book_5

Publications

2026

The regulation of Protein Phosphatase 4 by FBXO42 is required for cancer cell survival

DPC

Spangenberg SH, Garaffo N, Alcindor EM, Lusk B, Pandey V, Longhurst AD, Bolech E, Fu BX, Gilbert LA, Wohlschlegel JA, Toczyski DP

EMBO reports, 2026 Jul 14;1-27.

PMID: 42448956

Graphical and interactive spatial proteomics image analysis workflow

DRACC

Singh P, Wright JH, Smythe KS, Fukuda B, Hung LH, Yeung CC, Yeung KY

Gigabyte, 2026 Jun 22;2026:gigabyte186-0.

PMID: 42389189

Advancing the bioassay ontology through integrated PK/PD and safety pharmacology representation

DRACC

Glenny-Pescov J, Chung C, Ross N, Hu J, Sinclair M, Khurshid R, Karlsson A, Schürer SC

Journal of biomedical semantics, 2026 Mar 12;17(1):6.

PMID: 41821121

EcDNA-borne structural variants drive oncogenic fusion transcript amplification

DAV

Yi H, Zhang S, Swinderman J, Wang Y, Kanakaveti V, Hung KL, Wong IT, Srinivasan S, Curtis EJ, Bhargava-Shah A, Li R, et al.

Cell, 2026 Feb 5;189(3):906-21.

PMID: 41506267

FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry

DPC

Umhoefer JM, Arce MM, Kasinathan S, Whalen S, Dajani R, Subramanya S, Goudy L, Belk JA, Zhou R, Pham MT, Zhang W, et al.

Immunity, 2026 Jan 13;59(1):129-44.

PMID: 41237776

2025

Protocol to rapidly verify silent gene reporter in human pluripotent stem cells using CRISPR activation

MSK

Wu Y, Zhong A, Ramirez B, Wai SS, Zhou T

STAR protocols, 2025 Dec 19;6(4).

PMID: 41201092

Genome-wide CRISPR screen identifies Menin and SUZ12 as regulators of human developmental timing

MSK

Xu N, Cho HS, Hackland JO, Benito-Kwiecinski S, Saurat N, Harschnitz O, Russo MV, Garippa R, Ciceri G, Studer L

Nature Cell Biology, 2025 Sep;27(9):1411-21.

PMID: 40897805

Critical roles of IKAROS and HDAC1 in regulation of heterochromatin and tumor suppression in T-cell acute lymphoblastic leukemia

NWU

Ding Y, He B, Bogush D, Schramm J, Singh C, Dovat K, Randazzo J, Tukaramrao D, Hengst J, Annageldiyev C, Kudva A, et al.

Leukemia, 2025 Aug;39(8):2010-20.

PMID: 40555735

Systematic comparison and base-editing-mediated directed protein evolution and functional screening yield superior auxin-inducible degron technology

NWU

Xing D, Bai T, Neyisci O, Paylakhi SZ, Duval AJ, Tekin Y, Adli M

Nature Communications, 2025 Jul 18;16(1):6631.

PMID: 40681502

Comprehensive Proteomics Metadata and Integrative Web Portals Facilitate Sharing and Integration of LINCS Multiomics Data

Vidović D, Shamsaei B, Schürer SC, Kogan P, Chojnacki S, Kouril M, Medvedovic M, Niu W, Azeloglu EU, Birtwistle MR, Chen Y, et al.

Molecular & Cellular Proteomics, 2025 Jul 1;24(7).

PMID: 40089066

Leveraging CRISPR activation for rapid assessment of gene editing products in human pluripotent stem cells

MSK

Wu Y, Zhong A, Evangelisti A, Sidharta M, Huangfu D, Studer L, Zhou T

Stem Cell Reports, 2025 Jun 10;20(6).

PMID: 40345204

Pooled CRISPR screening with optical sequencing reveals regulators of 3D chromatin organization

NWU

Adli M

Nature methods, 2025 May;22(5):901-3.

PMID: 40211005

Unified molecular approach for spatial epigenome, transcriptome, and cell lineages

DAV

Huang YH, Belk JA, Zhang R, Weiser NE, Chiang Z, Jones MG, Mischel PS, Buenrostro JD, Chang HY

Proceedings of the National Academy of Sciences, 2025 Apr 22;122(16):e2424070122.

PMID: 40249782

HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCs

JAXDPC

Liu Z, Tan Y, Flynn WF, Sun L, Pratumkaew P, Diniz JA, Oliveira NA, McDonough JA, Skarnes WC, Robson P

Cell reports, 2025 Apr 22;44(4).

