Single Cell Analyses
November 8 - 11, 2023

You must register for the meeting in order to submit abstracts.
After registering you will be sent a web link for abstract submission by email.
You may copy and paste your abstract from Word, Google Docs, or Notepad; abstracts are limited to ~2900 characters.

Program information: An electronic version of the program abstract book will be sent three working days prior to the first day of the meeting, and hard copies will be available for collection upon your arrival at Cold Spring Harbor Laboratory. First night and keynote speakers are informed of their session date and time, otherwise program information is only available upon release of the electronic version of the abstract book. The reason we do this is to try and maximize interactions by encouraging participants to stay for the duration of the meeting.

Please check your email for talk length, poster instructions, and how to have your poster printed at CSHL for collection upon arrival. 

Abstract Status

Presenting Author

Abstract Title

Talk/Poster

Aggarwal, Manu

Inferring transition probabilities and cellular trajectories from single-cell RNA sequencing

poster

Aihara, Gohta

Rasterization framework for scalable spatially resolved omics data analysis

poster

Ak, Cigdem

EpiConfig—Multimodal topic modeling for single-cell multiomics

flash talk & poster

Aladyeva, Ekaterina

Spatial transcriptomics of human hippocampal brain tissues with active lesion in secondary progressive multiple sclerosis

poster

Alakhdar, Amira A

Apoptotic processes direct the matrix-induced fibrogenic conversion of aged muscle stem cells

poster

Alemayehu, Amare Eshetu

Ultra-high resolution spatial transcriptomics reveals HIV-induced immune dysfunction in tissue microenvironment

poster

Alessandri, Luca

SC-Admine—Sparsely connected autoencoder for comprehensive data mining in single-cell RNAseq

poster

Allbritton, Nancy

Single-cell assay systems—Beyond genomics and proteomics

talk

An, Min Ho

Exploring keratinocyte differences in central and peripheral vitiligo lesions with single-cell RNA analysis

poster

Andersen, Chris

De novo inference of cell signaling from multiplexed single-cell imaging data

poster

Annepureddy, Laasya Devi

Identifying transcription factors that regulate epithelial cellular functions in breast milk using single-cell multiomic analysis

poster

Arbabi, Keon

Transcriptomic pathology of neocortical microcircuit cell types across psychiatric disorders

poster

Ates-Kalkan, Seda

Genetic lineage tracing analysis of neuromesodermal progenitor at single cell level uncovers novel contributions to trunk neural crest derivatives in zebrafish embryos

poster

Atta, Lyla M

Gene count normalization in single-cell imaging-based spatially resolved transcriptomics

poster

Attenborough, Teresa

Challenges, surprises, and uncharacterised genes—Single cell RNA sequencing in Schistosoma mansoni

poster

Bafna, Mihir

CLARIFY—Cell-cell interaction and gene regulatory network refinement from spatially resolved transcriptomics

poster

Battistella, Mattia

Challenging the hypothesis of a neurodevelopmental component in Huntington's disease by single-cell RNA sequencing analysis of human fetal samples

poster

Becker, Timothy J

Associating intergenic genomic variation with locally integrated scATAC and scRNA

poster

Benthal, Joseph T

Gene regulatory network analysis via single cell multiomics of the developing Mus musculus enteric nervous system

poster

Bhaskaran, Jahnavi

Single-nucleus multiomic analysis of human spermatogonia dynamics

talk

Booeshaghi, Ali Sina

A machine-readable specification for genomics assays

flash talk & poster

Boufaied, Nadia

MYC drives aggressive prostate cancer by disrupting transcriptional pause release at androgen receptor targets

poster

Brand, Joshua

Integrated scRNA-Seq analysis identifies fallopian tube myeloid cell alteration associated with high-grade serous ovarian cancer progression

poster

Budhathoki, Yogesh

Building a single cell atlas for osteosarcoma

poster

Cai, Jinpu

Cell-ontology-aware marker identification and stratification with TAMER

poster

Cannon, Matthew V

Identification of tumor cells in mixed-sample scRNAseq datasets using genetic variants

