Blar i Bergen Open Research Archive på forfatter "Shigdel, Rajesh"

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    • Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action 

      D’Elia, Domenica; Truu, Jaak; Lahti, Leo; Berland, Magali; Papoutsoglou, Georgios; Ceci, Michelangelo; Zomer, Aldert; Lopes, Marta B.; Ibrahimi, Eliana; Gruca, Aleksandra; Nechyporenko, Alina; Frohme, Marcus; Klammsteiner, Thomas; Pau, Enrique Carrillo-de Santa; Marcos-Zambrano, Laura Judith; Hron, Karel; Pio, Gianvito; Simeon, Andrea; Suharoschi, Ramona; Moreno-Indias, Isabel; Temko, Andriy; Nedyalkova, Miroslava; Apostol, Elena-Simona; Truică, Ciprian-Octavian; Shigdel, Rajesh; Telalović, Jasminka Hasić; Bongcam-Rudloff, Erik; Przymus, Piotr; Jordamović, Naida Babić; Falquet, Laurent; Tarazona, Sonia; Sampri, Alexia; Isola, Gaetano; Pérez-Serrano, David; Trajkovik, Vladimir; Klucar, Lubos; Loncar-Turukalo, Tatjana; Havulinna, Aki S.; Jansen, Christian; Bertelsen, Randi Jacobsen; Claesson, Marcus Joakim (Journal article; Peer reviewed, 2023)
      The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which ...

    • Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment 

      Marcos-Zambrano, Laura Judith; Hadziabdic, Kanita Karaduzovic; Turukalo, Tatjana Loncar; Przymus, Piotr; Trajkovik, Vladimir; Aasmets, Oliver; Berland, Magali; Gruca, Aleksandra; Hasic, Jasminka; Hron, Karel; Klammsteiner, Thomas; Kolev, Mikhail; Lahti, Leo; Lopes, Marta B.; Moreno, Victor; Naskinova, Irina; Org, Elin; Paciencia, Ines; Papoutsoglou, Georgios; Shigdel, Rajesh; Stres, Blaz; Vilne, Baiba; Yousef, Malik; Zdravevski, Eftim; Tsamardinos, Ioannis; Carrillo de Santa Pau, Enrique; Claesson, Marcus J.; Moreno-Indias, Isabel; Truu, Jaak (Journal article; Peer reviewed, 2021)
      The number of microbiome-related studies has notably increased the availability of data on human microbiome composition and function. These studies provide the essential material to deeply explore host-microbiome associations ...

    • Association of oral bacteria with oral hygiene habits and self-reported gingival bleeding 

      Bertelsen, Randi Jacobsen; Perez Barrionuevo, Antonio Manuel; Shigdel, Rajesh; Lie, Stein Atle; Lin, Huang; Real, Francisco Gomez; Ringel-Kulka, Tamar; Åstrøm, Anne-Kristine N; Svanes, Cecilie (Journal article; Peer reviewed, 2022)
      Aim To describe associations of gingival bacterial composition and diversity with self-reported gingival bleeding and oral hygiene habits in a Norwegian regional-based population. Materials and Methods We examined the ...

    • Exposure to Antibacterial Chemicals Is Associated With Altered Composition of Oral Microbiome 

      Vindenes, Hilde Kristin; Lin, Huang; Shigdel, Rajesh; Ringel-Kulka, Tamar; Real, Francisco Gomez; Svanes, Cecilie; Peddada, Shyamal D.; Bertelsen, Randi Jacobsen (Journal article; Peer reviewed, 2022)
      Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional exposure in humans to such chemicals is well documented, ...

    • The Future of DNA Barcoding: Reflections from Early Career Researchers 

      Grant, Danielle M.; Brodnicke, Ole Bjørn; Evankow, Ann; Ferreira, André O.; Fontes, João T.; Hansen, Aslak Kappel; Jensen, Mads Reinholdt; Kalaycı, Tuğba Ergül; Leeper, Alexandra Eve Joyce; Patil, Shalaka Kiran; Prati, Sebastian; Reunamo, Anna; Roberts, Aradhana J; Shigdel, Rajesh; Tyukosova, Valentina; Bendiksby, Mika; Blaalid, Rakel; Costa, Filipe O.; Hollingsworth, Peter M.; Stur, Elisabeth; Ekrem, Torbjørn (Journal article; Peer reviewed, 2021)
      Over the last two decades, the use of DNA barcodes has transformed our ability to identify and assess life on our planet. Both strengths and weaknesses of the method have been exemplified through thousands of peer-reviewed ...

    • Indoor Airborne Microbiome and Endotoxin: Meteorological Events and Occupant Characteristics Are Important Determinants 

      Abouelhana, Hesham Amin Mohamed; Šantl-Temkiv, Tina; Cramer, Christine; Finster, Kai; Gomez Real, Francisco; Gislason, Thorarinn; Holm, Mathias; Janson, Christer; Jögi, Nils Oskar; Jogi, Rain; Malinovschi, Andrei; Marshall, Ian P. G.; Modig, Lars; Norbäck, Dan; Shigdel, Rajesh; Sigsgaard, Torben; Svanes, Cecilie; Thorarinsdottir, Hulda; Wouters, Inge M.; Schlünssen, Vivi; Bertelsen, Randi Jacobsen (Journal article; Peer reviewed, 2023)
      Airborne bacteria and endotoxin may affect asthma and allergies. However, there is limited understanding of the environmental determinants that influence them. This study investigated the airborne microbiomes in the homes ...

