Ritambhara Singh

发表

Jointly Embedding Multiple Single-Cell Omics Measurements

William Stafford Noble, Jean-Philippe Vert, Jie Liu, 2019, bioRxiv.

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

Mazhar Adli, A. Quinlan, Ritambhara Singh, 2015, Nucleic acids research.

Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9

Mustafa Mir, Ahmet Yildiz, Peiwu Qin, 2017, Nature Communications.

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

Mazhar Adli, Ritambhara Singh, Cem Kuscu, 2014, Nature Biotechnology.

Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

William Stafford Noble, Cole Trapnell, J. Shendure, 2020, Genome Biology.

A pitfall for machine learning methods aiming to predict across cell types

William Stafford Noble, Jacob M. Schreiber, J. Bilmes, 2020, Genome biology.

Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells

Hui Li, Mazhar Adli, Fujun Qin, 2015, PLoS genetics.

A pitfall for machine learning methods aiming to predict across cell types

Jeff A. Bilmes, William Stafford Noble, Jacob M. Schreiber, 2019, Genome Biology.

Unbalanced CO-Optimal Transport

N. Courty, Rémi Flamary, I. Redko, 2022, AAAI.

Exploring Graph-Based Neural Networks for Automatic Brain Tumor Segmentation

R. Munbodh, Ritambhara Singh, Camillo F Saueressig, 2020, DataMod@CIKM.

Multimodal Attention-based Deep Learning for Alzheimer's Disease Diagnosis

Ritambhara Singh, Carsten Eickhoff, Michal Golovanevsky, 2022, ArXiv.

Predicting Cell Type and Extracting Key Genes using Single Cell Multi-Omics Data and Graph Neural Networks

Ritambhara Singh, Hossam A. Zaki, 2022 .

cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9.

Mazhar Adli, X. Darzacq, Ritambhara Singh, 2017 .

Beyond DNA methylation: chromatin age of human tissues

Ritambhara Singh, M. Asif, 2022 .

Jointly Embedding Multiple Single-Cell Omics Measurements

William Stafford Noble, Jean-Philippe Vert, Jie Liu, 2019, bioRxiv.

Investigating the performance of deep learning methods for Hi-C resolution improvement

Ritambhara Singh, G. Murtaza, Atishay Jain, 2022, bioRxiv.

GrapHiC: An integrative graph based approach for imputing missing Hi-C reads

J. Zook, Justin Wagner, Ritambhara Singh, 2022, bioRxiv.

Predicting A/B compartments from histone modifications using deep learning

William Stafford Noble, M. Gerstein, Erez Lieberman-Aiden, 2022, bioRxiv.

Multimodal Attention-based Deep Learning for Alzheimer's Disease Diagnosis

Ritambhara Singh, Michal Golovanevsky, C. Eickhoff, 2022, J. Am. Medical Informatics Assoc..

Investigating the Complexity of Gene Co-expression Estimation for Single-cell Data

Ritambhara Singh, Jiaqi Zhang, 2023, bioRxiv.

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data

Yanhui Hu, Norbert Perrimon, Ritambhara Singh, 2020, bioRxiv.

Unsupervised manifold alignment for single-cell multi-omics data

William Stafford Noble, Ritambhara Singh, Pinar Demetci, 2020, bioRxiv.

Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks

E. Larschan, Ritambhara Singh, Shalin Patel, 2022, J. Comput. Biol..

Integrating long-range regulatory interactions to predict gene expression using graph convolutional neural networks

Ritambhara Singh, Erica Larschan, Jeremy Bigness, 2020, bioRxiv.

Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma

S. Toms, A. Fiser, Ritambhara Singh, 2021, bioRxiv.

DeepChrome: deep-learning for predicting gene expression from histone modifications

Yanjun Qi, Gabriel Robins, Ritambhara Singh, 2016, Bioinform..

Machine learning for profile prediction in genomics.

Jacob M. Schreiber, Ritambhara Singh, 2021, Current opinion in chemical biology.

Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

Beilun Wang, Yanjun Qi, Ritambhara Singh, 2016, PSB.

Deep Motif: Visualizing Genomic Sequence Classifications pdf

Yanjun Qi, Zeming Lin, Ritambhara Singh, 2016, ArXiv.

Gromov-Wasserstein optimal transport to align single-cell multi-omics data

William Stafford Noble, Björn Sandstede, Ritambhara Singh, 2020, bioRxiv.

SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport

Ritambhara Singh, Pinar Demetci, Bjorn Sandstede, 2022, J. Comput. Biol..

Single-Cell Multiomics Integration by SCOT

Ritambhara Singh, Pinar Demetci, Bjorn Sandstede, 2022, J. Comput. Biol..

DeepDiff: DEEP‐learning for predicting DIFFerential gene expression from histone modifications

Arshdeep Sekhon, Yanjun Qi, Ritambhara Singh, 2018, Bioinform..

Live cell imaging of low-and non-repetitive chromosome loci using CRISPR-Cas 9

Mazhar Adli, X. Darzacq, Ritambhara Singh, 2017 .

A pan-tissue DNA-methylation epigenetic clock based on deep learning

Ritambhara Singh, L. R. Lapierre, Lucas Paulo de Lima Camillo, 2021, npj Aging.

Degree of recruitment of DOT1L to MLL-AF9 defines level of H3K79 Di- and tri-methylation on target genes and transformation potential.

N. Zeleznik-Le, Mazhar Adli, Ritambhara Singh, 2015, Cell reports.

A pan-tissue DNA-methylation epigenetic clock based on deep learning

Ritambhara Singh, L. R. Lapierre, Lucas Paulo de Lima Camillo, 2022, npj Aging.