poster

Cao, Junyue

The panoramic view of organismal aging at single-cell resolution

talk

Chan, Kwan Pui

B cell repertoire differences induced by wild-type measles virus compared to live-attenuated measles vaccine

poster

Chang, Ting-Ya

Functional enhancer identification at sex-biased, growth hormone-responsive open chromatin regions in mouse liver

poster

Chari, Tara

Stochastic modeling for mapping biophysical effects of genetic and environmental perturbation

talk

Chen, Tianmeng

Multi-modal single-cell sequencing deconvolutes outcome-specific immune responses in trauma patients

poster

Chin, Christopher R

Single cell multiomics predicts germinal center B cell fate

poster

Chitra, Uthsav

Mapping spatial gene expression gradients with interpretable deep learning

poster

Clark, Kevin D

Deciphering the function of RNA modifications in the central nervous system and single cells—Strategies in sample preparation, separations, and mass spectrometry

poster

Clifton, Kalen

Alignment of spatial transcriptomics data using diffeomorphic metric mapping

talk

Coskun, Ahmet F

Subcellular spatial omics decode RNA and protein networks and neighborhoods in single cells

poster

Cotrim Chaves, Rodrigo

High-throughput nucleic acid cytometry with hydrogel beads

poster

Daccache, Joseph

Decoding epithelial inflammatory memory using single cell multiomics

poster

Das, Sankha Subhra

Human adipocyte subtypes and their expression profiles in subcutaneous adipose tissue differ based on liver fat amount and adipocyte characteristics

poster

Daswani, Rishika R

Measurement of single cell and spatial multiomics within the brains of rats following fentanyl self-administration

poster

deMello, Andrew

Microfluidic flow cytometry for blood-based diagnostics

talk

Dey, Siddharth S

Photo-sensitive barcodes combined with topologically imposed light gradients enable spatially-resolved single-cell transcriptomics and epigenomics

talk

Dhingra, Priyanka

Cellular and molecular impact of the melanocortin receptor agonist PL8177 in dextran sulfate sodium-induced colitis in rats

poster

Doratt, Brianna

Mild/asymptomatic COVID-19 in unvaccinated pregnant mothers impairs neonatal immune responses

poster

dos Santos Peixoto, Rafael

Multi-scale characterization of cell-type spatial relationships in spatially resolved omics data

poster

Duan, Xiaoyu

Deep learning cellular dynamics from single-cell RNA sequencing

poster

Ergen, Can

Comprehensive single-cell profiling of immune cells across the human lifespan reveals expression signatures of aging and tissue specificity

talk

Ergen, Can

Consensus prediction of cell type labels with popV

poster

Falk, Ariel

Patterns of aging across mouse tissues using global coordination level (GCL)—Insights from Tabula Muris Senis Dataset

poster

Feng, Site

Single-cell multi-omics analyses of colon mucosa reveal immune cell profiles of ulcerative colitis

poster

Ferrari, Ivan

Improved NK cell markers from single cell RNA-seq of PBMC populations by the new ROC-driven combiroc R package

poster

Franz, Emily

Trabectedin augments oncolytic herpes simplex virotherapy by reducing antiviral barriers to viral spread in pediatric bone sarcoma models

flash talk & poster

Fu, Yuntian

Single-cell landscape of tumor-infiltrating T cells in glioblastoma

poster

Ge, Xiaowei

SRS-FISH—Paving the way for single cell genotypic and phenotypic analysis

talk

Gironella Torrent, Marta

Single-cell quantification of secretory function and transcriptome delineates β-cell failure in type 2 diabetes

flash talk & poster

Go, Yunjin

HepScope—A new gene set identifying malignant hepatocytes at single-cell level

poster

Goggin, Sarah

A hyperparameter-randomized ensemble approach for robust clustering across diverse single-cell datasets

poster

Gomez, Nicholas

Topic modeling of epithelial to mesenchymal transition (EMT) in human iPSCs reveals dynamic gene expression substructure