    • Machine learning approaches in microbiome research: challenges and best practices 

      Papoutsoglou, Georgios; Tarazona, Sonia; Lopes, Marta B.; Klammsteiner, Thomas; Ibrahimi, Eliana; Eckenberger, Julia; Novielli, Pierfrancesco; Tonda, Alberto; Simeon, Andrea; Shigdel, Rajesh; Béreux, Stéphane; Vitali, Giacomo; Tangaro, Sabina; Lahti, Leo; Temko, Andriy; Claesson, Marcus J.; Berland, Magali (Journal article; Peer reviewed, 2023)
      Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model ...

    • Oral bacterial composition associated with lung function and lung inflammation in a community-based Norwegian population 

      Shigdel, Rajesh; Johannessen, Ane; Lin, Huang; Peddada, Shyamal D.; Gomez Real, Francisco; Ringel-Kulka, Tamar; Svanes, Cecilie; Bertelsen, Randi Jacobsen (Journal article; Peer reviewed, 2023)
      Background The oral cavity is the gateway to the bacteria community in the lung. Disruption of the symbiotic balance of the oral microbiota has been associated with respiratory diseases. However, little is known about ...

    • Overview of data preprocessing for machine learning applications in human microbiome research 

      Ibrahimi, Eliana; Lopes, Marta B.; Dhamo, Xhilda; Simeon, Andrea; Shigdel, Rajesh; Hron, Karel; Stres, Blaž; D’Elia, Domenica; Berland, Magali; Marcos-Zambrano, Laura Judith (Journal article; Peer reviewed, 2023)
      Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the statistical ...

    • Parental TB associated with offspring asthma and rhinitis 

      Lopez Cervantes, Juan Pablo; Shigdel, Rajesh; Accordini, S.; Mustafa, Tehmina; Bertelsen, Randi Jacobsen; Makvandi-Nejad, Shokouh; Lerm, M.; Horsnell, W.; Svanes, Cecilie (Journal article; Peer reviewed, 2022)
      BACKGROUND: Infections in early life are associated with asthma and allergies in one-generation settings; however, the link between parental infection and offspring phenotype is rarely investigated. We aim to study the ...

    • Previous tuberculosis infection associated with increased frequency of asthma and respiratory symptoms in a Nordic–Baltic multicentre population study 

      Gyawali, Sanjay; Lopez Cervantes, Juan Pablo; Jögi, Nils Oskar; Mustafa, Tehmina; Johannessen, Ane; Janson, Christer; Holm, Mathias; Modig, Lars; Cramer, Christine; Gislason, Thorarinn; Svanes, Cecilie; Shigdel, Rajesh (Journal article; Peer reviewed, 2023)
      Background: Tuberculosis (TB) infection induces profound local and systemic, immunological and inflammatory changes that could influence the development of other respiratory diseases; however, the association between TB ...

    • Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions 

      Moreno-Indias, Isabel; Lahti, Leo; Nedyalkova, Miroslava; Elbere, Ilze; Roshchupkin, Gennady V.; Adilovic, Muhamed; Aydemir, Onder; Bakir-Gungor, Burcu; Carrillo-de Santa Pau, Enrique; D’Elia, Domenica; Desai, Mahesh S.; Falquet, Laurent; Gundogdu, Aycan; Hron, Karel; Klammsteiner, Thomas; Lopes, Marta B.; Marcos-Zambrano, Laura Judith; Marques, Cláudia; Mason, Michael; May, Patrick; Pašić, Lejla; Pio, Gianvito; Pongor, Sándor; Promponas, Vasilis J.; Przymus, Piotr; Saez-Rodriguez, Julio; Sampri, Alexia; Shigdel, Rajesh; Stres, Blaz; Suharoschi, Ramona; Truu, Jaak; Truică, Ciprian-Octavian; Vilne, Baiba; Vlachakis, Dimitrios; Yilmaz, Ercument; Zeller, Georg; Zomer, Aldert L.; Gomez-Cabrero, David; Claesson, Marcus J. (Journal article; Peer reviewed, 2021)
      The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many ...

    • A toolbox of machine learning software to support microbiome analysis 

      Marcos-Zambrano, Laura Judith; López-Molina, Víctor Manuel; Bakir-Gungor, Burcu; Frohme, Marcus; Karaduzovic-Hadziabdic, Kanita; Klammsteiner, Thomas; Ibrahimi, Eliana; Lahti, Leo; Loncar-Turukalo, Tatjana; Dhamo, Xhilda; Simeon, Andrea; Nechyporenko, Alina; Pio, Gianvito; Przymus, Piotr; Sampri, Alexia; Trajkovik, Vladimir; Lacruz-Pleguezuelos, Blanca; Aasmets, Oliver; Araujo, Ricardo; Anagnostopoulos, Ioannis; Aydemir, Önder; Berland, Magali; Calle, M. Luz; Ceci, Michelangelo; Duman, Hatice; Gündoğdu, Aycan; Havulinna, Aki S.; Kaka Bra, Kardokh Hama Najib; Kalluci, Eglantina; Karav, Sercan; Lode, Daniel; Lopes, Marta B.; May, Patrick; Nap, Bram; Nedyalkova, Miroslava; Paciência, Inês; Pasic, Lejla; Pujolassos, Meritxell; Shigdel, Rajesh; Susín, Antonio; Thiele, Ines; Truică, Ciprian-Octavian; Wilmes, Paul; Yilmaz, Ercument; Yousef, Malik; Claesson, Marcus Joakim; Truu, Jaak; Carrillo de Santa Pau, Enrique (Journal article; Peer reviewed, 2023)
      The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high ...