De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

por Kosciolek, Tomasz, Jones, David T.
Publicado 2014

Accurate contact predictions using covariation techniques and machine learning

por Kosciolek, Tomasz, Jones, David T.
Publicado 2015

MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

por Jones, David T., Singh, Tanya, Kosciolek, Tomasz, Tetchner, Stuart
Publicado 2015

Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions

por Kosciolek, Tomasz, Buchan, Daniel W. A., Jones, David T.
Publicado 2017

The importance of template choice in homology modeling. A 5-HT(6)R case study

por Rataj, Krzysztof, Witek, Jagna, Mordalski, Stefan, Kościółek, Tomasz, Bojarski, Andrzej J
Publicado 2013

Application of Structural Interaction Fingerpints (SIFts) into post-docking analysis - insight into activity and selectivity

por Witek, Jagna, Rataj, Krzysztof, Mordalski, Stefan, Smusz, Sabina, Kosciolek, Tomasz, Bojarski, Andrzej J
Publicado 2013

Deep embeddings to comprehend and visualize microbiome protein space

por Odrzywolek, Krzysztof, Karwowska, Zuzanna, Majta, Jan, Byrski, Aleksander, Milanowska-Zabel, Kaja, Kosciolek, Tomasz
Publicado 2022

Individuals with substance use disorders have a distinct oral microbiome pattern

por Kosciolek, Tomasz, Victor, Teresa A., Kuplicki, Rayus, Rossi, Maret, Estaki, Mehrbod, Ackermann, Gail, Knight, Rob, Paulus, Martin P.
Publicado 2021

Treatment With Multi-Species Probiotics Changes the Functions, Not the Composition of Gut Microbiota in Postmenopausal Women With Obesity: A Randomized, Double-Blind, Placebo-Contr...

por Kaczmarczyk, Mariusz, Szulińska, Monika, Łoniewski, Igor, Kręgielska-Narożna, Matylda, Skonieczna-Żydecka, Karolina, Kosciolek, Tomasz, Bezshapkin, Valentyn, Bogdański, Paweł
Publicado 2022

Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method

por Maranga, Mary, Szczerbiak, Pawel, Bezshapkin, Valentyn, Gligorijevic, Vladimir, Chandler, Chris, Bonneau, Richard, Xavier, Ramnik J., Vatanen, Tommi, Kosciolek, Tomasz
Publicado 2023

Structure-based protein function prediction using graph convolutional networks

por Gligorijević, Vladimir, Renfrew, P. Douglas, Kosciolek, Tomasz, Leman, Julia Koehler, Berenberg, Daniel, Vatanen, Tommi, Chandler, Chris, Taylor, Bryn C., Fisk, Ian M., Vlamakis, Hera, Xavier, Ramnik J., Knight, Rob, Cho, Kyunghyun, Bonneau, Richard
Publicado 2021

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

por Estaki, Mehrbod, Jiang, Lingjing, Bokulich, Nicholas A., McDonald, Daniel, González, Antonio, Kosciolek, Tomasz, Martino, Cameron, Zhu, Qiyun, Birmingham, Amanda, Vázquez‐Baeza, Yoshiki, Dillon, Matthew R., Bolyen, Evan, Caporaso, J. Gregory, Knight, Rob
Publicado 2020

Sequence-structure-function relationships in the microbial protein universe

por Koehler Leman, Julia, Szczerbiak, Pawel, Renfrew, P. Douglas, Gligorijevic, Vladimir, Berenberg, Daniel, Vatanen, Tommi, Taylor, Bryn C., Chandler, Chris, Janssen, Stefan, Pataki, Andras, Carriero, Nick, Fisk, Ian, Xavier, Ramnik J., Knight, Rob, Bonneau, Richard, Kosciolek, Tomasz
Publicado 2023

IL-4Rα Blockade by Dupilumab Decreases Staphylococcus aureus Colonization and Increases Microbial Diversity in Atopic Dermatitis

por Callewaert, Chris, Nakatsuji, Teruaki, Knight, Rob, Kosciolek, Tomasz, Vrbanac, Alison, Kotol, Paul, Ardeleanu, Marius, Hultsch, Thomas, Guttman-Yassky, Emma, Bissonnette, Robert, Silverberg, Jonathan I., Krueger, James, Menter, Alan, Graham, Neil M.H., Pirozzi, Gianluca, Hamilton, Jennifer D., Gallo, Richard L.
Publicado 2019

The impact of skin care products on skin chemistry and microbiome dynamics

por Bouslimani, Amina, da Silva, Ricardo, Kosciolek, Tomasz, Janssen, Stefan, Callewaert, Chris, Amir, Amnon, Dorrestein, Kathleen, Melnik, Alexey V., Zaramela, Livia S., Kim, Ji-Nu, Humphrey, Gregory, Schwartz, Tara, Sanders, Karenina, Brennan, Caitriona, Luzzatto-Knaan, Tal, Ackermann, Gail, McDonald, Daniel, Zengler, Karsten, Knight, Rob, Dorrestein, Pieter C.
Publicado 2019

