Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia.

Baryawno, Ninib; Przybylski, Dariusz; Kowalczyk, Monika S; Kfoury, Youmna; Severe, Nicolas; Gustafsson, Karin; Kokkaliaris, Konstantinos D; Mercier, Francois; Tabaka, Marcin; Hofree, Matan; Dionne, Danielle; Papazian, Ani; Lee, Dongjun; Ashenberg, Orr; Subramanian, Ayshwarya; Vaishnav, Eeshit Dhaval; Rozenblatt-Rosen, Orit; Regev, Aviv; Scadden, David T.

Cell ; 177(7): 1915-1932.e16, 2019 06 13.

Artigo em Inglês | MEDLINE | ID: mdl-31130381

2.

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.

Parnas, Oren; Jovanovic, Marko; Eisenhaure, Thomas M; Herbst, Rebecca H; Dixit, Atray; Ye, Chun Jimmie; Przybylski, Dariusz; Platt, Randall J; Tirosh, Itay; Sanjana, Neville E; Shalem, Ophir; Satija, Rahul; Raychowdhury, Raktima; Mertins, Philipp; Carr, Steven A; Zhang, Feng; Hacohen, Nir; Regev, Aviv.

Cell ; 162(3): 675-86, 2015 Jul 30.

Artigo em Inglês | MEDLINE | ID: mdl-26189680

3.

Fas Promotes T Helper 17 Cell Differentiation and Inhibits T Helper 1 Cell Development by Binding and Sequestering Transcription Factor STAT1.

Meyer Zu Horste, Gerd; Przybylski, Dariusz; Schramm, Markus A; Wang, Chao; Schnell, Alexandra; Lee, Youjin; Sobel, Raymond; Regev, Aviv; Kuchroo, Vijay K.

Immunity ; 48(3): 556-569.e7, 2018 03 20.

Artigo em Inglês | MEDLINE | ID: mdl-29562202

4.

Lipid availability determines fate of skeletal progenitor cells via SOX9.

van Gastel, Nick; Stegen, Steve; Eelen, Guy; Schoors, Sandra; Carlier, Aurélie; Daniëls, Veerle W; Baryawno, Ninib; Przybylski, Dariusz; Depypere, Maarten; Stiers, Pieter-Jan; Lambrechts, Dennis; Van Looveren, Riet; Torrekens, Sophie; Sharda, Azeem; Agostinis, Patrizia; Lambrechts, Diether; Maes, Frederik; Swinnen, Johan V; Geris, Liesbet; Van Oosterwyck, Hans; Thienpont, Bernard; Carmeliet, Peter; Scadden, David T; Carmeliet, Geert.

Nature ; 579(7797): 111-117, 2020 03.

Artigo em Inglês | MEDLINE | ID: mdl-32103177

5.

The genomic substrate for adaptive radiation in African cichlid fish.

Brawand, David; Wagner, Catherine E; Li, Yang I; Malinsky, Milan; Keller, Irene; Fan, Shaohua; Simakov, Oleg; Ng, Alvin Y; Lim, Zhi Wei; Bezault, Etienne; Turner-Maier, Jason; Johnson, Jeremy; Alcazar, Rosa; Noh, Hyun Ji; Russell, Pamela; Aken, Bronwen; Alföldi, Jessica; Amemiya, Chris; Azzouzi, Naoual; Baroiller, Jean-François; Barloy-Hubler, Frederique; Berlin, Aaron; Bloomquist, Ryan; Carleton, Karen L; Conte, Matthew A; D'Cotta, Helena; Eshel, Orly; Gaffney, Leslie; Galibert, Francis; Gante, Hugo F; Gnerre, Sante; Greuter, Lucie; Guyon, Richard; Haddad, Natalie S; Haerty, Wilfried; Harris, Rayna M; Hofmann, Hans A; Hourlier, Thibaut; Hulata, Gideon; Jaffe, David B; Lara, Marcia; Lee, Alison P; MacCallum, Iain; Mwaiko, Salome; Nikaido, Masato; Nishihara, Hidenori; Ozouf-Costaz, Catherine; Penman, David J; Przybylski, Dariusz; Rakotomanga, Michaelle.

