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Maria Carilli @MariaCarilli

🧬 PhD candidate @Caltech in the lab of @lpachter | Computational biology, bioinformatics, biophysics | 🧬

Joined June 2022
  • Tweets 13
  • Following 105
  • Followers 140
Photos and videos
Maria Carilli retweeted
Nature Methods@naturemethods
25 Jul 2024
biVI models the biophysical processes generating nascent and mature single-cell transcriptomes using variational autoencoders. @MariaCarilli @GorinGennady @funion10 @lpachter nature.com/articles/s41592-0…
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Maria Carilli retweeted
Laura Luebbert, PhD@NeuroLuebbert
13 Dec 2023
We expanded kallisto to translated alignment (nucleotides <-> amino acids), and used it to detect novel viruses in RNA seq data. The single-cell resolution allowed us to determine whether the presence of these viruses affected host gene expression. 🧵 biorxiv.org/content/10.1101/…
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Maria Carilli retweeted
Gennady Gorin@GorinGennady
19 Jan 2023
We have another preprint out! Please see @lpachter's thread for an overview from the viewpoint of integration, or read on for 1/ biVI: THE CHEMICAL ENGINEER’S PERSPECTIVE
Lior Pachter@lpachter
19 Jan 2023
Interested in "integrating" multimodal #scRNAseq data? W/ @MariaCarilli, @GorinGennady, @funion10 & Tara Chari we introduce biVI, which combines the scVI variational autoencoder with biophysically motivated bivariate models for RNA distributions. 🧵 1/ biorxiv.org/content/10.1101/…
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Maria Carilli retweeted
Lior Pachter@lpachter
19 Jan 2023
Interested in "integrating" multimodal #scRNAseq data? W/ @MariaCarilli, @GorinGennady, @funion10 & Tara Chari we introduce biVI, which combines the scVI variational autoencoder with biophysically motivated bivariate models for RNA distributions. 🧵 1/ biorxiv.org/content/10.1101/…
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Laura Luebbert, PhD@NeuroLuebbert
6 Aug 2022
gget alphafold: Predict the 3D structure of a protein from its amino acid sequence using @DeepMind’s AlphaFold v2.0 from a Python or command-line environment in 3 lines of code. Runs on any laptop and requires only ~4 GB of disk space. Simply ‘pip install gget’ and:
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Maria Carilli retweeted
Slava Bobrov
@slava__bobrov
17 Jul 2022
Neuron vs viruses vs bacteria. Microorganisms size comparison: #biology
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Maria Carilli retweeted
bioRxiv Bioinfo@biorxiv_bioinfo
17 Jun 2022
Spectral neural approximations for models of transcriptional dynamics biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Maria Carilli retweeted
Lior Pachter@lpachter
17 Jun 2022
In a new preprint with @GorinGennady and Maria Carilli (co-first) along with Tara Chari, we show how neural networks can be used to efficiently approximate steady state solutions of two species (nascent and mature RNA) bursty transcription models. biorxiv.org/content/10.1101/… 🧵1/

Spectral neural approximations for models of transcriptional dynamics

Transcriptional systems involving discrete, stochastic events are naturally modeled using Chemical Master Equations (CMEs). These can be solved for microstate probabilities over time and state space...

biorxiv.org
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