PMID: 40220298

Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows

Hung LH, Fukuda B, Schmitz R, Hoang V, Lloyd W, Yeung KY

PLoS One, 2025 Mar 4;20(3):e0318676.

PMID: 40036210

Decoding heterogeneous single-cell perturbation responses

MSK

Song B, Liu D, Dai W, Mcmyn NF, Wang Q, Yang D, Krejci A, Vasilyev A, Untermoser N, Loregger A, Song D, et al.

Nature cell biology, 2025 Mar;27(3):493-504.

PMID: 40011559

MorPhiC Consortium: towards functional characterization of all human genes

All

Adli M, Przybyla L, Burdett T, Burridge PW, Cacheiro P, Chang HY, Engreitz JM, Gilbert LA, Greenleaf WJ, Hsu L, Huangfu D, et al.

Nature, 2025 Feb 13;638(8050):351-9.

PMID: 39939790

Biodepot Launcher: an app to install, manage and launch bioinformatics workflows

Hung LH, Dahlstrom TJ, Garnica J, Munoz E, Schmitz R, Yeung KY

Gigabyte, 2025 Jan 14;2025:gigabyte146-0.

PMID: 39850508

2024

Comparative analysis and directed protein evolution yield an improved degron technology with minimal basal degradation, rapid inducible depletion, and faster recovery of target proteins

NWUDPC

Adli M, Xing D, Bai T, Neyisci O, Paylakhi S, Duval A, Tekin Y

Research Square, 2024 Nov 15;rs-3.

PMID: 39606491

Parallel genome-scale CRISPR-Cas9 screens uncouple human pluripotent stem cell identity versus fitness

MSKDPC

Rosen BP, Li QV, Cho HS, Liu D, Yang D, Graff S, Yan J, Luo R, Verma N, Damodaran JR, Kale HT, et al.

Nature communications, 2024 Oct 17;15(1):8966.

PMID: 39419994

Single-nuclei sequencing of uterine serous carcinoma reveals racial differences in immune signaling

NWUDPC

Foley KG, Adli M, Kim JJ

Proceedings of the National Academy of Sciences, 2024 Aug 20;121(34):e2402998121.

PMID: 39133838

Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline

JAX

Mitchell JM, Chi Y, Thapa M, Pang Z, Xia J, Li S

PLOS Computational Biology, 2024 Jun 6;20(6):e1011912.

PMID: 38843301

Unveiling challenges in Mendelian randomization for gene–environment interaction

Fred Hutch

Gorfine M, Qu C, Peters U, Hsu L

Genetic epidemiology, 2024 Jun;48(4):164-89.

PMID: 38420714

Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism

NWUDPC

Pujadas Liwag EM, Wei X, Acosta N, Carter LM, Yang J, Almassalha LM, Jain S, Daneshkhah A, Rao SS, Seker-Polat F, MacQuarrie KL, et al.

Genome biology, 2024 Mar 22;25(1):77.

PMID: 38519987

Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types

NWUDPC

Buyukcelebi K, Duval AJ, Abdula F, Elkafas H, Seker-Polat F, Adli M

Nature communications, 2024 Feb 7;15(1):1169.

PMID: 38326302

Biology-driven therapy advances in high-grade serous ovarian cancer

NWUDPC

Wang Y, Duval AJ, Adli M, Matei D

The Journal of Clinical Investigation, 2024 Jan 2;134(1).

PMID: 38165032

2023

Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization

NWUDPC

Buyukcelebi K, Chen X, Abdula F, Elkafas H, Duval AJ, Ozturk H, Seker-Polat F, Jin Q, Yin P, Feng Y, Bulun SE, et al.

Nature communications, 2023 Jul 10;14(1):4057.

PMID: 37429859

Adenomyosis: single-cell transcriptomic analysis reveals a paracrine mesenchymal–epithelial interaction involving the WNT/SFRP pathway

NWUDPC

Yildiz S, Kinali M, Wei JJ, Milad M, Yin P, Adli M, Bulun SE

Fertility and sterility, 2023 May 1;119(5):869-82.

PMID: 36736810

Endometriosis and adenomyosis: shared pathophysiology

NWUDPC

Bulun SE, Yildiz S, Adli M, Chakravarti D, Parker JB, Milad M, Yang L, Chaudhari A, Tsai S, Wei JJ, Yin P

Fertility and Sterility, 2023 May 1;119(5):746-50.

PMID: 36925057