Cecil H. and Ida Green Center For Reproductive Biology Sciences

Research output

Research output per year 2003 2020 2021 2022 2023 2024

• 83 Article
• 24 Review article
• 6 Comment/debate
• 3 Chapter
• 4 More
  • 2 Editorial
  • 2 Letter

Research output per year

Research output per year

Search results

• 2024

  Coactivator condensation drives cardiovascular cell lineage specification

  Gan, P., Eppert, M., De La Cruz, N., Lyons, H., Shah, A. M., Veettil, R. T., Chen, K., Pradhan, P., Bezprozvannaya, S., Xu, L., Liu, N., Olson, E. N. & Sabari, B. R., Mar 2024, In: Science Advances. 10, 11, eadk7160.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • myocardin 100%
  • Cell Lineage 83%
  • Transcriptional Activation 43%
  • Smooth Muscle Myocytes 41%
  • Cellular Reprogramming 40%
• 2023

  Acetyl-Click Screening Platform Identifies Small-Molecule Inhibitors of Histone Acetyltransferase 1 (HAT1)

  Gaddameedi, J. D., Chou, T., Geller, B. S., Rangarajan, A., Swaminathan, T. A., Dixon, D., Long, K., Golder, C. J., Vuong, V. A., Banuelos, S., Greenhouse, R., Snyder, M. P., Lipchik, A. M. & Gruber, J. J., Apr 27 2023, In: Journal of Medicinal Chemistry. 66, 8, p. 5774-5801 28 p.

  Research output: Contribution to journal › Article › peer-review

  • histone acetyltransferase type B complex 100%
  • Histone 55%
  • isoalloxazine 13%
  • Growth 11%
  • Enzyme Activity 10%
  1 Scopus citations

• Beyond energy and growth: the role of metabolism in developmental signaling, cell behavior and diapause

  Tippetts, T. S., Sieber, M. H. & Solmonson, A., Oct 2023, In: Development (Cambridge). 150, 20, dev201610.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Diapause 100%
  • Signal Transduction 46%
  • Growth 29%
  • Nutrients 20%
  • Germ Cells 11%
  3 Scopus citations

• Breaking enhancers to gain insights into developmental defects

  Armendariz, D. A., Sundarrajan, A. & Hon, G. C., 2023, In: eLife. 12, e88187.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Developmental 100%
  • Enhancer 97%
  • Phenotype 24%
  • Gene Expression 12%

• Charles David Allis (1951-2023)

  Chi, P., Lewis, P. W., Lu, C., Lu, J., Ruthenburg, A. J., Sabari, B. R., Shechter, D., Wan, L. & Wang, G. G., Apr 1 2023, In: Nature genetics. 55, 4, p. 522-523 2 p.

  Research output: Contribution to journal › Editorial › peer-review

  Open Access

• CHD-associated enhancers shape human cardiomyocyte lineage commitment

  Armendariz, D. A., Goetsch, S. C., Sundarrajan, A., Sivakumar, S., Wang, Y., Xie, S., Munshi, N. V. & Hon, G. C., 2023, In: eLife. 12, e86206.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Enhancer 100%
  • Congenital Heart Defects 98%
  • Cardiac Myocytes 78%
  • Shape 54%
  • Epigenomics 36%
  1 Scopus citations

• Dissecting mammalian reproduction with spatial transcriptomics

  Zhang, X., Cao, Q., Rajachandran, S., Grow, E. J., Evans, M. & Chen, H., Nov 1 2023, In: Human Reproduction Update. 29, 6, p. 794-810 17 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Reproduction 100%
  • Technology 67%
  • Genitalia 41%
  • Gametogenesis 21%
  • Embryonic Development 20%

• Dissecting the spermatogonial stem cell niche using spatial transcriptomics

  Rajachandran, S., Zhang, X., Cao, Q., Caldeira-Brant, A. L., Zhang, X., Song, Y., Evans, M., Bukulmez, O., Grow, E. J., Nagano, M., Orwig, K. E. & Chen, H., Jul 25 2023, In: Cell Reports. 42, 7, 112737.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Stem Cell Niche 100%
  • Stem Cells 57%
  • Ephrin-A1 34%
  • Testis 34%
  • pleiotrophin 30%
  1 Scopus citations

