Publications by authors named "Srinivas Aluru"

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High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.
Chirag Jain, Luis M Rodriguez-R, Adam M Phillippy, Konstantinos T Konstantinidis, Srinivas Aluru

Nat Commun· November 2018

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Disambiguating a Soft Metagenomic Clustering.
Rahul Nihalani, Jaroslaw Zola, Srinivas Aluru

J Comput Biol· May 2025

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SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.
Sriram P Chockalingam, Maneesha Aluru, Srinivas Aluru

Bioinformatics· February 2025

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GraphSlimmer: Preserving Read Mappability with the Minimum Number of Variants.
Neda Tavakoli, Daniel Gibney, Srinivas Aluru

J Comput Biol· July 2024

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MCPNet: a parallel maximum capacity-based genome-scale gene network construction framework.
Tony C Pan, Sriram P Chockalingam, Maneesha Aluru, Srinivas Aluru

Bioinformatics· June 2023

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On the Hardness of Sequence Alignment on De Bruijn Graphs.
Daniel Gibney, Sharma V Thankachan, Srinivas Aluru

J Comput Biol· December 2022

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EnGRaiN: a supervised ensemble learning method for recovery of large-scale gene regulatory networks.
Maneesha Aluru, Harsh Shrivastava, Sriram P Chockalingam, Shruti Shivakumar, Srinivas Aluru

Bioinformatics· February 2022

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GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks.
Harsh Shrivastava, Xiuwei Zhang, Le Song, Srinivas Aluru

J Comput Biol· January 2022

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Fast alignment and preprocessing of chromatin profiles with Chromap.
Haowen Zhang, Li Song, Xiaotao Wang, Haoyu Cheng, Chenfei Wang, Srinivas Aluru

Nat Commun· November 2021

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Reply to: "Re-evaluating the evidence for a universal genetic boundary among microbial species".
Luis M Rodriguez-R, Chirag Jain, Roth E Conrad, Srinivas Aluru, Konstantinos T Konstantinidis

Nat Commun· July 2021

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Real-time mapping of nanopore raw signals.
Haowen Zhang, Haoran Li, Chirag Jain, Haoyu Cheng, Kin Fai Au, Srinivas Aluru

Bioinformatics· July 2021

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A variant selection framework for genome graphs.
Chirag Jain, Neda Tavakoli, Srinivas Aluru

Bioinformatics· July 2021

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Fast de Bruijn Graph Compaction in Distributed Memory Environments.
Tony Pan, Rahul Nihalani, Srinivas Aluru

IEEE/ACM Trans Comput Biol Bioinform· January 2021

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A comprehensive evaluation of long read error correction methods.
Haowen Zhang, Chirag Jain, Srinivas Aluru

BMC Genomics· December 2020

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An alignment-free heuristic for fast sequence comparisons with applications to phylogeny reconstruction.
Sriram P Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V Thankachan, Srinivas Aluru

BMC Bioinformatics· November 2020

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Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems.
Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru

IEEE/ACM Trans Comput Biol Bioinform· February 2020

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An SVM-based method for assessment of transcription factor-DNA complex models.
Rosario I Corona, Sanjana Sudarshan, Srinivas Aluru, Jun-Tao Guo

BMC Bioinformatics· December 2018

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A fast adaptive algorithm for computing whole-genome homology maps.
Chirag Jain, Sergey Koren, Alexander Dilthey, Adam M Phillippy, Srinivas Aluru

Bioinformatics· September 2018

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A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.
Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru, Adam M Phillippy

J Comput Biol· July 2018

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A greedy alignment-free distance estimator for phylogenetic inference.
Sharma V Thankachan, Sriram P Chockalingam, Yongchao Liu, Ambujam Krishnan, Srinivas Aluru

BMC Bioinformatics· June 2017

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Efficient detection of viral transmissions with Next-Generation Sequencing data.
Inna Rytsareva, David S Campo, Yueli Zheng, Seth Sims, Sharma V Thankachan, Srinivas Aluru

BMC Genomics· May 2017

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RD26 mediates crosstalk between drought and brassinosteroid signalling pathways.
Huaxun Ye, Sanzhen Liu, Buyun Tang, Jiani Chen, Zhouli Xie, Maneesha Aluru, Srinivas Aluru

Nat Commun· February 2017

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Microarray Data Processing Techniques for Genome-Scale Network Inference from Large Public Repositories.
Sriram Chockalingam, Maneesha Aluru, Srinivas Aluru

Microarrays (Basel)· September 2016

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SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations.
Yongchao Liu, Martin Loewer, Srinivas Aluru, Bertil Schmidt

BMC Syst Biol· August 2016

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ALFRED: A Practical Method for Alignment-Free Distance Computation.
Sharma V Thankachan, Sriram P Chockalingam, Yongchao Liu, Alberto Apostolico, Srinivas Aluru

J Comput Biol· June 2016

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