flash talk & poster

Gu, Weihong

Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells

flash talk & poster

Guo, Xiaofeng

Transcriptomic characterization of preoptic area in homeostatic sleep controls using single-nucleus RNA-sequencing

poster

Haag, Natja

Deciphering pain mechanisms with single cell resolution

poster

Hamidzada, Homaira

Single cell transcriptomics reveals a modular macrophage structure conserved across organs and species

flash talk & poster

Harens, Hannah

Multimodal sample preparation for RNA and proteins in single cells

poster

Hassanin, Ismail El-Shimy A

Deficient IFN response, excessive neutrophil reactivity, and cilia impairment distinguish RSV from SARS-CoV-2 infection in infants

poster

He, Jian

Leveraging single-cell RNA-seq for uncovering naïve B cells associated with better prognosis of hepatocellular carcinoma

poster

Holmes, Austin

Enhanced single cell DNA methylation analysis using combinatorial sequencing

poster

Hu, Zhiyuan

Reconstructing gene regulatory networks underlying neural crest cell fate decisions using single-cell multiomics

talk

Hughes, Jason J

Quantitative RNA-FISH probe design

poster

Imafuku, Tadashi

Development of the section-based transcriptomics analysis without enzymatic treatment for single-cell dissociation

poster

Jiang, Jenny

High-throughput and high-dimensional profiling of antigen-specific T cells

talk

Jiang, Jialong

D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response

flash talk & poster

Johnson, Courtney M

scRNA sequencing reveals differential gene expression of cancer-associated fibroblast markers in early vs. late-stage mycosis fungoides disease

talk

Jonsson, Vanessa D

CITA—A pan-cancer multi-omic immune T cell atlas and antigen specificity database for cancer immunotherapy

talk

Kafader, Jared

scPiMS—A novel strategy for profiling intact proteoform signals from single cells

talk

Karakose, Esra

Single cell RNA-seq analysis of regenerative drug-treated human pancreatic Islets identifies a cycling alpha cell population as key beta cell progenitors

poster

Karlsson, Filip

Molecular pixilation—Spatial proteomics on single-cells by sequencing

flash talk & poster

Keer, Frances R

Stitch-seq—A facile and high-throughput perturbation sequencing method

poster

Khan, Teka

Syncytiotrophoblast subtypes revealed by single nucleus RNA sequencing, immunocytochemistry and fluorescence activated nuclear sorting of trophoblast derived from primed-type human pluripotent stem cells

poster

Ko, kyungdae.ko@nih.gov

A deep learning adversarial autoencoder with dynamic batching has superior performance in denoising scRNA-seq data

poster

Koumadorakis, Dimitrios

Decoding the antigen-presenting stroma landscape of lung tumors

poster

Krishnaswamy, Smita

Multiscale diffusion geometry for (deep) learning of graphs, manifolds, and flows

talk

Kuwabara, Takayoshi

Application of scRNA-seq technology to explore the evolutionary dynamics of Kenyon cell types, which comprise the higher-order brain center, in Hymenoptera

poster

Lakra, Priya

Smarca4 regulated transcription factor activity in germinal center B-cells

poster

Lam, Gabriel

Profiling splicing isoforms in single cells in aging models

poster

Lam, Trinh

A synchronized barcoded vacuum-driven microfluidic device for single-cell ATAC sequencing

flash talk & poster

Large, Christopher R

Combining the conserved and defined developmental lineage of the Caenorhabditis nematode embryo with single-cell resolution to study the evolution of cellular gene expression

flash talk & poster

Laub, Shannon

Single-cell CRISPRi screen maps candidate regulatory Alzheimer’s variants to target genes and cellular pathways in a human microglial cell line

flash talk & poster

Leduc, Andrew

Droplet sample preparation enables protein covariation across single cells

poster

Lee, Chen-Yu

Single-cell spatial proteomics identifies intraglomerular myeloid cells in membranous lupus nephritis