Nature ; 513(7518): 375-381, 2014 Sep 18.

Artigo em Inglês | MEDLINE | ID: mdl-25186727

6.

Finished bacterial genomes from shotgun sequence data.

Ribeiro, Filipe J; Przybylski, Dariusz; Yin, Shuangye; Sharpe, Ted; Gnerre, Sante; Abouelleil, Amr; Berlin, Aaron M; Montmayeur, Anna; Shea, Terrance P; Walker, Bruce J; Young, Sarah K; Russ, Carsten; Nusbaum, Chad; MacCallum, Iain; Jaffe, David B.

Genome Res ; 22(11): 2270-7, 2012 Nov.

Artigo em Inglês | MEDLINE | ID: mdl-22829535

7.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

Gnerre, Sante; Maccallum, Iain; Przybylski, Dariusz; Ribeiro, Filipe J; Burton, Joshua N; Walker, Bruce J; Sharpe, Ted; Hall, Giles; Shea, Terrance P; Sykes, Sean; Berlin, Aaron M; Aird, Daniel; Costello, Maura; Daza, Riza; Williams, Louise; Nicol, Robert; Gnirke, Andreas; Nusbaum, Chad; Lander, Eric S; Jaffe, David B.

Proc Natl Acad Sci U S A ; 108(4): 1513-8, 2011 Jan 25.

Artigo em Inglês | MEDLINE | ID: mdl-21187386

8.

DNA read count calibration for single-molecule, long-read sequencing.

Soares, Luis M M; Hanscom, Terrence; Selby, Donald E; Adjei, Samuel; Wang, Wei; Przybylski, Dariusz; Thompson, John F.

Sci Rep ; 12(1): 17257, 2022 11 01.

Artigo em Inglês | MEDLINE | ID: mdl-36319642

9.

A transcriptomic taxonomy of Drosophila circadian neurons around the clock.

Ma, Dingbang; Przybylski, Dariusz; Abruzzi, Katharine C; Schlichting, Matthias; Li, Qunlong; Long, Xi; Rosbash, Michael.

Elife ; 102021 01 13.

Artigo em Inglês | MEDLINE | ID: mdl-33438579

10.

Powerful fusion: PSI-BLAST and consensus sequences.

Przybylski, Dariusz; Rost, Burkhard.

Bioinformatics ; 24(18): 1987-93, 2008 Sep 15.

Artigo em Inglês | MEDLINE | ID: mdl-18678588

11.

Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments.

Przybylski, Dariusz; Rost, Burkhard.

Nucleic Acids Res ; 35(7): 2238-46, 2007.

Artigo em Inglês | MEDLINE | ID: mdl-17369271

12.

Cancer immunogenomic approach to neoantigen discovery in a checkpoint blockade responsive murine model of oral cavity squamous cell carcinoma.

Zolkind, Paul; Przybylski, Dariusz; Marjanovic, Nemanja; Nguyen, Lan; Lin, Tianxiang; Johanns, Tanner; Alexandrov, Anton; Zhou, Liye; Allen, Clint T; Miceli, Alexander P; Schreiber, Robert D; Artyomov, Maxim; Dunn, Gavin P; Uppaluri, Ravindra.

Oncotarget ; 9(3): 4109-4119, 2018 Jan 09.

Artigo em Inglês | MEDLINE | ID: mdl-29423108

13.

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.

Mertins, Philipp; Przybylski, Dariusz; Yosef, Nir; Qiao, Jana; Clauser, Karl; Raychowdhury, Raktima; Eisenhaure, Thomas M; Maritzen, Tanja; Haucke, Volker; Satoh, Takashi; Akira, Shizuo; Carr, Steven A; Regev, Aviv; Hacohen, Nir; Chevrier, Nicolas.

Cell Rep ; 19(13): 2853-2866, 2017 06 27.

Artigo em Inglês | MEDLINE | ID: mdl-28658630

14.

Predicting transmembrane beta-barrels in proteomes.

