@nceglia

Principal Computational Biologist @ MSKCC 🧬💻 PhD in CS from UC Irvine

 NV CA NY
Joined December 2012
  • Tweets79
  • Following485
  • Followers242
Check out my recent work on GeneVector in @NatureComms using mutual information for dimensionality reduction in #scrna-seq! This framework generates gene embeddings to identify latent metagenes and annotate cell types. #research #singlecell nature.com/articles/s41467-0…

Identification of transcriptional programs using dense vector representations defined by mutual...

Nature Communications - In single-cell RNA-seq analyses, it would be critical to measure the relationships between genes. Here, the authors develop a framework for single-cell dimensionality...

nature.com
1
6
1
23
4,533
Nicholas Ceglia retweeted
biohub
@biohub2 Jan 2025
Our initial set of cell models all have cards, tutorials, notebooks + demo datasets to make understanding & running them easier. #AIML researchers can also access the source & processed data to train & validate new models with less data wrangling czi.co/3ZkysJh

AI-Supported Virtual Cells Platform From Biohub

Learn about Biohub's virtual cells platform, models and datasets — available for the scientific community for early access use and feedback.

virtualcellmodels.cziscience.com
6
13
2,031
Nicholas Ceglia retweeted
Adam Weiner@adamcweiner1 Oct 2024
Happy to announce that PERT is now published in @NatureComms ! With PERT, we explore replication timing variability (Fig 3-4), chrXi reactivation (Fig 5), and how S-phase fractions struggle to approximate clone fitness (Fig 6). nature.com/articles/s41467-0… 1/n

Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data

Nature Communications - Here the authors develop a probabilistic model for single-cell DNA sequencing of aneuploid tumors that infers clone-specific replication timing and S-phase fractions,...

nature.com
2
17
1
44
5,495
Nicholas Ceglia retweeted
Marc Williams@marcjwills_13 Sep 2024
We posted a couple of preprints recently, quick summary below 👇
2
6
16
1,492
Dr. @ivazquezgarcia spoke at a major symposium about evolutionary dynamics of whole-genome doubling in #ovariancancer at #AACR24. Learn more: bit.ly/3VUiA07
5
26
6,089
Nicholas Ceglia retweeted
Lior Pachter@lpachter5 Apr 2024
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.1101/… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
15
366
50
1,174
587,379
Excited to share our article in @Cancer_Cell on clinical and molecular features of acquired resistance to #immunotherapy in #lungcancer. We identify acquired resistance occurs in over >60% of initial responders and investigate underlying mechanisms. cell.com/cancer-cell/fulltex…

Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung...

Memon et al. demonstrate the relationship between persistent and upregulated interferon signaling and acquired resistance in tumors from patients with NSCLC who have developed acquired resistance to...

cell.com
8
36
118
14,022
Nicholas Ceglia retweeted
MSK Library
@MSKLibrary29 Sep 2023
Featured today by @MSKLibrary: Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector dx.doi.org/10.1038/s41467-02… @nceglia @fuhlitz @AndrewChowMDPhD @GreedyApple @farhia_kabeer @sajraparicio @bengrbm @SohrabShah
2
9
862
Our MSK scientists are much more than white coats in a lab. From postdocs to interns to faculty, hear why these brilliant scientists joined the field, and share your own reason below! #IAmAScientist
3
9
4
38
10,799
Nicholas Ceglia retweeted
UCIbrenICS@UCIbrenICS2 Sep 2023
Alumni Spotlight: Peter Sadowski Sadowski earned his Ph.D. in CS from UCI’s School of ICS. He is now an associate professor of information and computer sciences at the University of Hawaii at Māno leading the AI Precision Health Institute. Read: bit.ly/3Z0lqQK #uciics
Peter Sadowski

ALT Peter Sadowski

2
3
868
Extremely pleased that my joint work with amazing collaborators @dewolf_susan, @DrMvandenBrink and @tsonipeled came out yesterday in Science Translational Medicine, about TCR repertoires in tissue samples in GVHD patients and mouse models of GVHD.
1
1
12
450
.@nceglia @SohrabShah @bengrbm @CompOncMSK develop GeneVector, a framework for #scRNAseq dimensionality reduction that incorporates gene-specific relationships #CancerResearch @NatResCancer nature.com/articles/s41467-0…

Identification of transcriptional programs using dense vector representations defined by mutual...

Nature Communications - In single-cell RNA-seq analyses, it would be critical to measure the relationships between genes. Here, the authors develop a framework for single-cell dimensionality...

nature.com
10
1
29
11,334
Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplantation in human and mouse | Science Translational Medicine science.org/doi/10.1126/scit…

Tissue-specific features of the T cell repertoire after allogeneic hematopoietic cell transplanta...