• Dynamic states of cervical epithelia during pregnancy and epithelial barrier disruption

  Cooley, A., Madhukaran, S. P., Stroebele, E., Colon Caraballo, M., Wang, L., Akgul, Y., Hon, G. C. & Mahendroo, M., Feb 17 2023, In: iScience. 26, 2, 105953.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Epithelium 100%
  • Single-Cell Analysis 87%
  • Pregnancy 79%
  • Goblet Cells 78%
  • Spatial Analysis 42%
  4 Scopus citations

• Erratum: Mitochondrial Uncoupling Induces Epigenome Remodeling and Promotes Differentiation in Neuroblastoma (Cancer Res (2023) 83 (181–94) DOI: 10.1158/0008-5472.CAN-22-1029)

  Jiang, H., Greathouse, R., Tiche, S., Zhao, M., He, B., Li, Y., Li, A. M., Forgo, B., Yip, M., Li, A., Shih, M., Banuelos, S., Zhou, M. N., Gruber, J. J., Rankin, E. B., Hu, Z., Shimada, H., Chiu, B. & Ye, J., Jan 15 2023, In: Cancer research. 83, 2, p. 346 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Epigenome 100%
  • Neuroblastoma 80%
  • Progression-Free Survival 72%
  • Datasets 63%
  • Genes 32%

• FDA approved drugs with antiviral activity against SARS-CoV-2: From structure-based repurposing to host-specific mechanisms

  Ahmed, M. S., Farag, A. B., Boys, I. N., Wang, P., Menendez-Montes, I., Nguyen, N. U. N., Eitson, J. L., Ohlson, M. B., Fan, W., McDougal, M. B., Mar, K., Thet, S., Ortiz, F., Kim, S. Y., Solmonson, A., Williams, N. S., Lemoff, A., DeBerardinis, R. J., Schoggins, J. W. & Sadek, H. A., Jun 2023, In: Biomedicine and Pharmacotherapy. 162, 114614.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Atovaquone 100%
  • SARS Virus 91%
  • Mebendazole 57%
  • Antiviral Agents 53%
  • Inhibitory Concentration 50 35%
  5 Scopus citations

• Functional partitioning of transcriptional regulators by patterned charge blocks

  Lyons, H., Veettil, R. T., Pradhan, P., Fornero, C., De La Cruz, N., Ito, K., Eppert, M., Roeder, R. G. & Sabari, B. R., Jan 19 2023, In: Cell. 186, 2, p. 327-345.e28

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Block Like Crystal 100%
  • Transcriptional Activation 67%
  • Protein 61%
  • Proteins 54%
  • RNA Polymerase II 43%
  50 Scopus citations

• Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease

  Owen, D. M., Kwon, M., Huang, X., Nagari, A., Nandu, T. & Lee Kraus, W., Dec 1 2023, In: Biology of reproduction. 109, 6, p. 965-981 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Placentation 100%
  • Human Development 85%
  • Transcription Factors 59%
  • Genome 53%
  • Placenta 49%

• Global chromatin landscapes identify candidate noncoding modifiers of cardiac rhythm

  Bhattacharyya, S., Kollipara, R. K., Orquera-Tornakian, G., Goetsch, S., Zhang, M., Perry, C., Li, B., Shelton, J. M., Bhakta, M., Duan, J., Xie, Y., Xiao, G., Evers, B. M., Hon, G. C., Kittler, R. & Munshi, N. V., Feb 1 2023, In: Journal of Clinical Investigation. 133, 3, e153635.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genetic Enhancer Elements 100%
  • Chromatin 69%
  • Transcription Factors 59%
  • Transposases 55%
  • Biomass 48%
  2 Scopus citations

• H3.3 contributes to chromatin accessibility and transcription factor binding at promoter-proximal regulatory elements in embryonic stem cells

  Tafessu, A., O’Hara, R., Martire, S., Dube, A. L., Saha, P., Gant, V. U. & Banaszynski, L. A., Dec 2023, In: Genome biology. 24, 1, 25.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • embryonic stem cells 100%
  • Embryonic Stem Cells 84%
  • accessibility 75%
  • stem 71%
  • chromatin 70%
  10 Scopus citations

