Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study
Bagutti, Claudia, Alt Hug, Monica, Heim, Philippe, Maurer Pekerman, Laura, Ilg Hampe, Evelyn, Hübner, Philipp, Fuchs, Simon, Savic, Miodrag, Stadler, Tanja, Topolsky, Ivan, Icer Baykal, Pelin, Dreifuss, David, Beerenwinkel, Niko, Tschudin Sutter, Sarah
Published in Swiss medical weekly (27.06.2022)
Published in Swiss medical weekly (27.06.2022)
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Journal Article
Technology dictates algorithms: recent developments in read alignment
Alser, Mohammed, Rotman, Jeremy, Deshpande, Dhrithi, Taraszka, Kodi, Shi, Huwenbo, Baykal, Pelin Icer, Yang, Harry Taegyun, Xue, Victor, Knyazev, Sergey, Singer, Benjamin D, Balliu, Brunilda, Koslicki, David, Skums, Pavel, Zelikovsky, Alex, Alkan, Can, Mutlu, Onur, Mangul, Serghei
Published in Genome Biology (26.08.2021)
Published in Genome Biology (26.08.2021)
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Journal Article
Genomic reproducibility in the bioinformatics era
Baykal, Pelin Icer, Łabaj, Paweł Piotr, Markowetz, Florian, Schriml, Lynn M., Stekhoven, Daniel J., Mangul, Serghei, Beerenwinkel, Niko
Published in Genome Biology (09.08.2024)
Published in Genome Biology (09.08.2024)
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Journal Article
Analysis of heterogeneous genomic samples using image normalization and machine learning
Basodi, Sunitha, Baykal, Pelin Icer, Zelikovsky, Alex, Skums, Pavel, Pan, Yi
Published in BMC genomics (21.12.2020)
Published in BMC genomics (21.12.2020)
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Journal Article
SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework
Skums, Pavel, Mohebbi, Fatemeh, Tsyvina, Vyacheslav, Baykal, Pelin Icer, Nemira, Alina, Ramachandran, Sumathi, Khudyakov, Yury
Published in Cell systems (19.10.2022)
Published in Cell systems (19.10.2022)
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Journal Article
Unlocking capacities of genomics for the COVID-19 response and future pandemics
Knyazev, Sergey, Chhugani, Karishma, Sarwal, Varuni, Ayyala, Ram, Singh, Harman, Karthikeyan, Smruthi, Deshpande, Dhrithi, Baykal, Pelin Icer, Comarova, Zoia, Lu, Angela, Porozov, Yuri, Vasylyeva, Tetyana I, Wertheim, Joel O, Tierney, Braden T, Chiu, Charles Y, Sun, Ren, Wu, Aiping, Abedalthagafi, Malak S, Pak, Victoria M, Nagaraj, Shivashankar H, Smith, Adam L, Skums, Pavel, Pasaniuc, Bogdan, Komissarov, Andrey, Mason, Christopher E, Bortz, Eric, Lemey, Philippe, Kondrashov, Fyodor, Beerenwinkel, Niko, Lam, Tommy Tsan-Yuk, Wu, Nicholas C, Zelikovsky, Alex, Knight, Rob, Crandall, Keith A, Mangul, Serghei
Published in Nature methods (01.04.2022)
Published in Nature methods (01.04.2022)
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Journal Article
A Novel Network Representation of SARS-CoV-2 Sequencing Data
Knyazev, Sergey, Novikov, Daniel, Grinshpon, Mark, Singh, Harman, Ayyala, Ram, Sarwal, Varuni, Hosseini, Roya, Baykal, Pelin Icer, Skums, Pavel, Campbell, Ellsworth, Mangul, Serghei, Zelikovsky, Alex
Published in Bioinformatics Research and Applications
Published in Bioinformatics Research and Applications
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Book Chapter
Reproducibility of Bioinformatics Tools
Baykal, Pelin Icer, Beerenwinkel, Niko, Mangul, Serghei
Published in 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) (01.05.2022)
Published in 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) (01.05.2022)
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Conference Proceeding
Genomic reproducibility in the bioinformatics era
Baykal, Pelin Icer, Łabaj, Paweł P, Markowetz, Florian, Schriml, Lynn M, Stekhoven, Daniel J, Mangul, Serghei, Beerenwinkel, Niko
Year of Publication 18.08.2023
Year of Publication 18.08.2023
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Journal Article
SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework
Skums, Pavel, Mohebbi, Fatemeh, Tsyvina, Vyacheslav, Baykal, Pelin Icer, Nemira, Alina, Ramachandran, Sumathi, Khudyakov, Yury
Published in bioRxiv (05.05.2022)
Published in bioRxiv (05.05.2022)
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Paper
Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning
Baykal, Pelin Icer, Artyomenko, Alexander, Ramachandran, Sumathi, Khudyakov, Yury, Zelikovsky, Alex, Skums, Pavel
Published in 2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) (01.10.2017)
Published in 2017 IEEE 7th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) (01.10.2017)
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Conference Proceeding
Technology dictates algorithms: Recent developments in read alignment
Alser, Mohammed, Rotman, Jeremy, Taraszka, Kodi, Shi, Huwenbo, Baykal, Pelin Icer, Yang, Harry Taegyun, Xue, Victor, Knyazev, Sergey, Singer, Benjamin D, Balliu, Brunilda, Koslicki, David, Skums, Pavel, Zelikovsky, Alex, Alkan, Can, Mutlu, Onur, Serghei Mangul
Published in arXiv.org (09.07.2020)
Published in arXiv.org (09.07.2020)
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Paper
Journal Article
Modeling of Erosion-Corrosion In An Alkaline Environment By Machine Learning
Baykal, B Aydin, Singh, Preet M, Baykal, Pelin B Icer
Published in NACE International Corrosion Conference Proceedings (01.01.2019)
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Published in NACE International Corrosion Conference Proceedings (01.01.2019)
Conference Proceeding