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1
A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer
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A latent variable model for evaluating mutual exclusivity and co-occurrence between driver mutations in cancer

Shuaibi, Ahmed ; Chitra, Uthsav ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2024-04

United States

Sem texto completo

2
Mapping the topography of spatial gene expression with interpretable deep learning
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Mapping the topography of spatial gene expression with interpretable deep learning

Chitra, Uthsav ; Arnold, Brian J ; Sarkar, Hirak ; Ma, Cong ; Lopez-Darwin, Sereno ; Sanno, Kohei ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2023-10

United States

Sem texto completo

3
Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data
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Maximum Likelihood Inference of Time-scaled Cell Lineage Trees with Mixed-type Missing Data

Mai, Uyen ; Chu, Gillian ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2024-03

United States

Sem texto completo

4
A zero-agnostic model for copy number evolution in cancer
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A zero-agnostic model for copy number evolution in cancer

Schmidt, Henri ; Sashittal, Palash ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2023-04

United States

Sem texto completo

5
PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data
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PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data

Liu, Xinhao ; Zeira, Ron ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2023-01

United States

Sem texto completo

6
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data
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DeST-OT: Alignment of Spatiotemporal Transcriptomics Data

Halmos, Peter ; Liu, Xinhao ; Gold, Julian ; Chen, Feng ; Ding, Li ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2024-03

United States

Sem texto completo

7
HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data
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HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data

Myers, Matthew A ; Arnold, Brian J ; Bansal, Vineet ; Mullen, Katelyn M ; Zaccaria, Simone ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2023-07

United States

Sem texto completo

8
ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model
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ConDoR: Tumor phylogeny inference with a copy-number constrained mutation loss model

Sashittal, Palash ; Zhang, Haochen ; Iacobuzio-Donahue, Christine A ; Raphael, Benjamin J

bioRxiv : the preprint server for biology, 2023-01

United States

Sem texto completo

9
UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples
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UNSEG: unsupervised segmentation of cells and their nuclei in complex tissue samples

Kochetov, Bogdan ; Bell, Phoenix ; Garcia, Paulo S ; Shalaby, Akram S ; Raphael, Rebecca ; Raymond, Benjamin ; Leibowitz, Brian J ; Schoedel, Karen ; Brand, Rhonda M ; Brand, Randall E ; Yu, Jian ; Zhang, Lin ; Diergaarde, Brenda ; Schoen, Robert E ; Singhi, Aatur ; Uttam, Shikhar

bioRxiv : the preprint server for biology, 2024-04

United States

Sem texto completo

10
A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex
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A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex

Leydon, Alexander R ; Downing, Benjamin ; Sanchez, Janet Solano ; Loll-Krippleber, Raphael ; Belliveau, Nathan M ; Rodriguez-Mias, Ricard A ; Bauer, Andrew ; Watson, Isabella J ; Bae, Lena ; Villén, Judit ; Brown, Grant W ; Nemhauser, Jennifer L

bioRxiv : the preprint server for biology, 2024-04

United States

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