A comprehensive and quantitative exploration of thousands of viral genomes

Autor: Gita Mahmoudabadi, Rob Phillips

Publikováno v: eLife, Vol 7 (2018)

The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenom

Externí odkaz: https://doaj.org/article/4f765301be464a9e8cca2a9d0a0d5d53

The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

Autor: Robert C, Jones, Jim, Karkanias, Mark A, Krasnow, Angela Oliveira, Pisco, Stephen R, Quake, Julia, Salzman, Nir, Yosef, Bryan, Bulthaup, Phillip, Brown, William, Harper, Marisa, Hemenez, Ravikumar, Ponnusamy, Ahmad, Salehi, Bhavani A, Sanagavarapu, Eileen, Spallino, Ksenia A, Aaron, Waldo, Concepcion, James M, Gardner, Burnett, Kelly, Nikole, Neidlinger, Zifa, Wang, Sheela, Crasta, Saroja, Kolluru, Maurizio, Morri, Serena Y, Tan, Kyle J, Travaglini, Chenling, Xu, Marcela, Alcántara-Hernández, Nicole, Almanzar, Jane, Antony, Benjamin, Beyersdorf, Deviana, Burhan, Kruti, Calcuttawala, Matthew M, Carter, Charles K F, Chan, Charles A, Chang, Stephen, Chang, Alex, Colville, Rebecca N, Culver, Ivana, Cvijović, Gaetano, D'Amato, Camille, Ezran, Francisco X, Galdos, Astrid, Gillich, William R, Goodyer, Yan, Hang, Alyssa, Hayashi, Sahar, Houshdaran, Xianxi, Huang, Juan C, Irwin, SoRi, Jang, Julia Vallve, Juanico, Aaron M, Kershner, Soochi, Kim, Bernhard, Kiss, William, Kong, Maya E, Kumar, Angera H, Kuo, Rebecca, Leylek, Baoxiang, Li, Gabriel B, Loeb, Wan-Jin, Lu, Sruthi, Mantri, Maxim, Markovic, Patrick L, McAlpine, Antoine, de Morree, Karim, Mrouj, Shravani, Mukherjee, Tyler, Muser, Patrick, Neuhöfer, Thi D, Nguyen, Kimberly, Perez, Ragini, Phansalkar, Nazan, Puluca, Zhen, Qi, Poorvi, Rao, Hayley, Raquer-McKay, Nicholas, Schaum, Bronwyn, Scott, Bobak, Seddighzadeh, Joe, Segal, Sushmita, Sen, Shaheen, Sikandar, Sean P, Spencer, Lea C, Steffes, Varun R, Subramaniam, Aditi, Swarup, Michael, Swift, Will, Van Treuren, Emily, Trimm, Stefan, Veizades, Sivakamasundari, Vijayakumar, Kim Chi, Vo, Sevahn K, Vorperian, Wanxin, Wang, Hannah N W, Weinstein, Juliane, Winkler, Timothy T H, Wu, Jamie, Xie, Andrea R, Yung, Yue, Zhang, Angela M, Detweiler, Honey, Mekonen, Norma F, Neff, Rene V, Sit, Michelle, Tan, Jia, Yan, Gregory R, Bean, Vivek, Charu, Erna, Forgó, Brock A, Martin, Michael G, Ozawa, Oscar, Silva, Angus, Toland, Venkata N P, Vemuri, Shaked, Afik, Kyle, Awayan, Olga Borisovna, Botvinnik, Ashley, Byrne, Michelle, Chen, Roozbeh, Dehghannasiri, Adam, Gayoso, Alejandro A, Granados, Qiqing, Li, Gita, Mahmoudabadi, Aaron, McGeever, Julia Eve, Olivieri, Madeline, Park, Neha, Ravikumar, Geoff, Stanley, Weilun, Tan, Alexander J, Tarashansky, Rohan, Vanheusden, Peter, Wang, Sheng, Wang, Galen, Xing, Rebecca, Culver, Les, Dethlefsen, Po-Yi, Ho, Shixuan, Liu, Jonathan S, Maltzman, Ross J, Metzger, Koki, Sasagawa, Rahul, Sinha, Hanbing, Song, Bruce, Wang, Steven E, Artandi, Philip A, Beachy, Michael F, Clarke, Linda C, Giudice, Franklin W, Huang, Kerwyn Casey, Huang, Juliana, Idoyaga, Seung K, Kim, Mark, Krasnow, Christin S, Kuo, Patricia, Nguyen, Thomas A, Rando, Kristy, Red-Horse, Jeremy, Reiter, David A, Relman, Justin L, Sonnenburg, Albert, Wu, Sean M, Wu, Tony, Wyss-Coray

Publikováno v: Science
Tabula Sapiens Consortium* 2022, ' The Tabula Sapiens : A multiple-organ, single-cell transcriptomic atlas of humans ', Science (New York, N.Y.), vol. 376, no. 6594, pp. eabl4896 . https://doi.org/10.1126/science.abl4896

INTRODUCTION: Although the genome is often called the blueprint of an organism, it is perhaps more accurate to describe it as a parts list composed of the various genes that may or may not be used in the different cell types of a multicellular organi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f726fc016f86cd4ce8c15a69dce9f6be
https://pubmed.ncbi.nlm.nih.gov/36198687

Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions

Autor: Rob Phillips, Arbel D. Tadmor, Kelsey Homyk, Allison Cheung, Helen B. Foley, Gita Mahmoudabadi, Ana Mahmoudabadi, Adam Catching

Metagenomic studies have revolutionized the study of novel phages. However these studies trade the depth of coverage for breadth. In this study we show that the targeted sequencing of a phage genomic region as small as 200-300 base pairs, can provide

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::26aa42117bcac4e8a7dd06abf24f593b

Energetic cost of building a virus

Autor: Rob Phillips, Ron Milo, Gita Mahmoudabadi

Viruses are incapable of autonomous energy production. Although many experimental studies make it clear that viruses are parasitic entities that hijack the molecular resources of the host, a detailed estimate for the energetic cost of viral synthesis

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4bfcb0654e9550eeb176a5d23722cdc9
https://europepmc.org/articles/PMC5465929/

A Search for the Common Words within the Voluminous Phage Vocabulary

Autor: Gita Mahmoudabadi

Publikováno v: Biophysical Journal. 106(2)

4^(900) is a number that surpasses the estimated number of protons in our observable universe by roughly 462 orders of magnitude. Yet, this number corresponds to the number of sequences that can be encoded using just 900 DNA base pairs, the average g

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::210759d48ba2032d3cd9f13493b8ea76