• IL-1β mediates the induction of immune checkpoint regulators IDO1 and PD-L1 in lung adenocarcinoma cells

  Nawas, A. F., Solmonson, A., Gao, B., DeBerardinis, R. J., Minna, J. D., Conacci-Sorrell, M. & Mendelson, C. R., Dec 2023, In: Cell Communication and Signaling. 21, 1, 331.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Indoleamine-Pyrrole 2,3,-Dioxygenase 100%
  • Kynurenine 80%
  • Adenocarcinoma of Lung 78%
  • Interleukin-1 73%
  • Tryptophan 68%
  1 Scopus citations

• Large-scale production of human blastoids amenable to modeling blastocyst development and maternal-fetal cross talk

  Yu, L., Logsdon, D., Pinzon-Arteaga, C. A., Duan, J., Ezashi, T., Wei, Y., Ribeiro Orsi, A. E., Oura, S., Liu, L., Wang, L., Liu, K., Ding, X., Zhan, L., Zhang, J., Nahar, A., Stobbe, C., Katz-Jaffe, M., Schoolcraft, W. B., Tan, T., Hon, G. C., & 2 othersYuan, Y. & Wu, J., Sep 7 2023, In: Cell Stem Cell. 30, 9, p. 1246-1261.e9

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Blastocyst 100%
  • Fetal Development 90%
  • Mothers 55%
  • Trophoblasts 31%
  • Coculture Techniques 29%
  7 Scopus citations

• Modeling post-implantation stages of human development into early organogenesis with stem-cell-derived peri-gastruloids

  Liu, L., Oura, S., Markham, Z., Hamilton, J. N., Skory, R. M., Li, L., Sakurai, M., Wang, L., Pinzon-Arteaga, C. A., Plachta, N., Hon, G. C. & Wu, J., Aug 31 2023, In: Cell. 186, 18, p. 3776-3792.e16

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Sequencing 100%
  • Gastrulation 78%
  • Organogenesis 73%
  • Human Development 64%
  • Stem Cells 44%
  26 Scopus citations

• PASK links cellular energy metabolism with a mitotic self-renewal network to establish differentiation competence

  Xiao, M., Wu, C. H., Meek, G., Kelly, B., Castillo, D. B., Young, L. E. A., Martire, S., Dhungel, S., McCauley, E., Saha, P., Dube, A. L., Gentry, M. S., Banaszynski, L. A., Sun, R. C. & Kikani, C. K., Apr 2023, In: eLife. 12, e81717.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Glutamine 100%
  • Mental Competency 86%
  • Heterogeneity 83%
  • Energy Metabolism 81%
  • Pharmacological Metabolism 70%
  2 Scopus citations

• Phase Separation in Biology and Disease; Current Perspectives and Open Questions

  Boeynaems, S., Chong, S., Gsponer, J., Holt, L., Milovanovic, D., Mitrea, D. M., Mueller-Cajar, O., Portz, B., Reilly, J. F., Reinkemeier, C. D., Sabari, B. R., Sanulli, S., Shorter, J., Sontag, E., Strader, L., Stachowiak, J., Weber, S. C., White, M., Zhang, H., Zweckstetter, M., & 2 othersElbaum-Garfinkle, S. & Kriwacki, R., Mar 1 2023, In: Journal of Molecular Biology. 435, 5, 167971.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Gene Expression Regulation 100%
  • Biological Phenomena 89%
  • Synthetic Biology 64%
  • Phase Transition 58%
  • Protein Biosynthesis 50%
  9 Scopus citations

• Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution

  Mangiameli, S. M., Chen, H., Earl, A. S., Dobkin, J. A., Lesman, D., Buenrostro, J. D. & Chen, F., May 2023, In: Nature methods. 20, 5, p. 686-694 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Illumination 100%
  • Chromatin 99%
  • Epigenomics 98%
  • Oligodendrocyte Precursor Cells 75%
  • Corpus Callosum 62%
  2 Scopus citations

• Protocol to dissociate epithelia from non-pregnant and pregnant mouse cervical tissue for single-cell RNA-sequencing