T cell receptor sequencing reveals tissue-specific features of the posttransplant T cell repertoire in mouse and human.

science.org
6
223
Excited to share our work on #mRNAvaccines in #pancreaticcancer @Nature in a trial led by @TheVinodLab, @EileenMOReilly & the incredible team @MSKCancerCenter: nature.com/articles/s41586-0… Check out the epic tweetorial by @TheVinodLab 👇👇👇 - some thoughts below as well...

Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

Nature - A phase I clinical trial of an adjuvant personalized mRNA neoantigen vaccine, autogene cevumeran, in patients with pancreatic ductal carcinoma demonstrates that the vaccine can...

nature.com
Vinod BalachandranMD@TheVinodLab10 May 2023
1. ENTER #mRNAvaccines for #pancreaticcancer! Long-term #PDAC survivor story PART3. "Do #PDACs REALLY have vaccine neoantigens (NAs)"? (aren’t they lowly mutated?) If each patient = own NAs, how do you vaccinate? Maybe mRNA? But how? @Nature nature.com/articles/s41586-0… 👇🏽 [1/32]

Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

Nature - A phase I clinical trial of an adjuvant personalized mRNA neoantigen vaccine, autogene cevumeran, in patients with pancreatic ductal carcinoma demonstrates that the vaccine can...

nature.com
2
21
2
79
26,479
1. ENTER #mRNAvaccines for #pancreaticcancer! Long-term #PDAC survivor story PART3. "Do #PDACs REALLY have vaccine neoantigens (NAs)"? (aren’t they lowly mutated?) If each patient = own NAs, how do you vaccinate? Maybe mRNA? But how? @Nature nature.com/articles/s41586-0… 👇🏽 [1/32]

Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer

Nature - A phase I clinical trial of an adjuvant personalized mRNA neoantigen vaccine, autogene cevumeran, in patients with pancreatic ductal carcinoma demonstrates that the vaccine can...

nature.com
41
345
68
1,002
387,558
Nicholas Ceglia retweeted
Adam Weiner@adamcweiner11 Apr 2023
Interested in DNA replication and genomic instability? Our new method PERT identifies S-phase cells and estimates replication timing from single cell whole genome sequencing (scWGS) data with heterogeneous copy number biorxiv.org/content/10.1101/… 1/10

Modeling single cell DNA replication dynamics and aneuploidy in genomically unstable cancers

DNA replication is a highly coordinated cell cycle process that can become dysregulated in cancer, increasing both proliferation and mutation rates. Single-cell whole genome sequencing holds potent...

biorxiv.org
2
16
1
51
6,227
Nicholas Ceglia retweeted
Maryam Pourmaleki@MaryamPourm3 Apr 2023
Excited to see our In Focus article published in this month's issue of @CD_AACR! If you are interested in reading about the utility of multiplexed protein imaging and the needs for clinical implementation of these technologies, give this a read: aacrjournals.org/cancerdisco…

Moving Spatially Resolved Multiplexed Protein Profiling toward Clinical Oncology

Summary:. The shift in cancer therapy from broadly cytotoxic agents toward “personalized” treatments that target specific alterations in each patient's tumor requires diagnostic pathology approaches...

aacrjournals.org
2
6
32
4,090
Nicholas Ceglia retweeted
Florian Uhlitz
@fuhlitz15 Dec 2022
Super excited that we made it into @Nature — Big thanks to amazing supervision by @SohrabShah and @DmitriyZamarin, to my co-first @ivazquezgarcia, and to the whole MSK SPECTRUM team! nature.com/articles/s41586-0…

Ovarian cancer mutational processes drive site-specific immune evasion

Nature - Multi-modal analysis of genomically unstable ovarian tumours characterizes the contribution of anatomical sites and mutational processes to evolutionary phenotypic divergence and immune...

nature.com
2
9
100
8,250
Very excited to share that I recently started my lab in @CompOncMSK at @MSKCancerCenter! Looking for postdocs and graduate students interested in cell fate decisions/cancer evolution/computational single-cell genomics. Come join us in NYC! Spread the word & please #RT. Thanks!
10
48
4
147
The results of different methods applied to the same scRNA-seq data differ substantially. This is true even for fold changes, as shown below for Seurat and Scanpy. The differences between selected transcript "markers" are even larger: biorxiv.org/content/10.1101/… via @davisjmcc
8
88
8
382
Load more