zhou T
MSK
PMID: 41201092
Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing
Nature Cell Biology, 2025 Sep;27(9):1411-21.
Xu N, Cho HS, Hackland JO, Benito-Kwiecinski S, Saurat N, Harschnitz O, Russo MV, Garippa R, Ciceri G, Studer L
MSK
PMID: 40897805
Critical roles of IKAROS and HDAC1 in regulation of heterochromatin and tumor suppression in T-cell acute lymphoblastic leukemia
Leukemia, 2025 Aug;39(8):2010-20.
Ding Y, He B, Bogush D, Schramm J, Singh C, Dovat K, Randazzo J, Tukaramrao D, Hengst J, Annageldiyev C, Kudva A
NWU
PMID: 40555735
Systematic comparison and base-editing-mediated directed protein evolution and functional screening yield superior auxin-inducible degron technology
Nature Communications, 2025 Jul 18;16(1):6631.
Xing D, Bai T, Neyisci O, Paylakhi SZ, Duval AJ, Tekin Y, Adli M
NWU
PMID: 40681502
Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data
Molecular & Cellular Proteomics, 2025 Jul 1;24(7).
Vidović D, Shamsaei B, Schürer SC, Kogan P, Chojnacki S, Kouril M, Medvedovic M, Niu W, Azeloglu EU, Birtwistle MR, Chen Y
UM
PMID: 40089066
Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells
Stem Cell Reports, 2025 Jun 10;20(6).
Wu Y, Zhong A, Evangelisti A, Sidharta M, Huangfu D, Studer L, Zhou T
MSK
PMID: 40345204
Pooled CRISPR screening with optical sequencing reveals regulators of 3D chromatin organization
Nature methods, 2025 May;22(5):901-3.
Adli M
NWU
PMID: 40211005
HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCs
Cell reports, 2025 Apr 22;44(4).
Liu Z, Tan Y, Flynn WF, Sun L, Pratumkaew P, Diniz JA, Oliveira NA, McDonough JA, Skarnes WC, Robson P
JAXDPC
PMID: 40220298
Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows
PLoS One, 2025 Mar 4;20(3):e0318676.
Hung LH, Fukuda B, Schmitz R, Hoang V, Lloyd W, Yeung KY
UW
PMID: 40036210
Decoding heterogeneous single-cell perturbation responses
Nature cell biology, 2025 Mar;27(3):493-504.
Song B, Liu D, Dai W, Mcmyn NF, Wang Q, Yang D, Krejci A, Vasilyev A, Untermoser N, Loregger A, Song D
MSK
PMID: 40011559
MorPhiC Consortium: towards functional characterization of all human genes
Nature, 2025 Feb 13;638(8050):351-9.
Adli M, Przybyla L, Burdett T, Burridge PW, Cacheiro P, Chang HY, Engreitz JM, Gilbert LA, Greenleaf WJ, Hsu L, Huangfu D
All
PMID: 39939790
Biodepot Launcher: an app to install, manage and launch bioinformatics workflows
Gigabyte, 2025 Jan 14;2025:gigabyte146-0.
Hung LH, Dahlstrom TJ, Garnica J, Munoz E, Schmitz R, Yeung KY
UW
PMID: 39850508
Comparative analysis and directed protein evolution yield an improved degron technology with minimal basal degradation, rapid inducible depletion, and faster recovery of target proteins
Research Square, 2024 Nov 15;rs-3.
Adli M, Xing D, Bai T, Neyisci O, Paylakhi S, Duval A, Tekin Y
NWUDPC
PMID: 39606491
Comparative analysis and directed protein evolution yield an improved degron technology with minimal basal degradation, rapid inducible depletion, and faster recovery of target proteins
Research Square, 2024 Nov 15;rs-3.
Adli M, Xing D, Bai T, Neyisci O, Paylakhi S, Duval A, Tekin Y
NWU
PMID: 39606491
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Nature communications, 2024 Oct 17;15(1):8966.
Rosen BP, Li QV, Cho HS, Liu D, Yang D, Graff S, Yan J, Luo R, Verma N, Damodaran JR, Kale HT
MSKDPC
PMID: 39419994
Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness
Nature communications, 2024 Oct 17;15(1):8966.
Rosen BP, Li QV, Cho HS, Liu D, Yang D, Graff S, Yan J, Luo R, Verma N, Damodaran JR, Kale HT
MSK
PMID: 39419994
Single-nuclei sequencing of uterine serous carcinoma reveals racial differences in immune signaling
Proceedings of the National Academy of Sciences, 2024 Aug 20;121(34):e2402998121.
Foley KG, Adli M, Kim JJ
NWUDPC
PMID: 39133838
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
PLOS Computational Biology, 2024 Jun 6;20(6):e1011912.
Mitchell JM, Chi Y, Thapa M, Pang Z, Xia J, Li S
JAX
PMID: 38843301
Unveiling challenges in Mendelian randomization for gene–environment interaction
Genetic epidemiology, 2024 Jun;48(4):164-89.
Gorfine M, Qu C, Peters U, Hsu L
Fred Hutch
PMID: 38420714
Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism
Genome biology, 2024 Mar 22;25(1):77.
Pujadas Liwag EM, Wei X, Acosta N, Carter LM, Yang J, Almassalha LM, Jain S, Daneshkhah A, Rao SS, Seker-Polat F, MacQuarrie KL
NWUDPC
PMID: 38519987
Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism
Genome biology, 2024 Mar 22;25(1):77.
Pujadas Liwag EM, Wei X, Acosta N, Carter LM, Yang J, Almassalha LM, Jain S, Daneshkhah A, Rao SS, Seker-Polat F, MacQuarrie KL
NWU
PMID: 38519987
Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types
Nature communications, 2024 Feb 7;15(1):1169.
Buyukcelebi K, Duval AJ, Abdula F, Elkafas H, Seker-Polat F, Adli M
NWUDPC
PMID: 38326302
Biology-driven therapy advances in high-grade serous ovarian cancer
The Journal of Clinical Investigation, 2024 Jan 2;134(1).
Wang Y, Duval AJ, Adli M, Matei D
NWUDPC
PMID: 38165032
Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization
Nature communications, 2023 Jul 10;14(1):4057.
Buyukcelebi K, Chen X, Abdula F, Elkafas H, Duval AJ, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Bulun SE
NWUDPC
PMID: 37429859
Adenomyosis: single-cell transcriptomic analysis reveals a paracrine mesenchymal–epithelial interaction involving the WNT/SFRP pathway
Fertility and sterility, 2023 May 1;119(5):869-82.
Yildiz S, Kinali M, Wei JJ, Milad M, Yin P, Adli M, Bulun SE
NWUDPC
PMID: 36736810
Endometriosis and adenomyosis: shared pathophysiology
Fertility and Sterility, 2023 May 1;119(5):746-50.
Bulun SE, Yildiz S, Adli M, Chakravarti D, Parker JB, Milad M, Yang L, Chaudhari A, Tsai S, Wei JJ, Yin P
NWUDPC
PMID: 36925057