Spatial host–microbiome sequencing reveals niches in the mouse gut
Lötstedt, Britta, Stražar, Martin, Xavier, Ramnik, Regev, Aviv, Vickovic, Sanja
Published in Nature biotechnology (01.09.2024)
Published in Nature biotechnology (01.09.2024)
Get full text
Journal Article
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins
Stražar, Martin, Žitnik, Marinka, Zupan, Blaž, Ule, Jernej, Curk, Tomaž
Published in Bioinformatics (15.05.2016)
Published in Bioinformatics (15.05.2016)
Get full text
Journal Article
Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations
Stražar, Martin, Temba, Godfrey S., Vlamakis, Hera, Kullaya, Vesla I., Lyamuya, Furaha, Mmbaga, Blandina T., Joosten, Leo A. B., van der Ven, Andre J. A. M., Netea, Mihai G., de Mast, Quirijn, Xavier, Ramnik J.
Published in Nature communications (11.08.2021)
Published in Nature communications (11.08.2021)
Get full text
Journal Article
Democratized image analytics by visual programming through integration of deep models and small-scale machine learning
Godec, Primož, Pančur, Matjaž, Ilenič, Nejc, Čopar, Andrej, Stražar, Martin, Erjavec, Aleš, Pretnar, Ajda, Demšar, Janez, Starič, Anže, Toplak, Marko, Žagar, Lan, Hartman, Jan, Wang, Hamilton, Bellazzi, Riccardo, Petrovič, Uroš, Garagna, Silvia, Zuccotti, Maurizio, Park, Dongsu, Shaulsky, Gad, Zupan, Blaž
Published in Nature communications (07.10.2019)
Published in Nature communications (07.10.2019)
Get full text
Journal Article
Yeast as a cell factory: current state and perspectives
Kavšček, Martin, Stražar, Martin, Curk, Tomaž, Natter, Klaus, Petrovič, Uroš
Published in Microbial cell factories (30.06.2015)
Published in Microbial cell factories (30.06.2015)
Get full text
Journal Article
Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism
Vatanen, Tommi, Jabbar, Karolina S., Ruohtula, Terhi, Honkanen, Jarno, Avila-Pacheco, Julian, Siljander, Heli, Stražar, Martin, Oikarinen, Sami, Hyöty, Heikki, Ilonen, Jorma, Mitchell, Caroline M., Yassour, Moran, Virtanen, Suvi M., Clish, Clary B., Plichta, Damian R., Vlamakis, Hera, Knip, Mikael, Xavier, Ramnik J.
Published in Cell (22.12.2022)
Published in Cell (22.12.2022)
Get full text
Journal Article
The influence of the gut microbiome on BCG-induced trained immunity
Stražar, Martin, Mourits, Vera P, Koeken, Valerie A C M, de Bree, L Charlotte J, Moorlag, Simone J C F M, Joosten, Leo A B, van Crevel, Reinout, Vlamakis, Hera, Netea, Mihai G, Xavier, Ramnik J
Published in Genome Biology (22.09.2021)
Published in Genome Biology (22.09.2021)
Get full text
Journal Article
A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning
Vatanen, Tommi, Ang, Qi Yan, Siegwald, Léa, Sarker, Shafiqul Alam, Le Roy, Caroline I., Duboux, Stéphane, Delannoy-Bruno, Omar, Ngom-Bru, Catherine, Boulangé, Claire L., Stražar, Martin, Avila-Pacheco, Julian, Deik, Amy, Pierce, Kerry, Bullock, Kevin, Dennis, Courtney, Sultana, Shamima, Sayed, Sharika, Rahman, Mahbubar, Ahmed, Tahmeed, Modesto, Monica, Mattarelli, Paola, Clish, Clary B., Vlamakis, Hera, Plichta, Damian R., Sakwinska, Olga, Xavier, Ramnik J.
Published in Cell (10.11.2022)
Published in Cell (10.11.2022)
Get full text
Journal Article
Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria
Li, Chenhao, Stražar, Martin, Mohamed, Ahmed M.T., Pacheco, Julian A., Walker, Rebecca L., Lebar, Tina, Zhao, Shijie, Lockart, Julia, Dame, Andrea, Thurimella, Kumar, Jeanfavre, Sarah, Brown, Eric M., Ang, Qi Yan, Berdy, Brittany, Sergio, Dallis, Invernizzi, Rachele, Tinoco, Antonio, Pishchany, Gleb, Vasan, Ramachandran S., Balskus, Emily, Huttenhower, Curtis, Vlamakis, Hera, Clish, Clary, Shaw, Stanley Y., Plichta, Damian R., Xavier, Ramnik J.