  Madhukaran, S. P., Hon, G. C. & Mahendroo, M., Dec 15 2023, In: STAR Protocols. 4, 4, 102631.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Sequencing 100%
  • RNA Sequence Analysis 67%
  • Epithelium 46%
  • Dissociation 43%
  • Goblet Cells 36%

• Recessive pathogenic variants in MCAT cause combined oxidative phosphorylation deficiency

  Webb, B. D., Nowinski, S. M., Solmonson, A., Ganesh, J., Rodenburg, R. J., Leandro, J., Evans, A., Vu, H. S., Naidich, T. P., Gelb, B. D., Deberardinis, R. J., Rutter, J. & Houten, S. M., Mar 2023, In: eLife. 12, e68047.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Acyl Carrier Protein 100%
  • Malonyl Coenzyme A 96%
  • Mitochondrial Diseases 79%
  • Fibroblasts 28%
  • Electron Transport 28%
  2 Scopus citations
• 2022

  ADP-ribosyltransferases, an update on function and nomenclature

  Lüscher, B., Ahel, I., Altmeyer, M., Ashworth, A., Bai, P., Chang, P., Cohen, M., Corda, D., Dantzer, F., Daugherty, M. D., Dawson, T. M., Dawson, V. L., Deindl, S., Fehr, A. R., Feijs, K. L. H., Filippov, D. V., Gagné, J. P., Grimaldi, G., Guettler, S., Hoch, N. C., & 27 othersHottiger, M. O., Korn, P., Kraus, W. L., Ladurner, A., Lehtiö, L., Leung, A. K. L., Lord, C. J., Mangerich, A., Matic, I., Matthews, J., Moldovan, G. L., Moss, J., Natoli, G., Nielsen, M. L., Niepel, M., Nolte, F., Pascal, J., Paschal, B. M., Pawłowski, K., Poirier, G. G., Smith, S., Timinszky, G., Wang, Z. Q., Yélamos, J., Yu, X., Zaja, R. & Ziegler, M., Dec 2022, In: FEBS Journal. 289, 23, p. 7399-7410 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • ADP Ribose Transferases 100%
  • ADP-Ribosylation 91%
  • Terminology 67%
  • Poly ADP-ribosylation 58%
  • ADP-ribosylarginine hydrolase 53%
  128 Scopus citations

• Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression

  Hou, T. Y. & Kraus, W. L., Jun 14 2022, In: Cell Reports. 39, 11, 110944.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Enhancer 100%
  • Estrogens 69%
  • RNA 58%
  • Gene Expression 50%
  • Estrogen 45%
  8 Scopus citations

• A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes

  Gruber, J. J., Afghahi, A., Timms, K., DeWees, A., Gross, W., Aushev, V. N., Wu, H. T., Balcioglu, M., Sethi, H., Scott, D., Foran, J., McMillan, A., Ford, J. M. & Telli, M. L., Oct 2022, In: Nature Cancer. 3, 10, p. 1181-1191 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • talazoparib 100%
  • Homologous Recombination 60%
  • Mutation 30%
  • Breast Neoplasms 23%
  • Genes 21%
  32 Scopus citations

• A single factor elicits multilineage reprogramming of astrocytes in the adult mouse striatum

  Zhang, Y., Li, B., Cananzi, S., Han, C., Wang, L. L., Zou, Y., Fu, Y. X., Hon, G. C. & Zhang, C. L., Mar 15 2022, In: Proceedings of the National Academy of Sciences of the United States of America. 119, 11, e2107339119.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Astrocytes 100%
  • Transcription Factors 32%
  • Cell Plasticity 28%
  • Neural Stem Cells 24%
  • Oligodendroglia 23%
  20 Scopus citations

• Cell type-specific inference of differential expression in spatial transcriptomics

  Cable, D. M., Murray, E., Shanmugam, V., Zhang, S., Zou, L. S., Diao, M., Chen, H., Macosko, E. Z., Irizarry, R. A. & Chen, F., Sep 2022, In: Nature methods. 19, 9, p. 1076-1087 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Additive 100%
  • Simulation 93%
  • Mixture 64%
  • Cellular Microenvironment 28%
  • Cell Communication 10%
  23 Scopus citations

• Chromatin accessibility analysis from fresh and cryopreserved human ovarian follicles

  Shannon, J., Sundaresan, A., Bukulmez, O., Jiao, Z., Doody, K., Capelouto, S., Carr, B. & Banaszynski, L. A., Jun 1 2022, In: Molecular Human Reproduction. 28, 6, gaac020.

