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1michaellee1/CellSeg
https://github.com/michaellee1/CellSeg
a year ago by @becker
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cellseg
cell
segmentation
hande
he
image
images
yuqi
github
code
python
codex
cellsegcellsegmentationhandeheimageimagesyuqigithubcodepythoncodex
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1Single Cell Perturbation Dataset Explorer
https://www.scperturb.org/
2 years ago by @becker
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atac
cell
dataset
datasets
perturbation
seq
single
ataccelldatasetdatasetsperturbationseqsingle
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1scverse - single cell methods
https://scverse.org/
2 years ago by @becker
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analysis
cell
github
methods
single
software
analysiscellgithubmethodssinglesoftware
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1Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning | Nature Biotechnology
https://www.nature.com/articles/s41587-021-01094-0
2 years ago by @becker
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large
dataset
tissue
single
cell
different
technologies
largedatasettissuesinglecelldifferenttechnologies
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1DeepCell Label
https://label.deepcell.org/
2 years ago by @becker
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deepcell
label
cell
cells
platform
crowdsourcing
crowd
sourcing
workers
deepcelllabelcellcellsplatformcrowdsourcingcrowdsourcingworkers
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1Differential cellular immune response in pregnant and non-pregnant women upon vaccination against SARS-CoV-2 infection
C. Urbschat, K. Thiele, I. Stelzer, T. Zhang, Y. Zhao, T. Kehribar, M. Pagenkemper, G. Hansen, B. Gaudillière, A. Diemert and 1 other author(s). Journal of Reproductive Immunology, (2023)
7 months ago by @becker
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abstract
cell
covid
myown
pregnancy
single
vaccination
abstractcellcovidmyownpregnancysinglevaccination
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1Cross-species comparative analysis of single presynapses
E. Berson, C. Gajera, T. Phongpreecha, A. Perna, S. Bukhari, M. Becker, A. Chang, D. De Francesco, C. Espinosa, N. Ravindra and 1 other author(s). Scientific Reports, 13 (1): 13849 (2023)
7 months ago by @becker
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cell
cross
cytof
myown
presynapses
single
species
cellcrosscytofmyownpresynapsessinglespecies
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1Revealing the impact of lifestyle stressors on the risk of adverse pregnancy outcomes with multitask machine learning
M. Becker, J. Dai, A. Chang, D. Feyaerts, I. Stelzer, M. Zhang, E. Berson, G. Saarunya, D. De Francesco, C. Espinosa and 1 other author(s). Frontiers in Pediatrics, (2022)
a year ago by @becker
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adverse
cell
immune
immunology
learning
life
machine
multitask
myown
outcomes
pregnancy
single
stress
stressors
system
adversecellimmuneimmunologylearninglifemachinemultitaskmyownoutcomespregnancysinglestressstressorssystem
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1In-Silico Generation of High-Dimensional Immune Response Data in Patients using a Deep Neural Network
R. Fallahzadeh, N. Bidoki, I. Stelzer, M. Becker, I. Marić, A. Chang, A. Culos, T. Phongpreecha, M. Xenochristou, D. De Francesco and 1 other author(s). Cytometry Part A, (2022)
a year ago by @becker
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cell
dimensional
encoder
high
myown
network
neural
single
celldimensionalencoderhighmyownnetworkneuralsingle
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1CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images
M. Lee, J. Bedia, S. Bhate, G. Barlow, D. Phillips, W. Fantl, G. Nolan, and C. Schürch. BMC bioinformatics, 23 (1): 1--17 (2022)
a year ago by @becker
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cell
segmentation
he
staining
image
nucleus
fluorescence
yuqi
citedby:scholar:count:10
citedby:scholar:timestamp:2022-12-2
cellsegmentationhestainingimagenucleusfluorescenceyuqicitedby:scholar:count:10citedby:scholar:timestamp:2022-12-2
(0)
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1Predicting cell populations in single cell mass cytometry data
T. Abdelaal, V. van Unen, T. Höllt, F. Koning, M. Reinders, and A. Mahfouz. Cytometry Part A, 95 (7): 769--781 (2019)
a year ago by @becker
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cytof
single
cell
type
prediction
yuqi
mass
cytometry
citedby:scholar:count:35
citedby:scholar:timestamp:2022-11-22
cytofsinglecelltypepredictionyuqimasscytometrycitedby:scholar:count:35citedby:scholar:timestamp:2022-11-22
(0)
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1SiGra: Single-cell spatial elucidation through image-augmented graph transformer
Z. Tang, T. Zhang, B. Yang, J. Su, and Q. Song. bioRxiv, (2022)
2 years ago by @becker
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single
cell
spatial
image
graph
transformer
yuqi
singlecellspatialimagegraphtransformeryuqi
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1Mapping single-cell data to reference atlases by transfer learning
M. Lotfollahi, M. Naghipourfar, M. Luecken, M. Khajavi, M. Büttner, M. Wagenstetter, {. Avsec, A. Gayoso, N. Yosef, M. Interlandi and 1 other author(s). Nature Biotechnology, 40 (1): 121--130 (2022)
2 years ago by @becker
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single
cell
mapping
reference
atlas
transfer
learning
combine
datasets
dataset
nature
theiss
citedby:scholar:count:57
citedby:scholar:timestamp:2022-8-30
singlecellmappingreferenceatlastransferlearningcombinedatasetsdatasetnaturetheisscitedby:scholar:count:57citedby:scholar:timestamp:2022-8-30
(0)
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1Mapping the developing human immune system across organs
C. Suo, E. Dann, I. Goh, L. Jardine, V. Kleshchevnikov, J. Park, R. Botting, E. Stephenson, J. Engelbert, Z. Tuong and 1 other author(s). bioRxiv, (2022)
2 years ago by @becker
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cell
development
dna
immune
longitudinal
single
system
celldevelopmentdnaimmunelongitudinalsinglesystem
(0)
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1Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE
