Najafi, Mojtaba; Guo, Yongzhi; Andersson, Goran et. al 2022 Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells Research article (Peer reviewed) DOI:10.3390/genes13122342
De Panis, D.; Dopazo, H.; Bongcam-Rudloff, E. et. al 2022 Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species Research article (Peer reviewed) DOI:10.1186/s12864-022-08745-9
Mero, Herieth; Lyantagaye, Sylvester Leonard; Bongcam Rudloff, Erik 2022 Cassava Brown Streak Viruses express second 6-kilodalton (6K2) protein with varied polarity and three dimensional (3D) structures: Basis for trait discrepancy between the virus species Research article (Peer reviewed) DOI:10.1016/j.meegid.2022.105219
Diakou, Kalliopi Io; Mitsis, Thanasis; Pierouli, Katerina et. al 2022 Ebola virus disease and current therapeutic strategies: a review Conference paper (Peer reviewed) DOI:10.1007/978-3-030-78787-5_18
Mero, Herieth Rhodes; Lyantagaye, Sylvester Leonard; Bongcam-Rudloff, Erik 2021 Why has permanent control of cassava brown streak disease in Sub-Saharan Africa remained a dream since the 1930s? Review article (Peer reviewed) DOI:10.1016/j.meegid.2021.105001
Wambua, Sammy; Gourle, Hadrien; de Villiers, Etienne P. et. al 2021 Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean Research article (Peer reviewed) DOI:10.3389/fmicb.2021.673128
Rugumisa, Bernadether T.; Bongcam-Rudloff, Erik; Lukumay, Murate S. et. al 2021 Factors associated with risk of preterm delivery in Tanzania: A case-control study at Muhimbili National Hospital Research article (Peer reviewed) DOI:10.1002/ijgo.13520
Corduneanu, Alexandra; Mihalca, Andrei Daniel; Sandor, Attila D. et. al 2021 The heart microbiome of insectivorous bats from Central and South Eastern Europe Research article (Peer reviewed) DOI:10.1016/j.cimid.2020.101605
Van Damme, Renaud; Hoelzer, Martin; Viehweger, Adrian et. al 2021 Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN) Research article (Peer reviewed) DOI:10.1371/journal.pcbi.1008716
Hollmann , Susanne; Kremer, Andreas; Baebler, Špela et. al 2020 The need for standardisation in life science research - an approach to excellence and trust Research article (Peer reviewed) DOI:10.12688/f1000research.27500.2
Brandt, Christian; Bongcam-Rudloff, Erik; Mueller, Bettina 2020 Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants Research article (Peer reviewed) DOI:10.3390/app10217518
Senanayake, Kanchana S.; Soderberg, Jonas; Polajev, Aleksei et. al 2020 The Genome of Setaria digitata: A Cattle Nematode Closely Related to Human Filarial Parasites Research article (Peer reviewed) DOI:10.1093/gbe/evaa017
Jhamat, Naveed; Niazi, Adnan; Guo, Yongzhi et. al 2020 LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function Research article (Peer reviewed) DOI:10.1186/s12864-020-06777-7
Sole, Marina; Lindgren, Gabriella; Bongcam-Rudloff, Erik et. al 2020 Benefits and risks of barefoot harness racing in Standardbred trotters Research article (Peer reviewed) DOI:10.1111/asj.13380
Singh, Abhijeet; Nylander, Johan A. A.; Schnurer, Anna et. al 2020 High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure Research article (Peer reviewed) DOI:10.3389/fmicb.2020.02066
Guo, Yongzhi; van Schaik, Tom; Jhamat, Naveed et. al 2019 Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions Research article (Peer reviewed) DOI:10.1371/journal.pone.0222081
Guo, Yongzhi; Chankeaw, Wiruntita; Chanrot, Metasu et. al 2019 Changes induced by pathogens and metabolic stress on endometrial function in cattle: possible impacts of increased inflammation on fertility Conference paper (Peer reviewed)
Gourle, Hadrien; Karlsson-Lindsjo, Oskar; Hayer, Juliette et. al 2019 Simulating Illumina metagenomic data with InSilicoSeq Research article (Peer reviewed) DOI:10.1093/bioinformatics/bty630
Hollmann, Susanne; Attwood, Teresa K.; Bongcam-Rudloff, Erik et. al 2018 Standardization and Quality Assurance in Life-Science Research - Crucially Needed or Unnecessary and Annoying Regulation? Conference paper (Peer reviewed) DOI:10.1007/978-3-030-00825-3_2
Batmagnai, E.; Bongcam-Rudloff, Erik; Kent, Matthew Peter et. al 2018 The identification and classification of endogenous retroviruses in the horse genome Research article (Peer reviewed) DOI:10.5564/mjas.v23i01.1012
Malmberg, Maja; Mugisha, Lawrence; Balinandi, Stephen et. al 2018 An Interdisciplinary Approach Addressing Ticks and Tick-Borne Diseases of Cattle in Uganda Conference abstract
Fahlman, Åsa; Sunil-Chandra, N.P.; Perera, Vijitha et. al 2018 A One Health approach to emerging zoonoses and biodiversity conservation in Sri Lanka Conference poster
Malmberg, Maja; Mugisha, Lawrence; Balinandi, Stephen et. al 2018 An interdisciplinary approach addressing ticks and tick-borne diseases of cattle in Uganda Conference abstract (Peer reviewed)
Cardenas, Cesar A.; Gonzalez-Aravena, Marcelo; Font, Alejandro et. al 2018 High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas Research article (Peer reviewed) DOI:10.7717/peerj.4935
