2024
Abstract PO2-28-08: A spatial transcriptomic study of a triple-negative breast cancer (TNBC) patient-derived xenograft (PDX) model of residual disease refractory to conventional chemotherapy
B. Strope, K. Pendleton, W. Bowie, G. Echeverria, Q. Zhu
Cancer Research (2024) https://doi.org/10.1158/1538-7445.SABCS23-PO2-28-08
Abstract 2335: MultiNMF: multiview factorization for joint modeling of spatial multi-omics and histology images
W. Bowie, S. Wang, B. Strope, Q. Zhu
Cancer Research (2024) https://doi.org/10.1158/1538-7445.AM2024-2335
Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and
European American patients with TNBC
Q. Zhu*, A. Balasubramanian*, J.R. Asirvatham*, ..., S. Wang, ... , Y. Li, E. Chang, X. Li, R. Aneja, X. H.-F. Zhang, A. Sreekumar
BioRxiv (2024) https://doi.org/10.1101/2024.03.17.585428 * - co-first authors
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Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments
B.S. Strope, K.E. Pendleton, W.Z. Bowie, G.V. Echeverria, Q. Zhu
Bioinformatics (2024) Accepted
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Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions
T. Liu*, Q. Zhu*, Y. Kai, T. Bingham, S. Wang, H.J. Cha, S. Mehta, T.M. Schlaeger, G. Yuan & S.H. Orkin
Nature Communications (2024) https://doi.org/10.1038/s41467-024-45386-w * - co-first authors
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2023
In vivo CRISPR/Cas9 screening identifies Pbrm1 as a regulator of myeloid leukemia development in mice
B.E. Li, G.Y. Li, W. Cai, Q. Zhu, D. Seruggia, Y. Fujiwara, C.R. Vakoc, S.H. Orkin
Blood Advances (2023) doi:10.1182/bloodadvances.2022009455
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1026 – REWIRING OF TRANSCRIPTION FACTOR NETWORKS DURING THE FETAL TO ADULT TRANSITION IN HSCS
G. Rowe, M. Yano, D. Wang, B. Isaac, T. Liu, G.F.R. Luiz, E.L. da Rocha, S. Orkin, L. Sun, Q. Zhu
Experimental Hematology (2023) https://doi.org/10.1016/j.exphem.2023.06.032
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2022
Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells
S. Mehta, A. Buyanbat, Y. Kai, O. Karayel, S.R. Goldman, D. Seruggia, K. Zhang, Y. Fujiwara, K.A. Donovan, Q. Zhu, H. Yang, ... , K. Adelman, S.H. Orkin
Cell Chemical Biology (2022) DOI: 10.1016/j.chembiol.2022.06.007
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IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia
B.J. Aubrey, J.A. Cutler, W.Bourgeois, K.A.Donovan, ..., Q. Zhu, ... X.S. Liu & S.A. Armstrong
Nature Cancer (2022) https://doi.org/10.1038/s43018-022-00366-1
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Developmental maturation of the hematopoietic
system controlled by a Lin28b-let-7-Cbx2 axis
D. Wang, M. Tanaka-Yano, E. Meader, M.A. Kinney, V. Morris, E.L. da Rocha, N. Liu, T. Liu, Q. Zhu, S.H. Orkin, T.E. North, G.Q. Daley, R.G. Rowe
Cell Reports (2022) DOI: 10.1016/j.celrep.2022.110587
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A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia
T. Harada*, Y. Heshmati*, J. Kalfon*, M.W. Perez, ..., Q. Zhu, ..., S.H. Orkin, M. Pimkin
Genes & Development (2022) DOI: 10.1101/gad.349284.121 * - co-first author
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2021
Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture
H.J. Cha, O. Uyan, Y. Kai, T. Liu, Q. Zhu, Z. Tothova, G.A. Botten, J. Xu, G. Yuan, J. Dekker & S.H. Orkin
Nature Communications (2021) https://doi.org/10.1038/s41467-021-26574-4
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Transcription factor competition at the γ-globin promoters controls hemoglobin switching
N. Liu, S. Xu, Q. Yao, Q. Zhu, Y. Kai, J.Y. Hsu, P. Sakon, L. Pinello, G. Yuan, D.E. Bauer & S.H. Orkin
Nature Genetics (2021) https://doi.org/10.1038/s41588-021-00798-y
