Publications

We develop computational models for dissecting single-cell biology through the analyses of high-throughput omics datasets. See below the list of publications from the lab.

2022

scDREAMER: atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier

Ajita Shree, Musale Krushna Pavan, Hamim Zafar

  ·  14 Jul 2022

Data Integration VAE Adverserial learning.

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Mohammadamin Edrisi, Monica V Valecha, Sunkara B V Chowdary, Sergio Robledo, Huw A Ogilvie, David Posada, Hamim Zafar, Luay Nakhleh

Bioinformatics  ·  24 Jun 2022

Variant Calling Phylogeny Tumor

Inference of cell state transitions and cell fate plasticity from single-cell with MARGARET

Kushagra Pandey, Hamim Zafar

Nucleic Acids Research  ·  25 May 2022

Trajectory Inference Cell fate Development

FiMO: Inferring the Temporal Order of Mutations on Clonal Phylogeny under Finite-sites Models

Avesh Kumar Agrawal, Hamim Zafar

Cold Spring Harbor Laboratory  ·  24 Jan 2022

Phylogeny Tumor Mutation Order

2021

TruthBot: An Automated Conversational Tool for Intent Learning, Curated Information Presenting, and Fake News Alerting

Ankur Gupta, Yash Varun, Prarthana Das, Nithya Muttineni, Parth Srivastava, Hamim Zafar, Tanmoy Chakraborty, Swaprava Nath

arXiv  ·  02 Feb 2021

Pre-metastatic niche drives breast cancer invasion by modulating MSC homing and CAF differentiation

Neha Saxena, Garvit Bhardwaj, Sameer Jadhav, Hamim Zafar, Shamik Sen

Cold Spring Harbor Laboratory  ·  13 Jan 2021

2020

Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data

Hamim Zafar, Chieh Lin, Ziv Bar-Joseph

Nature Communications  ·  16 Jun 2020

Phylogeny Lineage Development

2019

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data

Hamim Zafar, Nicholas Navin, Ken Chen, Luay Nakhleh

Genome Research  ·  18 Oct 2019

Phylogeny Tumor Clone

A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference

Mohammadamin Edrisi, Hamim Zafar, Luay Nakhleh

Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH, Wadern/Saarbruecken, Germany  ·  01 Jan 2019

Variant Calling Phylogeny Tumor

2018

Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells

Brian J. Grindel, Jerahme R. Martinez, Tristen V. Tellman, Daniel A. Harrington, Hamim Zafar, Luay Nakhleh, Leland W. Chung, Mary C. Farach-Carson

Scientific Reports  ·  08 May 2018

Computational approaches for inferring tumor evolution from single-cell genomic data

Hamim Zafar, Nicholas Navin, Luay Nakhleh, Ken Chen

Current Opinion in Systems Biology  ·  01 Feb 2018

Variant Calling Single cell

2017

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models

Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh

Genome Biology  ·  19 Sep 2017

Phylogeny Tumor Clone

  ·  01 Jan 1900

Cell-cell Communication Spatial Transcriptomics Ligand-target activity.