Qiita: rapid, web-enabled microbiome meta-analysis

por Gonzalez, Antonio, Navas-Molina, Jose A., Kosciolek, Tomasz, McDonald, Daniel, Vázquez-Baeza, Yoshiki, Ackermann, Gail, DeReus, Jeff, Janssen, Stefan, Swafford, Austin D., Orchanian, Stephanie B., Sanders, Jon G., Shorenstein, Joshua, Holste, Hannes, Petrus, Semar, Robbins-Pianka, Adam, Brislawn, Colin J., Wang, Mingxun, Rideout, Jai Ram, Bolyen, Evan, Dillon, Matthew, Caporaso, J Gregory, Dorrestein, Pieter C., Knight, Rob
Publicado 2018

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

por Zhu, Qiyun, Mai, Uyen, Pfeiffer, Wayne, Janssen, Stefan, Asnicar, Francesco, Sanders, Jon G., Belda-Ferre, Pedro, Al-Ghalith, Gabriel A., Kopylova, Evguenia, McDonald, Daniel, Kosciolek, Tomasz, Yin, John B., Huang, Shi, Salam, Nimaichand, Jiao, Jian-Yu, Wu, Zijun, Xu, Zhenjiang Z., Cantrell, Kalen, Yang, Yimeng, Sayyari, Erfan, Rabiee, Maryam, Morton, James T., Podell, Sheila, Knights, Dan, Li, Wen-Jun, Huttenhower, Curtis, Segata, Nicola, Smarr, Larry, Mirarab, Siavash, Knight, Rob
Publicado 2019

A communal catalogue reveals Earth’s multiscale microbial diversity

por Thompson, Luke R., Sanders, Jon G., McDonald, Daniel, Amir, Amnon, Ladau, Joshua, Locey, Kenneth J., Prill, Robert J., Tripathi, Anupriya, Gibbons, Sean M., Ackermann, Gail, Navas-Molina, Jose A., Janssen, Stefan, Kopylova, Evguenia, Vázquez-Baeza, Yoshiki, González, Antonio, Morton, James T., Mirarab, Siavash, Zech Xu, Zhenjiang, Jiang, Lingjing, Haroon, Mohamed F., Kanbar, Jad, Zhu, Qiyun, Jin Song, Se, Kosciolek, Tomasz, Bokulich, Nicholas A., Lefler, Joshua, Brislawn, Colin J., Humphrey, Gregory, Owens, Sarah M., Hampton-Marcell, Jarrad, Berg-Lyons, Donna, McKenzie, Valerie, Fierer, Noah, Fuhrman, Jed A., Clauset, Aaron, Stevens, Rick L., Shade, Ashley, Pollard, Katherine S., Goodwin, Kelly D., Jansson, Janet K., Gilbert, Jack A., Knight, Rob
Publicado 2017

American Gut: an Open Platform for Citizen Science Microbiome Research

por McDonald, Daniel, Hyde, Embriette, Debelius, Justine W., Morton, James T., Gonzalez, Antonio, Ackermann, Gail, Aksenov, Alexander A., Behsaz, Bahar, Brennan, Caitriona, Chen, Yingfeng, DeRight Goldasich, Lindsay, Dorrestein, Pieter C., Dunn, Robert R., Fahimipour, Ashkaan K., Gaffney, James, Gilbert, Jack A., Gogul, Grant, Green, Jessica L., Hugenholtz, Philip, Humphrey, Greg, Huttenhower, Curtis, Jackson, Matthew A., Janssen, Stefan, Jeste, Dilip V., Jiang, Lingjing, Kelley, Scott T., Knights, Dan, Kosciolek, Tomasz, Ladau, Joshua, Leach, Jeff, Marotz, Clarisse, Meleshko, Dmitry, Melnik, Alexey V., Metcalf, Jessica L., Mohimani, Hosein, Montassier, Emmanuel, Navas-Molina, Jose, Nguyen, Tanya T., Peddada, Shyamal, Pevzner, Pavel, Pollard, Katherine S., Rahnavard, Gholamali, Robbins-Pianka, Adam, Sangwan, Naseer, Shorenstein, Joshua, Smarr, Larry, Song, Se Jin, Spector, Timothy, Swafford, Austin D., Thackray, Varykina G., Thompson, Luke R., Tripathi, Anupriya, Vázquez-Baeza, Yoshiki, Vrbanac, Alison, Wischmeyer, Paul, Wolfe, Elaine, Zhu, Qiyun, Knight, Rob
Publicado 2018