List of works - Hamidreza Chitsaz

A partition function algorithm for interacting nucleic acid strands

scientific article

ARYANA: Aligning Reads by Yet Another Approach

scientific article

An efficient algorithm for upper bound on the partition function of nucleic acids

scientific article published on 15 April 2013

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

scientific article

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

scientific article

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks

article

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

scientific article published on 12 December 2017

DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome

scientific article published on 11 November 2019

Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities

scientific article published on 05 August 2013

Draft genome of provides insights into conserved regulatory elements of the brain restriction gene in planarians

article

Efficient Synergistic Single-Cell Genome Assembly

scientific article published on 23 May 2016

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

scientific article

Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency

scientific article

Enrichment of ovine gonadotropes via adenovirus gene targeting enhances assessment of transcriptional changes in response to estradiol-17 beta†

scientific article published on 01 February 2020

Exact learning of RNA energy parameters from structure

scientific article

Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast

scientific article published on 31 July 2017

Graph Traversal Edit Distance and Extensions

scientific article published on 13 February 2020

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly

scientific article

Increased robustness of early embryogenesis through collective decision-making by key transcription factors

scientific article published on 2 June 2015

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

scientific article

PyGTED: Python Application for Computing Graph Traversal Edit Distance

scientific article published on 01 March 2020

SEQuel: improving the accuracy of genome assemblies

scientific article

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

scientific article published on 07 April 2017

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

scientific article

The RNA Newton polytope and learnability of energy parameters

scientific article published on July 2013

List of works by Hamidreza Chitsaz

A partition function algorithm for interacting nucleic acid strands

ARYANA: Aligning Reads by Yet Another Approach

An efficient algorithm for upper bound on the partition function of nucleic acids

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

Cell Identity Codes: Understanding Cell Identity from Gene Expression Profiles using Deep Neural Networks

DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism

DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome

Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities

Draft genome of provides insights into conserved regulatory elements of the brain restriction gene in planarians

Efficient Synergistic Single-Cell Genome Assembly

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

Enhancing Extraction of Drug-Drug Interaction from Literature Using Neutral Candidates, Negation, and Clause Dependency

Enrichment of ovine gonadotropes via adenovirus gene targeting enhances assessment of transcriptional changes in response to estradiol-17 beta†

Exact learning of RNA energy parameters from structure

Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast

Graph Traversal Edit Distance and Extensions

HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly

Increased robustness of early embryogenesis through collective decision-making by key transcription factors

Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.

PyGTED: Python Application for Computing Graph Traversal Edit Distance

SEQuel: improving the accuracy of genome assemblies

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

The RNA Newton polytope and learnability of energy parameters