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List of works by Niina Haiminen

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases.

scientific article published on 14 November 2017

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

scientific article

BAC sequencing using pooled methods

scientific article

Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations

scientific article published on 24 February 2022

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

scientific article published on 18 August 2020

Comparative exomics of Phalaris cultivars under salt stress

scientific article

Correction: Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results

scientific article (publication date: 5 October 2011)

Correction: Evaluation of Methods for De Novo Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results.

scientific article

Discovering patterns in gene order.

scientific article published on January 2012

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

scientific article published on 15 March 2021

Evaluation of BIC and cross validation for model selection on sequence segmentations.

scientific article published in January 2010

Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results

scientific article (publication date: 2011)

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

scientific article published on 25 February 2021

Food authentication from shotgun sequencing reads with an application on high protein powders

scientific article published on 19 November 2019

Functional pathways in respiratory tract microbiome separate COVID-19 from community-acquired pneumonia patients

scientific article published on 03 May 2020

Haplotype assembly of autotetraploid potato using integer linear programing

scientific article published on 01 September 2019

Haplotype assembly of autotetraploid potato using integer linear programing

scientific article published on 01 November 2019

Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes

scientific article published on 17 March 2020

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

scientific article published on 11 February 2020

Linear time algorithms to construct populations fitting multiple constraint distributions at genomic scales

scientific article

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

scientific article published on 22 November 2020

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

scientific article published on 6 June 2021

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

scientific article published on 04 April 2022

Randomization techniques for assessing the significance of gene periodicity results ⬇️

scientific article published on August 9, 2011

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

scientific article

Signal enrichment with strain-level resolution in metagenomes using topological data analysis

scientific article published on 04 April 2019

SimBA: simulation algorithm to fit extant-population distributions

scientific article published on 14 March 2015

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

scientific article

Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata

scientific article published on 01 October 2019

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data

scientific article published on 29 April 2021

iXora: exact haplotype inferencing and trait association.

scientific article

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