Publications
D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response
Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Vielmetter J, Gong Y, Hanna J
Revealing a coherent cell-state landscape across single-cell datasets with CONCORD
Zhu Q†, Jiang Z, Zuckerman B, Weinberger L, Thomson M, Gartner Z†
First and co-corresponding authorReducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC
Conrad DN, Phong KT, Korotkevich E, McGinnis CS, Zhu Q, Chow ED, et al.
HybriSeq: probe-based device-free single-cell RNA profiling
Foyt D, Brown D, Zhou S, Moser B, Zhu Q, Gartner ZJ, Huang B
APC loss promotes intestinal transformation through induction of bistable stem cell states
Li N, Myers RL, Zhu Q, Tian Y, Durning K, Wang X, Leu NA, Rhoades JH, Bankler-Jukes D, Monaghan KE, Adams-Tzivelekidis S, et al.
Patterning and folding of intestinal villi by active mesenchymal dewetting
Huycke TR, Häkkinen TJ, Miyazaki H, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, et al.
deMULTIplex2: robust sample demultiplexing for scRNA-seq
Zhu Q†, Conrad DN, Gartner ZJ†
First and co-corresponding authorMapping and modeling human colorectal carcinoma interactions with the tumor microenvironment
Li N*, Zhu Q*, Tian Y, Ahn KJ, Wang X, Cramer Z, Jou J, et al.
Co-first authorEndothelial MEKK3-KLF2/4 signaling integrates inflammatory and hemodynamic signals during definitive hematopoiesis
Yang Y, Mumau M, Tober J, Zhu Q, Bennett L, Hong C, Sung D, Keller T, Uzun Y, Gao P, Shewale S, et al.
Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell–like blasts in KMT2A-rearranged leukemia
Chen C*, Yu W*, Alikarami F, Qiu Q, Chen CH, Flournoy J, Gao P, Uzun Y, Fang L, Hu Y, Zhu Q, et al.
Integrative bulk and single-cell profiling of premanufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy
Chen GM*, Chen C*, Das RK*, Gao P, Chen CH, Bandyopadhyay S, Ding YY, Uzun Y, Yu W, Zhu Q, Myers RM, et al.
Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells
Gao P, Chen C, Howell ED, Li Y, Tober J, Uzun Y, He B, Gao L, Zhu Q, Siekmann AF, Speck NA, Tan K
Developmental trajectory of prehematopoietic stem cell formation from endothelium
Zhu Q*, Gao P*, Tober J*, Bennett L, Chen C, Uzun Y, Li Y, Howell ED, Mumau M, Yu W, He B, Speck NA, Tan K
Co-first authorscATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Yu W, Uzun Y, Zhu Q, Chen C, Tan K
The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution
Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, et al.; Human Tumor Atlas Network
Runx1 negatively regulates inflammatory cytokine production by neutrophils in response to Toll-like receptor signaling
Bellissimo DC, Chen CH, Zhu Q, Bagga S, Lee CT, He B, Wertheim GB, Jordan M, Tan K, Worthen GS, Gilliland DG, et al.
SCRABBLE: single-cell RNA-seq imputation constrained by bulk RNA-seq data
Peng T, Zhu Q, Yin P, Tan K
Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation
Tang AT, Sullivan KR, Hong CC, Goddard LM, Mahadevan A, Ren A, Pardo H, Peiper A, Griffin E, Tanes C, Mattei LM, Yang J, Li L, Mericko-Ishizuka P, Shen L, Hobson N, Girard R, Lightle R, Moore T, Shenkar R, Polster SP, Roedel CJ, Li N, Zhu Q, et al.
Single-cell profiling reveals sex, lineage, and regional diversity in the mouse kidney
Ransick A*, Lindström NO*, Liu J*, Zhu Q, Guo JJ, Alvarado GF, Kim AD, Black HG, Kim J, McMahon AP
A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution
Packer JS*, Zhu Q*, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI
Co-first authorPIVOT: platform for interactive analysis and visualization of transcriptomics data
Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J
First authorVERSE: a versatile and efficient RNA-Seq read counting tool
Zhu Q, Fisher SA, Shallcross J, Kim J
First authorBetaine reduces serum uric acid levels and improves kidney function in hyperuricemic mice
Liu YL, Pan Y, Wang X, Fan CY, Zhu Q, Li JM, Wang SJ, Kong LD
Morin reduces hepatic inflammation-associated lipid accumulation in high fructose-fed rats via inhibiting sphingosine kinase 1/sphingosine 1-phosphate signaling pathway
Wang X, Zhang DM, Gu TT, Ding XQ, Fan CY, Zhu Q, Shi YW, Hong Y, Kong LD
Beneficial effect of rutin on oxonate-induced hyperuricemia and renal dysfunction in mice
Chen YS, Hu QH, Zhang X, Zhu Q, Kong LD
Pharmacokinetic-pharmacodynamic modeling of monoamine oxidase A inhibitory activity and behavior improvement by curcumin in the mouse forced swimming test
Xia X, Pan Y, Ou-Yang Z, Wang J, Pan LL, Zhu Q, Huang JJ, Kong LD
Orthogonal array design for antidepressant compatibility of polysaccharides from Banxia-Houpu decoction, a traditional Chinese herb prescription in the mouse models of depression
Yi LT, Zhang L, Ding AW, Xu Q, Zhu Q, Kong LD
† Co-corresponding author · * Equal contribution. Publication details are based on the current CV; Google Scholar and My Bibliography remain linked above for live indexing.
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