T. Phongpreecha, C. Gajera, C. Liu, K. Vijayaragavan, A. Chang, M. Becker, R. Fallahzadeh, R. Fernandez, N. Postupna, E. Sherfield and 1 other author(s). Science advances, 7 (51): eabk0473 (2021)
2 years ago by @becker
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alzheimer
brain
cell
citedby:scholar:count:2
citedby:scholar:timestamp:2022-3-22
clustering
deep
learning
myown
network
neural
single
synapse
alzheimerbraincellcitedby:scholar:count:2citedby:scholar:timestamp:2022-3-22clusteringdeeplearningmyownnetworkneuralsinglesynapse
(0)
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1Integrated Single-cell and Plasma Proteomic Modeling to Predict Surgical Site Complications: A Prospective Cohort Study
K. Rumer, J. Hedou, A. Tsai, J. Einhaus, F. Verdonk, N. Stanley, B. Choisy, E. Ganio, A. Bonham, D. Jacobsen and 1 other author(s). Annals of surgery, 275 (3): 582--590 (2022)
2 years ago by @becker
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iti
single
cell
cytof
mass
cytometry
proteomics
itisinglecellcytofmasscytometryproteomics
(0)
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2CytoSet: Predicting clinical outcomes via set-modeling of cytometry data
H. Yi, and N. Stanley. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, page 1--8. (2021)
2 years ago by @becker
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set
sets
single
cell
immune
system
cytof
deep
learning
neural
network
citedby:scholar:count:1
citedby:scholar:timestamp:2022-2-25
setsetssinglecellimmunesystemcytofdeeplearningneuralnetworkcitedby:scholar:count:1citedby:scholar:timestamp:2022-2-25
(0)
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1Integrated intra-and intercellular signaling knowledge for multicellular omics analysis
D. Türei, A. Valdeolivas, L. Gul, N. Palacio-Escat, M. Klein, O. Ivanova, M. Ölbei, A. Gábor, F. Theis, D. Módos and 1 other author(s). Molecular systems biology, 17 (3): e9923 (2021)
2 years ago by @becker
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background
cell
cells
citedby:scholar:count:35
citedby:scholar:timestamp:2022-2-23
cytokines
database
immune
knowledge
mining
network
networks
project:iti-single-cell
pubmed
system
text
backgroundcellcellscitedby:scholar:count:35citedby:scholar:timestamp:2022-2-23cytokinesdatabaseimmuneknowledgeminingnetworknetworksproject:iti-single-cellpubmedsystemtext
(0)
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1Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed
K. Kveler, E. Starosvetsky, A. Ziv-Kenet, Y. Kalugny, Y. Gorelik, G. Shalev-Malul, N. Aizenbud-Reshef, T. Dubovik, M. Briller, J. Campbell and 1 other author(s). Nature biotechnology, 36 (7): 651--659 (2018)
2 years ago by @becker
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background
cell
cells
citedby:scholar:count:51
citedby:scholar:timestamp:2022-2-23
cytokines
database
immune
knowledge
mining
network
networks
project:iti-single-cell
pubmed
system
text
backgroundcellcellscitedby:scholar:count:51citedby:scholar:timestamp:2022-2-23cytokinesdatabaseimmuneknowledgeminingnetworknetworksproject:iti-single-cellpubmedsystemtext
(0)
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1Machine learning for perturbational single-cell omics
Y. Ji, M. Lotfollahi, F. Wolf, and F. Theis. Cell Systems, 12 (6): 522--537 (2021)
3 years ago by @becker
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single
cell
perturbation
survey
deep
learning
review
theis
wolf
machine
background
knowledge
integration
generative
modeling
models
model
omics
multi
multiomics
singlecellperturbationsurveydeeplearningreviewtheiswolfmachinebackgroundknowledgeintegrationgenerativemodelingmodelsmodelomicsmultimultiomics
(0)
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1RchyOptimyx: cellular hierarchy optimization for flow cytometry
N. Aghaeepour, A. Jalali, K. O'Neill, P. Chattopadhyay, M. Roederer, H. Hoos, and R. Brinkman. Cytometry Part A, 81 (12): 1022--1030 (2012)
3 years ago by @becker
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cell
citedby:scholar:count:63
citedby:scholar:timestamp:2021-6-15
cytometry
dynamic
gating
prgramming
single
subgroup
subgroups
visualization
cellcitedby:scholar:count:63citedby:scholar:timestamp:2021-6-15cytometrydynamicgatingprgrammingsinglesubgroupsubgroupsvisualization
(0)
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1scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses
J. Wang, A. Ma, Y. Chang, J. Gong, Y. Jiang, R. Qi, C. Wang, H. Fu, Q. Ma, and D. Xu. Nature communications, 12 (1): 1--11 (2021)
3 years ago by @becker
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single
cell
gnn
graph
neural
network
rna
seq
rna-seq
paper:fastcor
citedby:scholar:count:3
citedby:scholar:timestamp:2021-6-4
singlecellgnngraphneuralnetworkrnaseqrna-seqpaper:fastcorcitedby:scholar:count:3citedby:scholar:timestamp:2021-6-4
(0)
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1Automated identification of maximal differential cell populations in flow cytometry data
A. Yue, C. Chauve, M. Libbrecht, and R. Brinkman. bioRxiv, (2020)
3 years ago by @becker
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differential
cell
populations
population
different
identification
flow
cytometry
differentialcellpopulationspopulationdifferentidentificationflowcytometry
(0)
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1Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology
S. Palit, C. Heuser, G. de Almeida, F. Theis, and C. Zielinski. Frontiers in Immunology, (July 2019)
4 years ago by @becker
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cell
dimensional
gating
high
immune
immunology
learning
machine
manual
ml
single
system
celldimensionalgatinghighimmuneimmunologylearningmachinemanualmlsinglesystem
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2Dynamic graph cnn for learning on point clouds
Y. Wang, Y. Sun, Z. Liu, S. Sarma, M. Bronstein, and J. Solomon. Acm Transactions On Graphics (tog), 38 (5): 1--12 (2019)
4 years ago by @becker
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graph
cnn
point
cloud
classification
dynamic
single
cell
neural
network
nn
citedby:scholar:count:674
citedby:scholar:timestamp:2020-9-10
graphcnnpointcloudclassificationdynamicsinglecellneuralnetworknncitedby:scholar:count:674citedby:scholar:timestamp:2020-9-10
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BibSonomy