  Research output: Contribution to journal › Article › peer-review

  • Ovarian Follicle 100%
  • Chromatin 70%
  • Cryopreservation 70%
  • Transposases 56%
  • Fertility 56%
  2 Scopus citations

• CK2-mediated phosphorylation of SUZ12 promotes PRC2 function by stabilizing enzyme active site

  Gong, L., Liu, X., Jiao, L., Yang, X., Lemoff, A. & Liu, X., Dec 2022, In: Nature communications. 13, 1, 6781.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Polycomb Repressive Complex 2 100%
  • phosphorylation 91%
  • Casein Kinase II 87%
  • enzymes 69%
  • Catalytic Domain 58%
  5 Scopus citations

• Combinatorial Treatment with PARP-1 Inhibitors and Cisplatin Attenuates Cervical Cancer Growth through Fos-Driven Changes in Gene Expression

  Gupte, R., Lin, K. Y., Nandu, T., Lea, J. S. & Lee Kraus, W., Aug 2022, In: Molecular Cancer Research. 20, 8, p. 1183-1192 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Poly(ADP-ribose) Polymerase Inhibitors 100%
  • Uterine Cervical Neoplasms 69%
  • Cisplatin 68%
  • Gene Expression 45%
  • Growth 38%
  6 Scopus citations

• Compartmentalized metabolism supports midgestation mammalian development

  Solmonson, A., Faubert, B., Gu, W., Rao, A., Cowdin, M. A., Menendez-Montes, I., Kelekar, S., Rogers, T. J., Pan, C., Guevara, G., Tarangelo, A., Zacharias, L. G., Martin-Sandoval, M. S., Do, D., Pachnis, P., Dumesnil, D., Mathews, T. P., Tasdogan, A., Pham, A., Cai, L., & 6 othersZhao, Z., Ni, M., Cleaver, O., Sadek, H. A., Morrison, S. J. & DeBerardinis, R. J., Apr 14 2022, In: Nature. 604, 7905, p. 349-353 5 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Embryonic Structures 100%
  • Citric Acid Cycle 90%
  • Placenta 68%
  • Isotopes 52%
  • Tricarboxylic Acids 41%
  44 Scopus citations

• Computational identification of clonal cells in single-cell CRISPR screens

  Wang, Y., Xie, S., Armendariz, D. & Hon, G. C., Dec 2022, In: BMC Genomics. 23, 1, 135.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Clustered Regularly Interspaced Short Palindromic Repeats 100%
  • Clone Cells 12%
  • Transcriptome 7%
  • Genome 5%
  • Phenotype 4%
  2 Scopus citations

• Context is key: Modulated protein multivalency in disease

  Eppert, M. & Sabari, B. R., Nov 3 2022, In: Molecular cell. 82, 21, p. 3965-3967 3 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Gene Expression 100%
  • Mutation 93%
  • Proteins 61%
  1 Scopus citations

• Developmental dynamics of RNA translation in the human brain

  Duffy, E. E., Finander, B., Choi, G. H., Carter, A. C., Pritisanac, I., Alam, A., Luria, V., Karger, A., Phu, W., Sherman, M. A., Assad, E. G., Pajarillo, N., Khitun, A., Crouch, E. E., Ganesh, S., Chen, J., Berger, B., Sestan, N., O’Donnell-Luria, A., Huang, E. J., & 5 othersGriffith, E. C., Forman-Kay, J. D., Moses, A. M., Kalish, B. T. & Greenberg, M. E., Oct 2022, In: Nature neuroscience. 25, 10, p. 1353-1365 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA 100%
  • Brain 70%
  • Ribosomes 60%
  • Glycine 58%
  • Open Reading Frames 55%
  20 Scopus citations