poster

Lee, Jaehyun

Decoding Parkinson's disease—Single-cell insights into region-specific and age-related genetic responses to α-synuclein oligomer exposure

poster

Lee, Jiseok

Deciphering altered gene networks in schizophrenia using single-cell perturbation and transcriptomics (CROP-seq) in the developing mouse brain

poster

Lee, Sanghoon

S100A11 mediates recruitment of tumor-associated macrophages to epithelial cancer cells in the microenvironment of ER+ breast cancer—Insights from single-cell analysis

poster

Leviyang, Sivan

Quantifying the clustering resolution of single cell RNA-seq

poster

Li, Siran

Associating cancer and stromal genomes with transcriptomes by high-throughput single-cell hybrid sequencing

talk

Li, Xiang

Real-time mRNA enrichment in single-nuclei RNA data by selective sequencing

talk

Lian, Qiuyu

Total-mRNA-aware comparative analysis for droplet-based single cell sequencing

poster

Liao, Tzu-Chieh

Single-cell multi-omics reveals molecular dynamics of type 3 innate lymphoid cell plasticity during intestinal Salmonella typhimurium infection

poster

Lim, Hansol

Transcriptional, anatomical and functional divergence in BLA neurons in controlling emotional valence behaviors

poster

Lingatlu, Sidarth

Cracking the code without coding—Assessing scRNA-seq cell type annotation using AI and data integration

poster

Liu, Shiwei

Single-nucleus RNA-seq analysis unveils sex/APOE-specific and cell type-specific transcriptional signatures in Alzheimer’s disease

poster

Liu, Zian

Imputation approaches and quality standards for single-cell epigenetic age predictions

poster

Loske, Jennifer

Deciphering molecular effects of triple therapy in children with cystic fibrosis by single-cell transcriptomics

poster

Ma, Cong

Inferring spatial tumor evolution and allele-specific copy number aberrations in spatially resolved transcriptomics data

talk

Ma, Xiao

Single-cell RNA sequencing reveals enhanced endothelial differentiation via ETV2 overexpression during murine embryogenesis

poster

MacLean, Adam L

Gene regulatory network inference with popInfer reveals dynamic regulation of hematopoietic stem cell quiescence upon diet restriction and aging

poster

Madler, Sophia C

SPARCS, a platform for genome-scale CRISPR screening for spatial cellular phenotypes

talk

Mancera Miranda, Laura M

Phenotypically heterogeneous loci in the plant pathogen Pseudomonas syringae

poster

McConnell, Michael

Recurrent sites of somatic mosaicism in human neurons

talk

McEwen, Sophie

Exploring the differential host response to SARS-CoV-2 variants in pediatric patients

poster

Mellis, Ian A

Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells

flash talk & poster

Miao, Zhen

Model-based compound hypothesis testing for snATAC-seq data with PACS

talk

Montoya Mira, Jose Luis

An integrated, efficient, and scalable single-cell sequencing platform leveraging engineered ultrasound responsive nanowells

flash talk & poster

Mossi Albiach, Alejandro

Glioblastoma is spatially organized by neurodevelopmental programs and a glial-like wound healing response

poster

Murza, Dominykas

Development of droplet-based single-cell small RNA sequencing assay

poster

Najafabadi, Hamed S

A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data

poster

Navab, Roya

Spatially defined co-culture model of non-small cell lung cancer (NSCLC) organoids and cancer-associated fibroblasts to investigate phenotypic heterogeneity

poster

Niemoeller, Christoph

Development of scPICO—A high-sensitivity single cell antibody assay with dPCR readout for quantitative analysis of 4EBP1 protein phosphorylation in drug-perturbed cellular populations

flash talk & poster

Nouri, Nima

Target identification by comparative analysis of gene association networks using single cell RNA sequencing data

poster

Okada, Hiroyuki

Subcellular sampling and sequencing by iSCseq connects transcriptomics with morphological, physical, and physiological findings in osteoimmunology