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1michaellee1/CellSeg

1Single Cell Perturbation Dataset Explorer

1scverse - single cell methods

1Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning | Nature Biotechnology

1DeepCell Label

publications (hide)42
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1Differential cellular immune response in pregnant and non-pregnant women upon vaccination against SARS-CoV-2 infection

1Cross-species comparative analysis of single presynapses

1Revealing the impact of lifestyle stressors on the risk of adverse pregnancy outcomes with multitask machine learning

1In-Silico Generation of High-Dimensional Immune Response Data in Patients using a Deep Neural Network

1CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images

1Predicting cell populations in single cell mass cytometry data

1SiGra: Single-cell spatial elucidation through image-augmented graph transformer

1Mapping single-cell data to reference atlases by transfer learning

1Mapping the developing human immune system across organs

1Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE

1Integrated Single-cell and Plasma Proteomic Modeling to Predict Surgical Site Complications: A Prospective Cohort Study

2CytoSet: Predicting clinical outcomes via set-modeling of cytometry data

1Integrated intra-and intercellular signaling knowledge for multicellular omics analysis

1Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed

1Machine learning for perturbational single-cell omics

1RchyOptimyx: cellular hierarchy optimization for flow cytometry

1scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

1Automated identification of maximal differential cell populations in flow cytometry data

1Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology

2Dynamic graph cnn for learning on point clouds

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