Manzoor, Shahid; Schnurer, Anna; Bongcam-Rudloff, Erik et. al 2018 Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria Research article (Peer reviewed) DOI:10.3390/genes9040225
Klingstrom, Tomas; Bongcam-Rudloff, Erik; Reichel, Jane 2018 Legal & ethical compliance when sharing biospecimen Review article (Peer reviewed) DOI:10.1093/bfgp/elx008
Guo, Yongzhi; Jhamat, Naveed ; Van Schaik, Tom et. al 2017 Changes in gene expression following exposure of bovine endometrial epithelial cells (BEEC) to escherichia coli LPS; their possible effect on implantation Conference abstract DOI:10.1071/RDv29n1Ab124
D'Elia, Domenica; Hernandez, Emiliano Barreto; Klucar, Lubos et. al 2017 2016 EMBnet Annual General Meeting – Executive Board Report Research article DOI:10.14806/ej.22.0.887
Manzoor, Shahid; Niazi, Adnan; Bongcam-Rudloff, Erik 2017 A stepping-stone to developing bioinformatics in Pakistan Research article DOI:10.14806/ej.23.0.891
Loftsdottir, Heiour; Soderlund, Robert; Jinnerot, Tomas et. al 2017 Dynamics of insertion sequence element IS629 inactivation of verotoxin 2 genes in Escherichia coli O157:H7 Research article (Peer reviewed) DOI:10.1093/femsle/fnx074
Klingström, Tomas; Hernandez De Diego, Rafael; Collard, Theo et. al 2017 Galaksio, a user friendly workflow-centric front end for Galaxy Research article (Peer reviewed) DOI:10.14806/ej.23.0.897
Hernandez-de-Diego, R; de, Villiers EP; Klingstrom, T et. al 2017 The eBioKit, a stand-alone educational platform for bioinformatics Research article (Peer reviewed) DOI:10.1371/journal.pcbi.1005616
Jhamat, Naveed ; Guo, Yongzhi; Niazi, Adnan et. al 2016 Identification of Differentially Methylated Regions (DMR) in the genome of bovine endometrial epithelial cells (bEEC)challenged by E.Coli LPS and its effect on transcription Conference abstract
Klingström, Tomas; Mendy, Maimuna: Meunier, Dominique; Berger, Anouk et. al 2016 Supporting the Development of Biobanks in Low and Medium Income Countries Conference paper (Peer reviewed) DOI:10.1109/ISTAFRICA.2016.7530672
Manzoor, Shahid; Bongcam-Rudloff, Erik; Schnürer, Anna et. al 2016 Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii Research article (Peer reviewed) DOI:10.1371/journal.pone.0166520
Truvé, Katarina; Fuxelius, Hans-Henrik; Andersson, Göran et. al 2016 Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus Research article (Peer reviewed) DOI:10.1371/journal.pgen.1006000
Norling, Martin; Karlsson-Lindsjö, Oskar E.; Karlsson Lindsjö, Oskar et. al 2016 MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies Research article (Peer reviewed) DOI:10.1371/journal.pone.0160334
Manzoor, Shahid; Schnürer, Anna; Bongcam-Rudloff, Erik et. al 2016 Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB) Research article (Peer reviewed) DOI:10.1186/s40793-016-0199-x
Mushtaq, Mamoona; Loftsdottir, Heidur; Bongcam-Rudloff, Erik et. al 2016 Genetic analysis of a Treponema phagedenis locus encoding antigenic lipoproteins with potential for antigenic variation Research article (Peer reviewed) DOI:10.1016/j.vetmic.2016.04.027
Söderlund, Robert; Hurel, Julie; Jinnerot, Tomas et. al 2016 Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs Research article (Peer reviewed) DOI:10.3402/iee.v6.30246
Spjuth, Ola; Bongcam-Rudloff, Erik; Dahlberg, Johan et. al 2016 Recommendations on e-Infrastructures for next-generation sequencing Review article (Peer reviewed) DOI:10.1186/s13742-016-0132-7
Bongcam-Rudloff, Erik 2015 Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training Other publication (Peer reviewed) DOI:10.1371/journal.pcbi.1004281
Attwood, Teresa K.; Bongcam-Rudloff, Erik; Zanzoni, Andreas 2015 GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training Research article (Peer reviewed) DOI:10.1371/journal.pcbi.1004143
Dahlö, Martin; Haziza, Frédéric; Kallio, Aleksi et. al 2015 BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences Research article (Peer reviewed) DOI:10.4137/BBI.S28636
Zubair, Saima; Fischer, Anne; Liljander, Anne et. al 2015 Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel Research article (Peer reviewed) DOI:10.1186/s40793-015-0098-6
Mushtaq, Mamoona; Manzoor, Shahid; Pringle, Märit et. al 2015 Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis Research article (Peer reviewed) DOI:10.1186/s40793-015-0059-0
Manzoor, Shahid; Müller, Bettina; Niazi, Adnan et. al 2015 Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3 Research article (Peer reviewed) DOI:10.1186/s40793-015-0092-z
Mushtaq, Mamoona; Zubair, Saima; Råsbäck, Therese et. al 2015 Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics Research article (Peer reviewed) DOI:10.1186/s12866-015-0537-y
Norling, Martin; Bongcam-Rudloff, Erik; Silva, Joana C. 2015 The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence Research article (Peer reviewed) DOI:10.1186/s12864-015-1910-9
Spjuth, Ola; Bongcam-Rudloff, Erik; Vassilev, Dimitar 2015 Experiences with workflows for automating data-intensive bioinformatics Review article (Peer reviewed) DOI:10.1186/s13062-015-0071-8