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Giotto, a toolbox for integrative analysis and visualization of spatial expression data
R. Dries*, Q. Zhu*, R. Dong, CH.L. Eng, H. Li, K. Liu, Y. Fu, T. Zhao, A. Sarkar, F. Bao, R.E. George, N. Pierson, L. Cai & G. Yuan
Genome Biology (2021) https://doi.org/10.1101/701680v2. * - co-first authors
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2020
Enhancer dependence of cell-type–specific gene expression increases with developmental age
W. Cai, J. Huang, Q. Zhu, B.E. Li, D. Seruggia, P. Zhou, M. Nguyen, Y. Fujiwara, H. Xie, Z. Yang, D. Hong, P. Ren, J. Xu, W.T. Pu, G. Yuan & S.H. Orkin
PNAS (2020) DOI: 10.1073/pnas.2008672117
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Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations
Q. Zhu, X. Tekpli, O.G. Troyanskaya, V.N. Kristensen
Bioinformatics (2020) https://doi.org/10.1093/bioinformatics/btz709
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2019
CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis
Q. Zhu, N. Liu, S.H. Orkin & G. Yuan
Genome Biology (2019) https://doi.org/10.1186/s13059-019-1802-4
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Accurate estimation of cell-type composition from gene expression data
D. Tsoucas, R. Dong, H. Chen, Q. Zhu, G. Guo & G. Yuan
Nature Communications (2019) https://doi.org/10.1038/s41467-019-10802-z
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Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
C.L. Eng, M. Lawson, Q. Zhu, R. Dries, N. Koulena, Y. Takei, J. Yun, C. Cronin, C. Karp, G. Yuan & L. Cai
Nature (2019) https://doi.org/10.1038/s41586-019-1049-y
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A Hidden Markov Random Field Model for Detecting Domain Organizations from Spatial Transcriptomic Data
Q. Zhu
Computational Methods for Single-Cell Data Analysis (2019) https://doi.org/10.1007/978-1-4939-9057-3_16
2018
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data
Q. Zhu, S. Shah, R. Dries, L. Cai & G. Yuan
Nature Biotechnology (2018) https://doi.org/10.1038/nbt.4260
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Revealing the Critical Regulators of Cell Identity in
the Mouse Cell Atlas
S. Suo, Q. Zhu, A. Saadatpour, L. Fei, G. Guo, G. Yuan
Cell Reports (2018) DOI: 10.1016/j.celrep.2018.10.045
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A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data
A.V. Rangan, C.C. McGrouther, J. Kelsoe, N. Schork, E. Stahl, Q. Zhu, A. Krishnan, ... ,Bipolar Disorders Working Group of the Psychiatric Genomics Consortium
PLoS Computational Biology (2018) https://doi.org/10.1371/journal.pcbi.1006105
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Direct Promoter Repression by BCL11A Controls the
Fetal to Adult Hemoglobin Switch
N. Liu*, V.V. Hargreaves*, Q. Zhu*, J.V. Kurland, J. Hong, W. Kim, F. Sher, C. Macias-Trevino, ... , G. Yuan, D.E. Bauer, J. Xu, M.L. Bulyk, S.H. Orkin
Cell (2018) https://doi.org/10.1016/j.cell.2018.03.016 * - co-first authors
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2017
Fetal Hemoglobin (HbF) Silencer BCL11A Acts through a Novel DNA-Motif in the Gamma-Globin Promoters, Simplifying the Model for Hemoglobin Switching
N. Liu, V.V. Hargreaves, J. Hong, W. Kim, J. Kurland, Q. Zhu, F. Sher, C. Macias-Trevino, J. Rogers, G. Yuan, D.E. Bauer, J. Xu, M.L. Bulyk, S.H. Orkin
Blood (2017) https://doi.org/10.1182/blood.V130.Suppl_1.283.283
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IFNγ-Dependent Tissue-Immune Homeostasis Is Co-opted in the Tumor Microenvironment
C.J. Nirschl, M. Suárez-Fariñas, B. Izar, S. Prakadan, R. Dannenfelser, I. Tirosh, Y. Liu, Q. Zhu, ..., N. Anandasabapathy
Cell (2017) https://doi.org/10.1016/j.cell.2017.06.016
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2015
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms
C.Y. Park, A. Krishnan, Q. Zhu, A.K. Wong, Y.S. Lee, O.G. Troyanskaya
Bioinformatics (2015) https://doi.org/10.1093/bioinformatics/btu786
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Targeted exploration and analysis of large cross-platform human transcriptomic compendia
Q. Zhu, A.K. Wong, A. Krishnan, M.R. Aure, A. Tadych, R. Zhang, D.C. Corney, C.S. Greene, L.A. Bongo, V.N. Kristensen, M. Charikar, K. Li & O.G. Troyanskaya
Nature Methods (2015) https://doi.org/10.1038/nmeth.3249
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2013
Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies
Y.S. Lee, A. Krishnan, Q. Zhu, O.G. Troyanskaya
Bioinformatics (2013) https://doi.org/10.1093/bioinformatics/btt529
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Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors
M.R. Aure, S.K. Leivonen, T. Fleischer, Q. Zhu, J. Overgaard, J. Alsner, T. Tramm, R. Louhimo, ..., K.K. Sahlberg & V.N. Kristensen
Genome Biology (2013) https://doi.org/10.1186/gb-2013-14-11-r126
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Defining cell-type specificity at the transcriptional level in human disease
W.Ju, C.S. Greene, F. Eichinger, V. Nair, J.B. Hodgin, M. Bitzer, Y.S. Lee, Q. Zhu, M. Kehata, ... , C.D. Cohen, O.G. Troyanskaya & M. Kretzler
Genome Research (2013) doi:10.1101/gr.155697.113
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2010
Scaffold filling, contig fusion and comparative gene order inference
A. Muñoz, C. Zheng, Q. Zhu, V.A. Albert, S. Rounsley & D. Sankoff
BMC Bioinformatics (2010) https://doi.org/10.1186/1471-2105-11-304
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The collapse of gene complement following whole genome duplication
D. Sankoff, C. Zheng & Q. Zhu
BMC Genomics (2010) https://doi.org/10.1186/1471-2164-11-313
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Issues in the Reconstruction of Gene Order Evolution
D. Sankoff, C. Zheng, A. Muñoz, Z. Yang, Z. Adam, R. Warren, V. Choi & Q. Zhu
Journal of Computer Science and Technology (2010) https://doi.org/10.1007/s11390-010-9301-9
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2009
Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution
Q. Zhu, Z. Adam, V. Choi, D. Sankoff
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2009) doi: 10.1109/TCBB.2008.121
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2008
Descendants of Whole Genome Duplication within Gene Order Phylogeny
C. Zheng, Q. Zhu & D. Sankoff
Journal of Computational Biology (2008) https://doi.org/10.1089/cmb.2008.0118
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes
C. Zheng, Q. Zhu, Z. Adam, D. Sankoff
Bioinformatics (2008) https://doi.org/10.1093/bioinformatics/btn146
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2007
Removing Noise and Ambiguities from Comparative Maps in Rearrangement Analysis
C. Zheng, Q. Zhu, D. Sankoff
IEEE/ACM Transactions on Computational Biology and Bioinformatics (2007) doi: 10.1109/TCBB.2007.1075
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Polyploids, genome halving and phylogeny
D. Sankoff, C. Zheng, Q. Zhu
Bioinformatics (2007) https://doi.org/10.1093/bioinformatics/btm169
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Parts of the Problem of Polyploids in Rearrangement Phylogeny
C. Zheng, Q. Zhu, D. Sankoff
Comparative Genomics (2007) https://doi.org/10.1007/978-3-540-74960-8_13
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Algorithms for the Extraction of Synteny Blocks from Comparative Maps
V. Choi, C. Zheng, Q. Zhu & D. Sankoff
Algorithms in Bioinformatics (2007) https://doi.org/10.1007/978-3-540-74126-8_26
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2006
Genome Halving with an Outgroup
C. Zheng, Q. Zhu & D. Sankoff
Evolutionary Bioinformatics (2006) https://doi.org/10.1177/117693430600200028
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