• Development and characterization of new tools for detecting poly(ADP-ribose) in vitro and in vivo

  Challa, S., Ryu, K. W., Whitaker, A. L., Abshier, J. C., Camacho, C. V. & Kraus, W. L., Apr 2022, In: eLife. 11, e72464.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Adenosine Diphosphate Ribose 100%
  • Poly Adenosine Diphosphate Ribose 96%
  • Poly(ADPribose) 93%
  • Modification 38%
  • ADP-Ribosylation 31%
  10 Scopus citations

• Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells

  Wu, D., Poddar, A., Ninou, E., Hwang, E., Cole, M. A., Liu, S. J., Horlbeck, M. A., Chen, J., Replogle, J. M., Carosso, G. A., Eng, N. W. L., Chang, J., Shen, Y., Weissman, J. S. & Lim, D. A., Nov 9 2022, In: Cell Genomics. 2, 11, 100177.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Induced Pluripotent Stem Cells 100%
  • Long Noncoding RNA 95%
  • Genome 60%
  • Clustered Regularly Interspaced Short Palindromic Repeats 25%
  • Genes 17%
  7 Scopus citations

• Endogenous retroviruses steer transcriptional condensates away from pluripotency

  Grow, E. J., Aug 2022, In: Nature genetics. 54, 8, p. 1068-1069 2 p.

  Research output: Contribution to journal › Comment/debate › peer-review

• Functional Characterization of lncRNA152 as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers

  Kim, D. S., Camacho, C. V., Setlem, R., Kim, K., Malladi, S., Hou, T. Y., Nandu, T., Gadad, S. S. & Kraus, W. L., Nov 2022, In: Molecular Cancer Research. 20, 11, p. 1623-1635 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Triple Negative Breast Neoplasms 100%
  • Neoplasms 26%
  • Breast Neoplasms 26%
  • Heterografts 24%
  • Down-Regulation 19%
  6 Scopus citations

• High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways

  Marshall, J. L., Noel, T., Wang, Q. S., Chen, H., Murray, E., Subramanian, A., Vernon, K. A., Bazua-Valenti, S., Liguori, K., Keller, K., Stickels, R. R., McBean, B., Heneghan, R. M., Weins, A., Macosko, E. Z., Chen, F. & Greka, A., Apr 15 2022, In: iScience. 25, 4, 104097.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Kidney 100%
  • Macrophages 87%
  • Unfolded Protein Response 77%
  • Diabetic Nephropathies 65%
  • Poisons 46%
  22 Scopus citations

• In vivo hypermutation and continuous evolution

  Molina, R. S., Rix, G., Mengiste, A. A., Álvarez, B., Seo, D., Chen, H., Hurtado, J. E., Zhang, Q., García-García, J. D., Heins, Z. J., Almhjell, P. J., Arnold, F. H., Khalil, A. S., Hanson, A. D., Dueber, J. E., Schaffer, D. V., Chen, F., Kim, S., Fernández, L. Á., Shoulders, M. D., & 1 othersLiu, C. C., Dec 2022, In: Nature Reviews Methods Primers. 2, 1, 36.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Mutation 100%
  • Protein Engineering 80%
  • Genes 47%
  • Protein 24%
  35 Scopus citations

• Machine learning predicts translation initiation sites in neurologic diseases with nucleotide repeat expansions

  Gleason, A. C., Ghadge, G., Chen, J., Sonobe, Y. & Roos, R. P., Jun 2022, In: PloS one. 17, 6 June, e0256411.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Machine Learning 100%
  • Nervous System Diseases 82%
  • Nucleotides 71%
  • Initiator Codon 36%
  • Amyotrophic Lateral Sclerosis 31%
  9 Scopus citations

• Multiomics analysis of the NAD⁺–PARP1 axis reveals a role for site-specific ADP-ribosylation in splicing in embryonic stem cells

  Jones, A. & Kraus, W. L., May 1 2022, In: Genes and Development. 36, 9-10, p. 601-617 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • ADP-Ribosylation 100%
  • Mouse Embryonic Stem Cells 89%
  • Embryonic Stem Cells 77%
  • NAD 74%
  • Metabolomics 26%
  5 Scopus citations