talk

Olsen, Timothy

Scalable co-sequencing of RNA and DNA from individual nuclei

talk

Orvis, Joshua D

The gene Expression Analysis Resource (gEAR) Portal—Making single-cell analysis and multi-experiment visualization accessible

flash talk & poster

Osmanbeyoglu, Hatice U

Single-cell analysis reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of ovarian cancer

poster

Osmanbeyoglu, Hatice U

Spatial landscape of malignant pleural and peritoneal mesothelioma tumor immune microenvironment

poster

Osmanbeyoglu, Hatice U

STAN, a computational framework for inferring spatially informed transcription factor activity networks

poster

Osmani, Lais

Investigating the functional heterogeneity of monocytes and macrophages in systemic lupus erythematosus

poster

Paddock, Lucinda

Intravesical BCG induces epigenetic changes in hematopoietic stem and progenitor cells that drive the anti-tumor immune response against bladder cancer

poster

Paek, Seung-Jun

Interplay of HBV-Infected tumor cells on the fibrotic microenvironment in hepatocellular carcinoma by single-cell RNA sequencing

poster

Page, Nicole M

Single-cell profiling of Anopheles gambiae spermatogenesis to identify novel regulatory elements for mosquito control

poster

Park, Soon Sang

Cellular senescence drives spatial evolution in colorectal cancer

poster

Passalacqua, Michael J

Leveraging coexpression to improve cross-species single cell integration in plants

poster

Patikas, Nikolaos

Harmony powers robust integration of single-cell data at scale

poster

Pham, Nhu-An

Mutant EGFR lung adenocarcinoma PDX model of osimertinib-induced drug tolerant persister is sensitized with an epigenetic modulator

poster

Polonsky, Michal

Deciphering cellular interactions in acute kidney injury using spatial transcriptomics

poster

Poo, Haryoung

Poly-γ-glutamic acid/Alum adjuvanted pH1N1 vaccine-immunized aged mice exhibit a significant increase in vaccine efficacy with a decrease in age-associated CD8+ T cell proportion in splenocytes

poster

Prazanowska, Karolina

An integrated single-cell transcriptomic dataset for non-small cell lung cancer

poster

Preka, Efthalia

Long-term microglia dynamics in the mouse hippocampus following cranial irradiation

poster

Qiao, Qi

Integrated single cell analysis shows chronic alcohol drinking disrupts monocyte differentiation in the bone marrow niche

poster

Qiao, Zhen

Population-scale single-cell transcriptomics of clonal haematopoiesis

poster

Quevedo, Laura

Targeting the tumor microenvironment by Duvelisib in peripheral T-cell lymphomas

poster

Quinn, Katelynn D

Single-cell DNA sequencing analysis of AML clones with an early signaling mutation show development of a novel immunophenotype

poster

Rajasekaran, Bhavna

A deep learning based quantitative framework for investigating spatiotemporal regulation of actin microridge patterns

poster

Rajendran, Ashmitha

Identification of pediatric brain cancer neurodevelopmental origins using spatiotemporal landscapes

poster

Ranade, Nissim

Identifying tumor sub populations in low coverage single cell data

poster

Reed, Jason

Single cell biomass tracking proves that tumor cells can escape from therapy-induced senescence

poster

Reed, Xylena

Building a single cell multiome ATAC + expression atlas in human frontal cortex

poster

Rozenwald, Michal

Mapping protein-DNA interactions with DiMeLo-seq

poster

Ruchiy, Yana

Genomic analysis of single-cell data allows the identification of tumour evolution culprits in medulloblastoma

poster

Sashittal, Palash

ConDoR—Tumor phylogeny inference with a copy-number constrained mutation loss model

flash talk & poster

Schippel, Natascha N

Single cell analysis of human early erythroid progenitor heterogeneity

poster

Schlueter, Hannah

Detecting lineage-related gene expression patterns

talk

Schmidt, Michael J

GeTMoR—Simultaneous genomic, transcriptomic, and morphological profiling of rare single cells

