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Probably Learning!
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Probably Learning!
173 followers · 162 following

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Achievement: YOLOAchievement: Pull Shark

Achievements

Achievement: YOLOAchievement: Pull Shark

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@chiralbd @deepbioacademy

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hossainlab/README.md

Jubayer Hossain

I study which tumor cells survive therapy, using public single-cell and spatial data. I test my tools before I trust their results, and I release everything needed to check my work.

Website · Google Scholar · ORCID

Selected projects

Project Question and result Output
dmg_atlas Which diffuse midline glioma cell states replicate across 6 studies and 311,618 cells? Only cycling and hypoxia met a pre-registered replication rule. [Preprint] · Zenodo
sc-cnv-fps How often do copy-number callers label normal cells as malignant? I ran three callers on 14 tumor-free datasets; an empirical null cut false calls about 90-fold. [Preprint]
dmg_mh_states Do mouse DMG models reproduce human tumor cell states? [Status]
ews_atlas A harmonized single-cell atlas of Ewing sarcoma. [Status]
cfm_eval Do single-cell foundation models work zero-shot on cancer data? [Status]
fezf2-loss-multi-omics How does Fezf2 dosage shape cortical neuron development? 121,889 cells, with effect sizes calibrated against replicate noise. bioRxiv

How I work

  • Every README lists the limitations and open issues.
  • Code, software versions and data checksums are released with each project.

Teaching

I founded CHIRAL Bangladesh and DeepBio to train students in reproducible bioinformatics. Course material lives at DeepBio Academy.

Pinned Loading

  1. spatial-niche-gbm spatial-niche-gbm Public

    Graph Neural Network for Predicting Immunosuppressive Spatial Niches in Glioblastoma

    Jupyter Notebook

  2. fezf2-loss-multi-omics fezf2-loss-multi-omics Public

    Single-cell multi-omics re-analysis reveals dosage-dependent disruption of corticofugal neuron development by Fezf2 loss

    Jupyter Notebook

  3. cella cella Public

    Cella: Decoding Cell-Type Identity Beyond Raw Expression

    Python

  4. gbm-bulk-deconvolution gbm-bulk-deconvolution Public

    Deconvolved myeloid infiltration and malignant-mesenchymal state are coupled but do not independently predict survival in IDH-wildtype glioblastoma: a multi-cohort, multi-method bulk RNA-seq analysis

    R 1

  5. sc-cnv-fps sc-cnv-fps Public

    Evaluating the false-positive rate of single-cell copy-number and malignant-cell classifiers

    Python

  6. perturb-bench perturb-bench Public

    Perturbation Response Prediction

    Jupyter Notebook