Bigelow, Henry R; Petrey, Donald S; Liu, Jinfeng; Przybylski, Dariusz; Rost, Burkhard.

Nucleic Acids Res ; 32(8): 2566-77, 2004.

Artigo em Inglês | MEDLINE | ID: mdl-15141026

15.

EVA: Evaluation of protein structure prediction servers.

Koh, Ingrid Y Y; Eyrich, Volker A; Marti-Renom, Marc A; Przybylski, Dariusz; Madhusudhan, Mallur S; Eswar, Narayanan; Graña, Osvaldo; Pazos, Florencio; Valencia, Alfonso; Sali, Andrej; Rost, Burkhard.

Nucleic Acids Res ; 31(13): 3311-5, 2003 Jul 01.

Artigo em Inglês | MEDLINE | ID: mdl-12824315

16.

Improving fold recognition without folds.

Przybylski, Dariusz; Rost, Burkhard.

J Mol Biol ; 341(1): 255-69, 2004 Jul 30.

Artigo em Inglês | MEDLINE | ID: mdl-15312777

17.

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

Jovanovic, Marko; Rooney, Michael S; Mertins, Philipp; Przybylski, Dariusz; Chevrier, Nicolas; Satija, Rahul; Rodriguez, Edwin H; Fields, Alexander P; Schwartz, Schraga; Raychowdhury, Raktima; Mumbach, Maxwell R; Eisenhaure, Thomas; Rabani, Michal; Gennert, Dave; Lu, Diana; Delorey, Toni; Weissman, Jonathan S; Carr, Steven A; Hacohen, Nir; Regev, Aviv.

Science ; 347(6226): 1259038, 2015 Mar 06.

Artigo em Inglês | MEDLINE | ID: mdl-25745177

18.

CAFASP3 in the spotlight of EVA.

Eyrich, Volker A; Przybylski, Dariusz; Koh, Ingrid Y Y; Grana, Osvaldo; Pazos, Florencio; Valencia, Alfonso; Rost, Burkhard.

Proteins ; 53 Suppl 6: 548-60, 2003.

Artigo em Inglês | MEDLINE | ID: mdl-14579345

19.

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver.

Bochkis, Irina M; Przybylski, Dariusz; Chen, Jenny; Regev, Aviv.

Cell Rep ; 9(3): 996-1006, 2014 Nov 06.

Artigo em Inglês | MEDLINE | ID: mdl-25437555

20.

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.

Maccallum, Iain; Przybylski, Dariusz; Gnerre, Sante; Burton, Joshua; Shlyakhter, Ilya; Gnirke, Andreas; Malek, Joel; McKernan, Kevin; Ranade, Swati; Shea, Terrance P; Williams, Louise; Young, Sarah; Nusbaum, Chad; Jaffe, David B.

Genome Biol ; 10(10): R103, 2009.

Artigo em Inglês | MEDLINE | ID: mdl-19796385

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A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia.

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.

Fas Promotes T Helper 17 Cell Differentiation and Inhibits T Helper 1 Cell Development by Binding and Sequestering Transcription Factor STAT1.

Lipid availability determines fate of skeletal progenitor cells via SOX9.

The genomic substrate for adaptive radiation in African cichlid fish.

Finished bacterial genomes from shotgun sequence data.

High-quality draft assemblies of mammalian genomes from massively parallel sequence data.

DNA read count calibration for single-molecule, long-read sequencing.

A transcriptomic taxonomy of Drosophila circadian neurons around the clock.

Powerful fusion: PSI-BLAST and consensus sequences.

Consensus sequences improve PSI-BLAST through mimicking profile-profile alignments.

Cancer immunogenomic approach to neoantigen discovery in a checkpoint blockade responsive murine model of oral cavity squamous cell carcinoma.

An Integrative Framework Reveals Signaling-to-Transcription Events in Toll-like Receptor Signaling.

Predicting transmembrane beta-barrels in proteomes.

EVA: Evaluation of protein structure prediction servers.

Improving fold recognition without folds.

Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.

CAFASP3 in the spotlight of EVA.

Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver.

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.