• Oncohistone Mutations Occur at Functional Sites of Regulatory ADP-Ribosylation

  Huang, D., Camacho, C. V., Martire, S., Nagari, A., Setlem, R., Gong, X., Edwards, A. D., Chiu, S. P., Banaszynski, L. A. & Lee Kraus, W., Jul 1 2022, In: Cancer research. 82, 13, p. 2361-2377 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • ADP-Ribosylation 100%
  • Histones 68%
  • Mutation 40%
  • Growth 26%
  • Neoplasms 20%
  4 Scopus citations

• PRC2, Chromatin Regulation, and Human Disease: Insights From Molecular Structure and Function

  Liu, X. & Liu, X., Jun 21 2022, In: Frontiers in Oncology. 12, 894585.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Polycomb Repressive Complex 2 100%
  • Molecular Structure 78%
  • Chromatin 57%
  • Methylation 17%
  • Histones 12%
  10 Scopus citations

• Standardized annotation of translated open reading frames

  Mudge, J. M., Ruiz-Orera, J., Prensner, J. R., Brunet, M. A., Calvet, F., Jungreis, I., Gonzalez, J. M., Magrane, M., Martinez, T. F., Schulz, J. F., Yang, Y. T., Albà, M. M., Aspden, J. L., Baranov, P. V., Bazzini, A. A., Bruford, E., Martin, M. J., Calviello, L., Carvunis, A. R., Chen, J., & 15 othersCouso, J. P., Deutsch, E. W., Flicek, P., Frankish, A., Gerstein, M., Hubner, N., Ingolia, N. T., Kellis, M., Menschaert, G., Moritz, R. L., Ohler, U., Roucou, X., Saghatelian, A., Weissman, J. S. & van Heesch, S., Jul 2022, In: Nature biotechnology. 40, 7, p. 994-999 6 p.

  Research output: Contribution to journal › Letter › peer-review

  Open Access
  59 Scopus citations

• The dark proteome: translation from noncanonical open reading frames

  Wright, B. W., Yi, Z., Weissman, J. S. & Chen, J., Mar 2022, In: Trends in Cell Biology. 32, 3, p. 243-258 16 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Proteome 100%
  • Open Reading Frames 92%
  • Genome 65%
  • Biological Phenomena 30%
  • Technology 20%
  47 Scopus citations

• The expanding universe of PARP1-mediated molecular and therapeutic mechanisms

  Huang, D. & Kraus, W. L., Jun 16 2022, In: Molecular cell. 82, 12, p. 2315-2334 20 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • ADP-Ribosylation 100%
  • Poly(ADP-ribose) Polymerase Inhibitors 96%
  • Post Translational Protein Processing 74%
  • Biological Phenomena 70%
  • Gene Expression Regulation 39%
  71 Scopus citations

• Two birds, one stone: Non-canonical therapeutic effects of the PARP inhibitor Talazoparib

  Challa, S. & Kraus, W. L., Feb 17 2022, In: Cell Chemical Biology. 29, 2, p. 171-173 3 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • talazoparib 100%
  • Poly(ADP-ribose) Polymerase Inhibitors 71%
  • Birds 58%
  • Therapeutic Uses 44%
  • Cell Biology 23%
  2 Scopus citations
• 2021

  A crispr/cas9-engineered arid1a-deficient human gastric cancer organoid model reveals essential and nonessential modes of oncogenic transformation

  Lo, Y. H., Kolahi, K. S., Du, Y., Chang, C. Y., Krokhotin, A., Nair, A., Sobba, W. D., Karlsson, K., Jones, S. J., Longacre, T. A., Mah, A. T., Tercan, B., Sockell, A., Xu, H., Seoane, J. A., Chen, J., Shmulevich, I., Weissman, J. S., Curtis, C., Califano, A., & 3 othersFu, H., Crabtree, G. R. & Kuo, C. J., 2021, In: Cancer discovery. 11, 6, p. 1562-1581 20 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Organoids 100%
  • Stomach Neoplasms 65%
  • Survivin 30%
  • Clustered Regularly Interspaced Short Palindromic Repeats 29%
  • Mutation 28%
  75 Scopus citations