Publications

Olsson, A; Venkatasubramanian, M; Chaudhri, VK; Aronow, BJ; Salomonis, N; Singh, H; Grimes, HL. Single-cell analysis of mixed-lineage states leading to a binary cell fate choice. Nature. 2016; 537:698-702.

Avellino, R; Mulet-Lazaro, R; Havermans, M; Hoogenboezem, R; Smeenk, L; Salomonis, N; Schneider, RK; Rombouts, E; Bindels, E; Grimes, L; et al. Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice. Blood Advances. 2022; 6:1406-1419.

Bono, C; Guerrero, P; Jordán-Pla, A; Erades, A; Salomonis, N; Grimes, HL; Gil, ML; Yáñez, A. GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection. Frontiers in Immunology. 2021; 12.

Zhang, X; Grimes, HL. Why Single-Cell Sequencing Has Promise in MDS. Frontiers in Oncology. 2021; 11.

Li, G; Song, B; Singh, H; Prasath, S; Grimes, L; Salomonis, N. scTriangulate, a game-theory based framework for optimal solutions of uni- and multimodal single-cell data. 2021.

Steele, H; Song, B; Willicut, A; Grimes, HL; Herro, R. Isolation of primary immune cells from fibrotic skin, esophageal, and gut tissue. Journal of Immunological Methods. 2021; 497.

Basu, J; Reis, BS; Peri, S; Zha, J; Hua, X; Ge, L; Ferchen, K; Nicolas, E; Czyzewicz, P; Cai, KQ; et al. Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4+ T cell identity and function. Nature Immunology. 2021; 22:969-982.

Serrano-Lopez, J; Hegde, S; Kumar, S; Serrano, J; Fang, J; Wellendorf, AM; Roche, PA; Rangel, Y; Carrington, LJ; Geiger, H; et al. Inflammation rapidly recruits mammalian GMP and MDP from bone marrow into regional lymphatics. eLife. 2021; 10.

Serrano-Lopez, J; Hegde, S; Kumar, S; Serrano, J; Fang, J; Wellendorf, AM; Roche, PA; Rangel, Y; Carrington, LJ; Geiger, H; et al. Systemic inflammation recruits fast-acting anti-inflammatory innate myeloid progenitors from BM into lymphatics. eLife. 2021; 10:1-60.

Zhang, J; Wu, Q; Johnson, CB; Pham, G; Kinder, JM; Olsson, A; Slaughter, A; May, M; Weinhaus, B; D’Alessandro, A; et al. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature. 2021; 590:457-462.

Ye, H; Minhajuddin, M; Krug, A; Pei, S; Chou, C; Culp-Hill, R; Ponder, J; De Bloois, E; Schniedewind, B; Amaya, ML; et al. The Hepatic Microenvironment Uniquely Protects Leukemia Cells through Induction of Growth and Survival Pathways Mediated by LIPG. Cancer Discovery. 2021; 11:500-519.

Dwivedi, P; Chutipongtanate, S; Muench, DE; Azam, M; Grimes, HL; Greis, KD. SWATH-Proteomics of Ibrutinib's Action in Myeloid Leukemia Initiating Mutated G-CSFR Signaling. Proteomics - Clinical Applications. 2020; 14.

Kwok, I; Becht, E; Xia, Y; Ng, M; Teh, YC; Tan, L; Evrard, M; Li, JL Y; Tran, HT N; Tan, Y; et al. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Immunity. 2020; 53:303-318.e5.

Muench, DE; Olsson, A; Ferchen, K; Pham, G; Serafin, RA; Chutipongtanate, S; Dwivedi, P; Song, B; Hay, S; Chetal, K; et al. Mouse models of neutropenia reveal progenitor-stage-specific defects. Nature. 2020; 582:109-114.

Hinge, A; He, J; Bartram, J; Javier, J; Xu, J; Fjellman, E; Sesaki, H; Li, T; Yu, J; Wunderlich, M; et al. Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell. 2020; 26:420-430.e6.

Yue, L; Sharma, V; Horvat, NP; Akuffo, AA; Beatty, MS; Murdun, C; Colin, C; Billington, JM R; Goodheart, WE; Sahakian, E; et al. HDAC11 deficiency disrupts oncogene-induced hematopoiesis in myeloproliferative neoplasms. Blood. 2020; 135:191-207.

Lucas, D; Salomonis, N; Grimes, HL. Unraveling bone marrow architecture. Nature Cell Biology. 2020; 22:5-6.

DePasquale, EA K; Schnell, D; Dexheimer, P; Ferchen, K; Hay, S; Chetal, K; Valiente-Alandi, I; Blaxall, BC; Grimes, HL; Salomonis, N. cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes. Nucleic Acids Research. 2019; 47.

Lee, C; Rudneva, VA; Erkek, S; Zapatka, M; Chau, LQ; Tacheva-Grigorova, SK; Garancher, A; Rusert, JM; Aksoy, O; Lea, R; et al. Lsd1 as a therapeutic target in Gfi1-activated medulloblastoma. Nature Communications. 2019; 10.

Dwivedi, P; Muench, DE; Wagner, M; Azam, M; Grimes, HL; Greis, KD. Phospho serine and threonine analysis of normal and mutated granulocyte colony stimulating factor receptors. Scientific data. 2019; 6.

DePasquale, EA K; Schnell, DJ; Van Camp, P; Valiente-Alandi, I; Blaxall, BC; Grimes, HL; Singh, H; Salomonis, N. DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data. Cell Reports. 2019; 29:1718-1727.e8.

