Laraib Malik

Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis

Fatemeh Almodaresi, Robert Patro, Laraib Malik, 2018, Bioinform..

Crow: Fast and accurate expression estimation from long reads

Avi Srivastava, Laraib Malik, Rob Patro, 2018, RECOMB 2018.

Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes pdf

Robert Patro, Avi Srivastava, Hirak Sarkar, 2016, ArXiv.

Rich Chromatin Structure Prediction from Hi-C Data

Robert Patro, Laraib Malik, Laraib Malik, 2019, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification

Robert Patro, Hirak Sarkar, Laraib Malik, 2017, bioRxiv.

Towards Selective-Alignment: Producing Accurate And Sensitive Alignments Using Quasi-Mapping

Hirak Sarkar, Laraib Malik, Rob Patro, 2017 .

Alignment and mapping methodology influence transcript abundance estimation

Fatemeh Almodaresi, Charlotte Soneson, Carl Kingsford, 2019, Genome Biology.

Graph regularized, semi-supervised learning improves annotation of de novo transcriptomes

Laraib Malik, Rob Patro, Shravya Thatipally, 2016, bioRxiv.

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data

Avi Srivastava, Laraib Malik, Rob Patro, 2018, Genome Biology.