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M. Stoeckius · SciRah

Researcher profile · Semantic Scholar

M. Stoeckius

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M. Stoeckius — researcher profile on SciRah

h-index: 21
Works: 46
Citations: 32K

Most-cited papers

Comprehensive integration of single-cell data
T. Stuart, Andrew W. Butler, Paul J. Hoffman, C. Hafemeister +6 more
2018bioRxiv14K citations Open access
Semantic Scholar
Integrated analysis of multimodal single-cell data
Yu-Han Hao, S. Hao, E. Andersen-Nissen, W. Mauck +21 more
2020bioRxiv13K citations Open access
Semantic Scholar
Large-scale simultaneous measurement of epitopes and transcriptomes in single cells
M. Stoeckius, C. Hafemeister, William Stephenson, B. Houck-Loomis +4 more
2017Nature Methods2,305 citations Open access
Semantic Scholar
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
M. Stoeckius, Shi-Wei Zheng, B. Houck-Loomis, S. Hao +4 more
2018Genome Biology935 citations Open access
Semantic Scholar
Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay
Eleni P. Mimitou, A. Cheng, A. Montalbano, S. Hao +10 more
2019Nature Methods453 citations Open access
Semantic Scholar
Paternal diet defines offspring chromatin state and intergenerational obesity.
Anita Öst, Adelheid M. Lempradl, Eduard Casas, M. Weigert +15 more
2014Cell380 citations Open access
Semantic Scholar
A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation
Ranit Kedmi, T. Najar, Kailin R. Mesa, Allyssa Grayson +19 more
2022Nature222 citations Open access
Semantic Scholar
Integrated protein and transcriptome spatial profiling
N. Ben-Chetrit, Xiang Niu, Ariel D. Swett, Jesus Sotelo +7 more
2023Nature Biotechnology168 citations Open access
Semantic Scholar
In vivo and transcriptome-wide identification of RNA binding protein target sites
AC Jungkamp, M. Stoeckius, D. Mecenas, D. Grün +3 more
2011Molecules and Cells159 citations Open access
Semantic Scholar
Conservation of mRNA and protein expression during development of C. elegans.
D. Grün, Marieluise Kirchner, Nadine Thierfelder, M. Stoeckius +2 more
2014Cell Reports111 citations Open access
Semantic Scholar
Large scale sorting of C. elegans embryos reveals the dynamics of small RNA expression
M. Stoeckius, J. Maaskola, T. Colombo, H. Rahn +5 more
2009Nature Methods96 citations Open access
Semantic Scholar
Global characterization of the oocyte‐to‐embryo transition in Caenorhabditis elegans uncovers a novel mRNA clearance mechanism
M. Stoeckius, D. Grün, Marieluise Kirchner, Salah Ayoub +5 more
2014EMBO Journal85 citations Open access
Semantic Scholar
Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells
Jue Feng, Joseph N. Pucella, Geunhyo Jang, M. Alcántara-Hernández +10 more
2022Immunity76 citations Open access
Semantic Scholar
Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28
Nathan Lawlor, Djamel Nehar-Belaid, Jessica D. S. Grassmann, M. Stoeckius +6 more
2021Frontiers in Immunology72 citations Open access
Semantic Scholar
Select microRNAs are essential for early development in the sea urchin
Jia L. Song, M. Stoeckius, J. Maaskola, M. Friedländer +6 more
2011Developmental Biology68 citations Open access
Semantic Scholar
Paternal RNA contributions in the Caenorhabditis elegans zygote
M. Stoeckius, D. Grün, N. Rajewsky
2014EMBO Journal66 citations Open access
Semantic Scholar
Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
C. Vejnar, Mario Abdelmessih, Carter M. Takacs, V. Yartseva +12 more
2019Genome Research59 citations Open access
Semantic Scholar
Multiplexed single-cell analysis reveals prognostic and nonprognostic T cell types in human colorectal cancer
K. Masuda, Adam E. Kornberg, Jonathan Miller, Sijie Lin +17 more
2022JCI Insight58 citations Open access
Semantic Scholar
Tracing tumorigenesis in a solid tumor model at single-cell resolution
Samantha D. Praktiknjo, B. Obermayer, Qiong-Hua Zhu, L. Fang +6 more
2020Nature Communications55 citations Open access
Semantic Scholar
Intratumor heterogeneity and T cell exhaustion in primary CNS lymphoma
Michael O. Heming, Svea Haessner, Jolien Wolbert, I-Na Lu +15 more
2022Genome Medicine52 citations Open access
Semantic Scholar
Essential Roles of Raf/Extracellular Signal-regulated Kinase/Mitogen-activated Protein Kinase Pathway, YY1, and Ca2+ Influx in Growth Arrest of Human Vascular Smooth Muscle Cells by Bilirubin*
M. Stoeckius, Anna Erat, Tatsuya Fujikawa, M. Hiromura +7 more
2012Journal of Biological Chemistry34 citations Open access
Semantic Scholar
Single-cell stabilization method identifies gonadotrope transcriptional dynamics and pituitary cell type heterogeneity
F. Ruf-zamojski, Yongchao Ge, V. Nair, M. Zamojski +14 more
2018Nucleic Acids Research20 citations Open access
Semantic Scholar
Cell “hashing” with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
M. Stoeckius, Shi-Wei Zheng, B. Houck-Loomis, S. Hao +3 more
2017bioRxiv17 citations Open access
Semantic Scholar
Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay
Eleni P. Mimitou, A. Cheng, A. Montalbano, S. Hao +10 more
2018bioRxiv14 citations Open access
Semantic Scholar
Tonic type I interferon signaling optimizes the antiviral function of plasmacytoid dendritic cells
Joseph N. Pucella, R. Maqueda-Alfaro, Hai Ni, Fernando Bandeira Sulczewski +21 more
2025Nature Immunology12 citations Open access
Semantic Scholar
Integrated protein and transcriptome high-throughput spatial profiling
N. Ben-Chetrit, Xiang Niu, Ariel D. Swett, Jesus Sotelo +4 more
2022bioRxiv12 citations Open access
Semantic Scholar
Passenger mutations link cellular origin and transcriptional identity in human lung adenocarcinomas
S. Panja, Padmaja Mantri, K. E. Johnson, J. Andrade-Martínez +13 more
2025Nature Genetics4 citations Open access
Semantic Scholar
Microbiota-instructed regulatory T cell differentiation is mediated by a distinct RORγt+ antigen presenting cell subset
Ranit Kedmi, T. Najar, Kailin R. Mesa, Allyssa Grayson +19 more
2022bioRxiv3 citations Open access
Semantic Scholar
FEM: mining biological meaning from cell level in single-cell RNA sequencing data
Yun-Qing Liu, Na Lu, Chang-Wei Bi, Ting-Yu Han +247 more
2021PeerJ3 citations Open access
Semantic Scholar
Single cell analysis of blood mononuclear cells stimulated through CD3 and CD28 shows collateral activation of B and NK cells and demise of monocytes
Nathan Lawlor, Djamel Nehar-Belaid, Jessica D. S. Grassmann, M. Stoeckius +6 more
2020bioRxiv3 citations Open access
Semantic Scholar
Publisher Correction: A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation
Ranit Kedmi, T. Najar, Kailin R. Mesa, Allyssa Grayson +19 more
2022Nature2 citations Open access
Semantic Scholar
The functional and phenotypic diversity of single T-cell infiltrates in human colorectal cancer as correlated with clinical outcome
K. Masuda, Adam E. Kornberg, Sijie Lin, P. Ho +14 more
20202 citations Open access
Semantic Scholar
Global characterization of the oocyte-to-embryo transition in C . elegans uncovers a novel mRNA clearance mechanism
M. Stoeckius, Marieluise Kirchner, Salah Ayoub, F. Torti +4 more
20142 citations
Semantic Scholar
Antigen presentation by type 3 innate lymphoid cells instructs the differentiation of gut microbiota-specific regulatory T cells
Ranit Kedmi, T. Najar, Kailin R. Mesa, Allyssa Grayson +15 more
20211 citations Open access
Semantic Scholar
A post-transcriptional regulatory code for mRNA stability during the zebrafish maternal-to-zygotic transition
C. Vejnar, Mario Abdel Messih, Carter M. Takacs, V. Yartseva +11 more
2018bioRxiv1 citations Open access
Semantic Scholar
ENHANCING HISTOLOGICAL TISSUE AND CELL CHARACTERIZATION WITH SIMULTANEOUS GENE EXPRESSION AND PROTEIN MEASUREMENTS
C. Uytingco, J. Chew, R. Spalinskas, Yifeng Yin +18 more
2022Journal of Pathology Informatics0 citations Open access
Semantic Scholar
Tumor Microenvironment Characterization using a Spatial Multiomic Assay to Simultaneously Profile Protein and Gene Expression in FFPE Tumors
J. Chew, C. Uytingco, Naishitha Anaparthy, Jun Chiang +18 more
2022The FASEB Journal0 citations
Semantic Scholar
Abstract 3814: Multiomic characterization of the tumor microenvironment in FFPE tissue by simultaneous protein and gene expression profiling
C. Uytingco, J. Chew, Naishitha Anaparthy, Jun Chiang +17 more
2022Cancer Research0 citations
Semantic Scholar
SINGLE-SECTION MULTIOMICS MAPPED ACROSS FFPE TISSUE
Paulius Mielinis, M. Turkekul, Dan Walker, T. Drennon +16 more
2022Journal of Pathology Informatics0 citations Open access
Semantic Scholar
83 Spatially resolved transcriptomic and proteomic investigation of breast cancer and its immune microenvironment
J. Chew, Cedric Uytingco, Rapolas Spalinskas, Yifeng Yin +18 more
2021Journal for ImmunoTherapy of Cancer0 citations Open access
Semantic Scholar
Abstract 2696: Spatially resolved whole transcriptome molecular investigation of FFPE triple positive breast cancer tumors using the Visium platform
Stephen R. Williams, M. Turkekul, A. Jurek, Marco Mignardi +4 more
2021Tumor Biology0 citations
Semantic Scholar
Abstract 909: Single-cell transcriptomic profiling of non-small cell lung cancer uncovers inter- and intracell population structure across TCGA lung adenocarcinoma and lung squamous cancer subtypes
K. Gyan, Aditya Deshpande, Shaham Beg, Huasong Tian +6 more
2019Bioinformatics, Convergence Science, and Systems Biology0 citations
Semantic Scholar
Heterogeneity and Functional Programming of Inflammatory Monocytes
A. Wolf, A. Yáñez, Simon G. Coetzee, Dennis J. Hazelett +3 more
2018Experimental Hematology0 citations Open access
Semantic Scholar
CITE-seq and Cell Hashing
M. Stoeckius
20180 citations Open access
Semantic Scholar
Caenorhabditis elegans is one of the most elegant model organisms
M. Stoeckius
20120 citations
Semantic Scholar
Identification of microRNA Targets by Azra Krek
A. Krek, N. Rajewsky, K. Rajewsky, S. Muljo +7 more
20090 citations
Semantic Scholar

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