Publications

2020

A Random Matrix Theory Approach to Denoise Single-Cell Data

Aparicio L,

Bordyuh M,

Blumberg AJ

Rabadan R

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

Blattman S B

Jiang W

Oikonomou P

Tavazoie S

Dose-response modeling in high-throughput cancer drug screenings: An end-to-end approach

Tansey W

Li K

Zhang H

....

Wiggins H

Time Course of Changes in Sorafenib‐Treated Hepatocellular Carcinoma (HCC) Cells Suggests Involvement of Phospho‐Regulated Signaling in Ferroptosis Induction

Werth E G

Rajbhandari P

Stockwell B

Brown L M

Cysteine depletion induces pancreatic tumor ferroptosis in mice

Badgley M A

Kremer DM

Maurer H C

....

Olive K P

SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses

Satas G

Zaccaria S

Mon G

Raphael B J

Fibroblastic reticular cells predict response to immune checkpoint inhibitors

Biasci D

Thaventhiran J Simon Tavaré

Tavaré S

Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.

Jiang W

Oikonomou P

Tavazoie S

Non-invasive optical biomarkers distinguish and track the metabolic status of single hematopoietic stem cells

Zhou H

Nguyen L

Arnesano C

....

Shen K

High-contrast, synchronous volumetric imaging with selective volume illumination microscopy

Truong T V

Holland D B

Madaan S

....

Fraser S E

Pathway and network analysis of more than 2500 whole cancer genomes

Reyna M A

Haan D

Paczkowska M

....

Raphael B J

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

Elyanow R

Dumitrascu B

Engelhardt B E

Raphael2 B J

Patient-derived glioblastoma cultures as a tool for small-molecule drug discovery

Ye L F,1 Eduard Reznik,1 Joshua M. Korn,

Reznik E

Korn J M

....

Stockwell B R

Radiation-Induced Lipid Peroxidation Triggers Ferroptosis and Synergizes with Ferroptosis Inducers

LF Ye

Chaudhary KR

Zandkarimi F

....

Stockwell BR

Discovering Transcription Factor Noncoding RNA Targets Using ChIP-Seq Analysis

Fomin V

Prives C

Efficient and accurate inference of microbial trajectories from longitudinal count data

Joseph T A, Amey P. Pasarkar, Itsik Pe’er

Pasarkar A P, Itsik Pe’er

Pe’er I

The Blessings of Multiple Causes: Rejoinder

Y Wang

DM Blei

Efficient and accurate inference of microbial trajectories from longitudinal count data

Joseph, TA

2019

Optimizing Esophageal Cancer Surveillance and Prevention Using a Comparative Simulation Modeling Approach

Omidvari AH

Ali A

Hazelton WD

....

Luebeck G

Hur C

GTP Cyclohydrolase 1/Tetrahydrobiopterin Counteract Ferroptosis through Lipid Remodeling

Kraft VAN

Bezjian CT

Pfeiffer S

...

Stockwell BR

Schick JA

Leveraging insights into cancer metabolism—a symposium report

Cable J

Finley L

Tu B P

....

Kaelin W

Tissue-Resident Memory T Cells in Mice and Humans: Towards a Quantitative Ecology

Morris S E

Farber D L

Yates A J

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Laks E

McPherson A

Zahn H

....

Aparicio S

Genomic architecture and introgression shape a butterfly radiation

Edelman NB,

Frandsen PB,

Miyagi M,

....

Blumberg AJ,

Mallet J

Random Matrices

Borodin A

Corwin I

Guionnet A

Relational Dose-Response Modeling for Cancer Drug Studies

W Tansey

C Tosh

DM Blei

Some recent progress in singular stochastic partial differential equations

Corwin I

Shen H

Particle Smoothing Variational Objectives

Moretti A K

Wang Z

Wu L

....

Pe'er I

Topological Data Analysis for Genomics and Evolution: Topology in Biology

Rabadán RJ

Blumberg AJ

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Publications

2020

A Random Matrix Theory Approach to Denoise Single-Cell Data

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing

Dose-response modeling in high-throughput cancer drug screenings: An end-to-end approach

Time Course of Changes in Sorafenib‐Treated Hepatocellular Carcinoma (HCC) Cells Suggests Involvement of Phospho‐Regulated Signaling in Ferroptosis Induction

Cysteine depletion induces pancreatic tumor ferroptosis in mice

SCARLET: Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses

Fibroblastic reticular cells predict response to immune checkpoint inhibitors

Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.

Non-invasive optical biomarkers distinguish and track the metabolic status of single hematopoietic stem cells

High-contrast, synchronous volumetric imaging with selective volume illumination microscopy

Pathway and network analysis of more than 2500 whole cancer genomes

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

Patient-derived glioblastoma cultures as a tool for small-molecule drug discovery

Radiation-Induced Lipid Peroxidation Triggers Ferroptosis and Synergizes with Ferroptosis Inducers

Discovering Transcription Factor Noncoding RNA Targets Using ChIP-Seq Analysis

Efficient and accurate inference of microbial trajectories from longitudinal count data

The Blessings of Multiple Causes: Rejoinder

Efficient and accurate inference of microbial trajectories from longitudinal count data

2019

Optimizing Esophageal Cancer Surveillance and Prevention Using a Comparative Simulation Modeling Approach

GTP Cyclohydrolase 1/Tetrahydrobiopterin Counteract Ferroptosis through Lipid Remodeling

GTP Cyclohydrolase 1/Tetrahydrobiopterin Counteract Ferroptosis through Lipid Remodeling

Leveraging insights into cancer metabolism—a symposium report

Tissue-Resident Memory T Cells in Mice and Humans: Towards a Quantitative Ecology

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Genomic architecture and introgression shape a butterfly radiation

Random Matrices

Relational Dose-Response Modeling for Cancer Drug Studies

Some recent progress in singular stochastic partial differential equations

Particle Smoothing Variational Objectives

Topological Data Analysis for Genomics and Evolution: Topology in Biology

edit publication

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