Adelman, ER; Huang, HT; Roisman, A; Olsson, A; Colaprico, A; Qin, T; Lindsley, RC; Bejar, R; Salomonis, N; Grimes, HL; et al. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discovery. 2019; 9:1080-1101.

Duy, C; Teater, M; Garrett-Bakelman, FE; Lee, TC; Meydan, C; Glass, JL; Li, M; Hellmuth, JC; Mohammad, HP; Smitheman, KN; et al. Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML. Cancer Discovery. 2019; 9:872-889.

Park, DS; Akuffo, AA; Muench, DE; Grimes, HL; Epling-Burnette, PK; Maini, PK; Anderson, AR A; Bonsall, MB. Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation. PLoS Computational Biology. 2019; 15.

Dwivedi, P; Muench, DE; Wagner, M; Azam, M; Grimes, HL; Greis, KD. Time resolved quantitative phospho-tyrosine analysis reveals Bruton's Tyrosine kinase mediated signaling downstream of the mutated granulocyte-colony stimulating factor receptors. Leukemia. 2019; 33:75-87.

Hay, SB; Ferchen, K; Chetal, K; Grimes, HL; Salomonis, N. The Human Cell Atlas bone marrow single-cell interactive web portal. Experimental Hematology. 2018; 68:51-61.

Muench, DE; Ferchen, K; Velu, CS; Pradhan, K; Chetal, K; Chen, X; Weirauch, MT; Colmenares, C; Verma, A; Salomonis, N; et al. SKI controls MDS-associated chronic TGF-β signaling, aberrant splicing, and stem cell fitness. Blood. 2018; 132:e24-e34.

Lu, Y; Xavier-Ferrucio, J; Wang, L; Zhang, P; Grimes, HL; Venkatasubramanian, M; Chetal, K; Aronow, B; Salomonis, N; Krause, DS. The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Reports. 2018; 25:2083-2093.e4.

Hayashi, Y; Zhang, Y; Yokota, A; Yan, X; Liu, J; Choi, K; Li, B; Sashida, G; Peng, Y; Xu, Z; et al. Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. Cancer Discovery. 2018; 8:1438-1457.

DePasquale, EA K; Dexheimer, P; Schnell, D; Ferchen, K; Hay, S; Valiente-Alandí, Í; Blaxall, B; Grimes, L; Salomonis, N. cellHarmony: Cell-level matching and holistic comparison of single-cell transcriptomes. 2018.

Muench, D; Ferchen, K; Pham, G; Hay, S; Zhang, K; Myers, K; Kappes, D; Way, SS; Salomonis, N; Grimes, HL. 3121 Severe Congenital Neutropenia-Associated Mutations Reveal Stage-Specific GFI1-Dependent Checkpoints in Myeloid Development. Experimental Hematology. 2018; 64.

Muench, D; Ferchen, K; Olsson, A; Dwivedi, P; Greis, K; Verma, A; Salomonis, N; Grimes, HL. 3122 Understanding Early Stage Myelodysplastic Syndrome Pathobiology. Experimental Hematology. 2018; 64.

Yáñez, A; Coetzee, S; Olsson, A; Muench, D; Berman, B; Hazelett, D; Salomonis, N; Grimes, HL; Goodridge, H. 3195 Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Experimental Hematology. 2018; 64.

Grimes, H; Venkatasubramanian, M; Chou, C; Olsson, A; Chen, X; Chetal, K; Newkold, T; Kulkarni, A; Meyers, K; Weirauch, M; et al. 3050 Global Unsupervised Splicing Analysis of Leukemia Reveals a Persistent Prognostic Signature That Precurses Oncogenesis. Experimental Hematology. 2018; 64.

DePasquale, EA K; Schnell, D; Valiente-Alandí, Í; Blaxall, B; Grimes, L; Singh, H; Salomonis, N. DoubletDecon: Cell-State Aware Removal of Single-Cell RNA-Seq Doublets. 2018.

Zhou, Y; Yan, X; Feng, X; Bu, J; Dong, Y; Lin, P; Hayashi, Y; Huang, R; Olsson, A; Andreassen, PR; et al. Setd2 regulates quiescence and differentiation of adult hematopoietic stem cells by restricting RNA polymerase II elongation. Haematologica. 2018; 103:1110-1123.

Zhang, C; D'Alessandro, A; Wellendorf, AM; Mohmoud, F; Serrano-Lopez, J; Perentesis, JP; Komurov, K; Alexe, G; Stegmaier, K; Whitsett, JA; et al. KLF5 controls glutathione metabolism to suppress p190-BCR-ABL+ B-cell lymphoblastic leukemia. Oncotarget. 2018; 9:29665-29679.

Kleeman, B; Olsson, A; Newkold, T; Kofron, M; DeLay, M; Hildeman, D; Grimes, HL. A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Cytometry. Part A : the journal of the International Society for Analytical Cytology. 2018; 93:556-562.

Bu, J; Chen, A; Yan, X; He, F; Dong, Y; Zhou, Y; He, J; Zhan, D; Lin, P; Hayashi, Y; et al. SETD2-mediated crosstalk between H3K36me3 and H3K79me2 in MLL-rearranged leukemia. Leukemia. 2018; 32:890-899.

Lee, J; Govindarajah, V; Goddard, B; Hinge, A; Muench, DE; Filippi, M; Aronow, B; Cancelas, JA; Salomonis, N; Grimes, HL; et al. Obesity alters the long-term fitness of the hematopoietic stem cell compartment through modulation of Gfi1 expression. Journal of Experimental Medicine. 2018; 215:627-644.