GaKCo: a Fast Gapped k-mer string Kernel using Counting pdf

Beilun Wang, Arshdeep Sekhon, Yanjun Qi, 2017, bioRxiv.

Character based String Kernels for Bio-Entity Relation Detection

Yanjun Qi, Ritambhara Singh, Yanjun Qi, 2016, BioNLP@ACL.

A pitfall for machine learning methods aiming to predict across cell types

William Stafford Noble, Jacob M. Schreiber, Ritambhara Singh, 2020, Genome Biology.

Unsupervised integration of single-cell multi-omics datasets with disparities in cell-type representation

Ritambhara Singh, Pinar Demetci, Bjorn Sandstede, 2021, bioRxiv.

SCOTv2: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation

Ritambhara Singh, Pinar Demetci, Bjorn Sandstede, 2022, J. Comput. Biol..

AltumAge: A Pan-Tissue DNA-Methylation Epigenetic Clock Based on Deep Learning

Ritambhara Singh, L. R. Lapierre, Lucas Paulo de Lima Camillo, 2021, bioRxiv.

An automated COVID-19 triage pipeline using artificial intelligence based on chest radiographs and clinical data

Raymond Y Huang, R. Sebro, I. Kamel, 2022, npj Digital Medicine.

GrapHiC: An integrative graph based approach for imputing missing Hi-C reads

J. Zook, Justin Wagner, Ritambhara Singh, 2023, bioRxiv.

FastSK: fast sequence analysis with gapped string kernels.

Yanjun Qi, Jack Lanchantin, Ritambhara Singh, 2020, Bioinformatics.

FastSK: Fast Sequence Analysis with Gapped String Kernels

Yanjun Qi, Derrick Blakely, Eamon Collins, 2020, bioRxiv.

Prototype Matching Networks for Large-Scale Multi-label Genomic Sequence Classification pdf

Arshdeep Sekhon, Yanjun Qi, Ritambhara Singh, 2017, ArXiv.

Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin

Arshdeep Sekhon, Yanjun Qi, Ritambhara Singh, 2017, bioRxiv.

Chi3l1 Is a Modulator of Glioma Stem Cell States and a Therapeutic Target in Glioblastoma

S. Toms, A. Fiser, J. Fajardo, 2023, Cancer research.

Advance Access Publication Date: Day Month Year Manuscript Category Deepchrome: Deep-learning for Predicting Gene Expression from Histone Modifications

Yanjun Qi, G. Robins, Jack Lanchantin, 2022 .

A Joint Graph and Image Convolution Network for Automatic Brain Tumor Segmentation

R. Munbodh, Ritambhara Singh, Camillo F. Saueressig, 2021, BrainLes@MICCAI.

Revisiting invariances and introducing priors in Gromov-Wasserstein distances

I. Redko, Ritambhara Singh, Quang-Huy Tran, 2023, ArXiv.

GrapHiC: An integrative graph based approach for imputing missing Hi-C reads

J. Zook, Justin Wagner, Ritambhara Singh, 2023, bioRxiv.

A comprehensive evaluation of generalizability of deep-learning based Hi-C resolution improvement methods

Justin Wagner, Ritambhara Singh, G. Murtaza, 2023, bioRxiv.

Investigating the performance of deep learning methods for Hi-C resolution improvement

Ritambhara Singh, Madeline Y. Hughes, G. Murtaza, 2022 .

Memory Matching Networks for Genomic Sequence Classification pdf

Yanjun Qi, Ritambhara Singh, Jack Lanchantin, 2017, ICLR.

One of the fundamental tasks in understanding genomics is the problem of predicting Transcription

Yanjun Qi, Ritambhara Singh, Arshdeep Sekhon, 2018 .

Jointly aligning cells and genomic features of single-cell multi-omics data with co-optimal transport

I. Redko, Ritambhara Singh, Quang-Huy Tran, 2022, bioRxiv.

One-Versus-Others Attention: Scalable Multimodal Integration

Carsten Eickhoff, Ritambhara Singh, Michal Golovanevsky, 2023, arXiv.org.

Histone mark age of human tissues and cells

E. Larschan, Ritambhara Singh, Lucas Paulo de Lima Camillo, 2023, bioRxiv.

Transfer String Kernel for Cross-Context DNA-Protein Binding Prediction

Yanjun Qi, Gabriel Robins, Ritambhara Singh, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A constrained $$\ell $$ℓ1 minimization approach for estimating multiple sparse Gaussian or nonparanormal graphical models

Yanjun Qi, Beilun Wang, Ritambhara Singh, 2016, Machine Learning.

A constrained $$\ell $$ℓ1 minimization approach for estimating multiple sparse Gaussian or nonparanormal graphical models

Beilun Wang, Yanjun Qi, Ritambhara Singh, 2016, Machine Learning.

Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks

E. Larschan, Ritambhara Singh, Shalin Patel, 2022, J. Comput. Biol..

Unbalanced CO-Optimal Transport

N. Courty, Rémi Flamary, I. Redko, 2022, AAAI.

Clinical capability of modern brain tumor segmentation models.

R. Munbodh, Ritambhara Singh, U. Shukla, 2023, Medical physics.

Advance Access Publication Date: Day Month Year Manuscript Category Deepchrome: Deep-learning for Predicting Gene Expression from Histone Modifications

Yanjun Qi, G. Robins, Jack Lanchantin, 2022 .

DeMo Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

Yanjun Qi, Beilun Wang, Jack Lanchantin, 2016 .

Deep GDashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks pdf

Beilun Wang, Yanjun Qi, Ritambhara Singh, 2016, ArXiv.