R
Raivo Kolde
Researcher at Harvard University
Publications - 58
Citations - 4906
Raivo Kolde is an academic researcher from Harvard University. The author has contributed to research in topics: Medicine & Internal medicine. The author has an hindex of 28, co-authored 43 publications receiving 3794 citations. Previous affiliations of Raivo Kolde include Broad Institute & Massachusetts Institute of Technology.
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Journal ArticleDOI
Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans
Tommi Vatanen,Tommi Vatanen,Aleksandar Kostic,Aleksandar Kostic,Eva d'Hennezel,Heli Siljander,Eric A. Franzosa,Eric A. Franzosa,Moran Yassour,Raivo Kolde,Hera Vlamakis,Timothy D. Arthur,Anu Maaria Hämäläinen,Aleksandr Peet,Vallo Tillmann,Raivo Uibo,Sergei Mokurov,Natalya Dorshakova,Jorma Ilonen,Jorma Ilonen,Suvi M. Virtanen,Suvi M. Virtanen,Susanne J. Szabo,Jeffrey A. Porter,Harri Lähdesmäki,Curtis Huttenhower,Curtis Huttenhower,Dirk Gevers,Thomas W. Cullen,Mikael Knip,Ramnik J. Xavier +30 more
TL;DR: It is shown that Bacteroides LPS is structurally distinct from E. coli LPS and inhibits innate immune signaling and endotoxin tolerance, and that early colonization by immunologically silencing microbiota may preclude aspects of immune education.
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Robust rank aggregation for gene list integration and meta-analysis
TL;DR: This work proposes a novel robust rank aggregation (RRA) method that detects genes that are ranked consistently better than expected under null hypothesis of uncorrelated inputs and assigns a significance score for each gene.
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Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation
Marta Wlodarska,Chengwei Luo,Raivo Kolde,Eva d'Hennezel,John W. Annand,Cortney E. Heim,Cortney E. Heim,Philipp Krastel,Esther K. Schmitt,Abdifatah S. Omar,Elizabeth A. Creasey,Ashley L. Garner,Sina Mohammadi,Daniel J. O’Connell,Sahar Abubucker,Timothy D. Arthur,Eric A. Franzosa,Curtis Huttenhower,Curtis Huttenhower,Leon Murphy,Henry J. Haiser,Hera Vlamakis,Jeffrey A. Porter,Ramnik J. Xavier,Ramnik J. Xavier +24 more
TL;DR: The data suggest that stimulating IA production could promote anti-inflammatory responses and have therapeutic benefits, and the genetic capability of microbes to utilize mucins and metabolize tryptophan is diminished in IBD patients.
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DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
Kaie Lokk,Kaie Lokk,Kaie Lokk,Vijayachitra Modhukur,Balaji Rajashekar,Kaspar Märtens,Reedik Mägi,Raivo Kolde,Marina Koltšina,Torbjörn K. Nilsson,Jaak Vilo,Andres Salumets,Neeme Tõnisson,Neeme Tõnisson +13 more
TL;DR: This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues, and a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases.
Journal ArticleDOI
Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach
Anne K. Krug,Raivo Kolde,John Antonydas Gaspar,Eugen Rempel,Nina V. Balmer,Kesavan Meganathan,Kinga Vojnits,Mathurin Baquié,Tanja Waldmann,Roberto Ensenat-Waser,Smita Jagtap,Richard Evans,Stéphanie Julien,Hedi Peterson,Dimitra Zagoura,Suzanne Kadereit,Daniel Gerhard,Isaia Sotiriadou,Michael Heke,Karthick Natarajan,Margit Henry,Johannes Winkler,Rosemarie Marchan,Luc Stoppini,Sieto Bosgra,Joost Westerhout,Miriam Verwei,Jaak Vilo,Andreas Kortenkamp,Jürgen Hescheler,Ludwig A. Hothorn,Susanne Bremer,Christoph van Thriel,Karl-Heinz Krause,Jan G. Hengstler,Jörg Rahnenführer,Marcel Leist,Agapios Sachinidis +37 more
TL;DR: The ESNATS assay battery allows classification of human DNT/RT toxicants on the basis of their transcriptome profiles and a relatively large ‘common response’ to VPA and MeHg could be distinguished from ‘compound-specific’ responses.