Jérémie Kalfon

TangentXY: Improved copy-number estimation of sex chromosomes reveals features associated with aneuploidies in chromosomes X and Y across cancers

TangentXY improves copy-number estimation for sex chromosomes, revealing associations between chrX and chrY copy-number alterations and cancer features.

Towards foundation models that learn across biological scales

The paper introduces Xpressor, a framework for cross-scale learning in biology, improving cell-type prediction and embedding quality.

scPRINT-2: Towards the next-generation of cell foundation models and benchmarks

scPRINT-2 is a single-cell foundation model pre-trained on 350 million cells across 16 organisms, achieving state-of-the-art performance in expression denoising, cell embedding, and cell type prediction.

scPRINT: pre-training on 50 million cells allows robust gene network predictions

scPRINT pre-trains on 50 million cells to predict gene networks, outperforming existing methods in inference and zero-shot tasks.

geneRNIB: a living benchmark for gene regulatory network inference

geneRNIB provides a benchmark for gene regulatory network inference, showing simpler models often outperform complex ones in perturbation-informed metrics.

Rapid-kinetics degron benchmarking reveals off-target activities and mixed agonism-antagonism of MYB inhibitors

The paper benchmarks six MYB inhibitors using a nascent transcriptomics assay, revealing partial specificity, off-target activity, and mixed agonism-antagonism effects.

Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops

The paper reconstructs a sparsely interconnected transcriptional hierarchy in leukemia cells stabilized by incoherent feed-forward loops and shows inhibitors disrupt core regulators' programs.

Transcriptional plasticity drives leukemia immune escape

The paper identifies transcription factors regulating MHC-II expression in AML and shows their role in immune evasion and relapse.

A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

The paper identifies a modular core regulatory circuitry in AML that enforces oncogene expression in KMT2A-rearranged leukemias.

Hidden patterns of codon usage bias across kingdoms

The paper develops a mathematical model to quantify codon usage bias across fungal and bacterial genomes, revealing taxonomic variation and implications for model organisms.

CaImAn: An open source tool for scalable Calcium Imaging data Analysis

CaImAn, an open-source library, automates motion correction, source extraction, deconvolution and cross-session registration for calcium imaging, detecting neurons near human level (F1 0.75 batch, 0.76 online).