poster

Sharif, Behrang

Exploring hierarchical linear and multilevel statistical modeling for biological inferences from integrated single nucleus transcriptomics of human dorsal root ganglia

poster

Shim, Jae Hyun

Single-cell resolution analysis of GPC3 and S100A10 in human liver tumor microarrays through automated cellular analysis

poster

Sienkiewicz, Karolina M

Changes in circulating cell-free DNA as a biomarker of immune response to short-duration spaceflight

poster

Slavov, Nikolai

Biological and technological frontiers for single-cell proteomics

talk

Snyder, Grace A

Single-cell sequencing of novel immune cells in an early-diverging metazoan

poster

Thakral, Deepshi

Comparative single cell whole transcriptome analysis of CD34 positive versus CD34 negative leukemic stem cells in acute myeloid leukemia

poster

Torous, William

Visualizing scRNA-Seq data at population scale with GloScope

talk

Tremblay, Simon

Cascading binomial classification framework for supervised scRNA-seq cell type classification

poster

Tsubosaka, Ayumu

Integrated single-cell RNA sequencing and spatial transcriptomic analyses of human normal and metaplastic gastric mucosa

poster

Uhler, Caroline

Causal representation learning—A proposal

talk

Volteras, Dimitrios

Scalable inference reveals global transcription regulation from time-resolved single-cell RNA-sequencing

flash talk & poster

Wang, Siyuan

A genome-wide single-cell 3D genome atlas of lung cancer progression

talk

Warrier, Tushar

Enhancer transposition at single-cell resolution—A tool to decipher enhancer kinetics and transcriptional regulation in cancer genomes

flash talk & poster

Wei, Yulong

Single-cell epigenetic, transcriptional, and protein states of HIV-infected cells

flash talk & poster

Weinstein, Joshua A

DNA microscopy in three dimensions

poster

Wekhande, Siddarth

Combinomics—Multiomic single cell processing and analysis pipeline

poster

Wong, Michelle E

Tracking the spatiotemporal dynamics of CD4+ T cell immune responses during HIV infection using single-cell multiomic profiling

poster

Woods, Mae L

Single cell pathway analysis isolates viral and tumor specific T cell receptors in cells with low activation marker transcript abundance

poster

Xin, Hongyi

Cross-modal, subtype-aware cell type clustering and classification in single-cell sequencing

poster

Xue, Angli

Population-scale single-cell transcriptomics reveals genetic associations with intra-individual variability of gene expression

flash talk & poster

Xue, Tianchun

Evaluating methods to extract genome structure information from single cell Hi-C data

poster

Yardimci, Galip G

Robust CNV detection using single-cell ATAC-seq

poster

Yokoyama, Masataka

Organ-specific transcriptional regulations of endothelial cells to aging and obesity stress

poster

Yu, Zhijun

Single cell technologies decipher the heterogeneity of colorectal tissue

poster

Yuan, Qiuyue

Continuous lifelong learning for modeling of gene regulation from single cell multiome data by leveraging atlas-scale external data

poster

Yunusov, Dinar

Accurate quantification of multi-mapping reads in single-cell RNA-seq with STARsolo

flash talk & poster

Zaragoza, Michael V

Single-cell transcriptomics of human iPSC differentiation to cardiomyocytes reveal cell type and lineage-specific molecular mechanisms of LMNA-related dilated cardiomyopathy

poster

Zhang, Pengfei

Mapping embryonic mouse lung development using single-cell and spatial transcriptomics

poster

Zhang, Tianran

Uncover molecular mechanisms of novel therapies for diabetic kidney disease by single-cell transcriptomics

poster

Zhang, Xinyi

Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer’s disease

flash talk & poster

Zhang, Xiuwei

scMultiSim—Simulation of single cell multi-omics and spatial data guided by cell-cell interactions and gene regulatory networks

flash talk & poster

Zhang, Ziqi

CeSpGRN—Inferring cell-specific gene regulatory networks from single cell multi-omics and spatial data

poster