Published in Cell (11.04.2024)
Published in Cell (11.04.2024)
Get full text
Journal Article
HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery
Stražar, Martin, Park, Jihye, Abelin, Jennifer G., Taylor, Hannah B., Pedersen, Thomas K., Plichta, Damian R., Brown, Eric M., Eraslan, Basak, Hung, Yuan-Mao, Ortiz, Kayla, Clauser, Karl R., Carr, Steven A., Xavier, Ramnik J., Graham, Daniel B.
Published in Immunity (Cambridge, Mass.) (11.07.2023)
Published in Immunity (Cambridge, Mass.) (11.07.2023)
Get full text
Journal Article
Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course
Schirmer, Melanie, Stražar, Martin, Avila-Pacheco, Julian, Rojas-Tapias, Daniel F., Brown, Eric M., Temple, Emily, Deik, Amy, Bullock, Kevin, Jeanfavre, Sarah, Pierce, Kerry, Jin, Shen, Invernizzi, Rachele, Pust, Marie-Madlen, Costliow, Zach, Mack, David R., Griffiths, Anne M., Walters, Thomas, Boyle, Brendan M., Kugathasan, Subra, Vlamakis, Hera, Hyams, Jeffrey, Denson, Lee, Clish, Clary B., Xavier, Ramnik J.
Published in Cell host & microbe (14.02.2024)
Published in Cell host & microbe (14.02.2024)
Get full text
Journal Article
Annotating metabolite mass spectra with domain-inspired chemical formula transformers
Goldman, Samuel, Wohlwend, Jeremy, Stražar, Martin, Haroush, Guy, Xavier, Ramnik J., Coley, Connor W.
Published in Nature machine intelligence (01.09.2023)
Published in Nature machine intelligence (01.09.2023)
Get full text
Journal Article
Commensal consortia decolonize Enterobacteriaceae via ecological control
Furuichi, Munehiro, Kawaguchi, Takaaki, Pust, Marie-Madlen, Yasuma-Mitobe, Keiko, Plichta, Damian R., Hasegawa, Naomi, Ohya, Takashi, Bhattarai, Shakti K., Sasajima, Satoshi, Aoto, Yoshimasa, Tuganbaev, Timur, Yaginuma, Mizuki, Ueda, Masahiro, Okahashi, Nobuyuki, Amafuji, Kimiko, Kiridoshi, Yuko, Sugita, Kayoko, Stražar, Martin, Avila-Pacheco, Julian, Pierce, Kerry, Clish, Clary B., Skelly, Ashwin N., Hattori, Masahira, Nakamoto, Nobuhiro, Caballero, Silvia, Norman, Jason M., Olle, Bernat, Tanoue, Takeshi, Suda, Wataru, Arita, Makoto, Bucci, Vanni, Atarashi, Koji, Xavier, Ramnik J., Honda, Kenya
Published in Nature (London) (26.09.2024)
Published in Nature (London) (26.09.2024)
Get full text
Journal Article
Author Correction: Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations
Stražar, Martin, Temba, Godfrey S., Vlamakis, Hera, Kullaya, Vesla I., Lyamuya, Furaha, Mmbaga, Blandina T., Joosten, Leo A. B., van der Ven, Andre J. A. M., Netea, Mihai G., de Mast, Quirijn, Xavier, Ramnik J.
Published in Nature communications (29.09.2021)
Published in Nature communications (29.09.2021)
Get full text
Journal Article
Publisher Correction: Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations
Stražar, Martin, Temba, Godfrey S., Vlamakis, Hera, Kullaya, Vesla I., Lyamuya, Furaha, Mmbaga, Blandina T., Joosten, Leo A. B., van der Ven, Andre J. A. M., Netea, Mihai G., de Mast, Quirijn, Xavier, Ramnik J.
Published in Nature communications (24.08.2021)
Published in Nature communications (24.08.2021)
Get full text
Journal Article
A bistable genetic switch based on designable DNA-binding domains
Lebar, Tina, Bezeljak, Urban, Golob, Anja, Jerala, Miha, Kadunc, Lucija, Pirš, Boštjan, Stražar, Martin, Vučko, Dušan, Zupančič, Uroš, Benčina, Mojca, Forstnerič, Vida, Gaber, Rok, Lonzarić, Jan, Majerle, Andreja, Oblak, Alja, Smole, Anže, Jerala, Roman
Published in Nature communications (29.09.2014)
Published in Nature communications (29.09.2014)
Get full text
Journal Article