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3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. Hoencamp C, et al. Among authors: di pierro m, di palma f. Science. 2021 May 28;372(6545):984-989. doi: 10.1126/science.abe2218. Science. 2021. PMID: 34045355 Free PMC article.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Grabherr MG, Russell P, Meyer M, Mauceli E, Alföldi J, Di Palma F, Lindblad-Toh K. Grabherr MG, et al. Among authors: di palma f. Bioinformatics. 2010 May 1;26(9):1145-51. doi: 10.1093/bioinformatics/btq102. Epub 2010 Mar 5. Bioinformatics. 2010. PMID: 20208069 Free PMC article.
Why sequence all eukaryotes?
Blaxter M, Archibald JM, Childers AK, Coddington JA, Crandall KA, Di Palma F, Durbin R, Edwards SV, Graves JAM, Hackett KJ, Hall N, Jarvis ED, Johnson RN, Karlsson EK, Kress WJ, Kuraku S, Lawniczak MKN, Lindblad-Toh K, Lopez JV, Moran NA, Robinson GE, Ryder OA, Shapiro B, Soltis PS, Warnow T, Zhang G, Lewin HA. Blaxter M, et al. Among authors: di palma f. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115636118. doi: 10.1073/pnas.2115636118. Proc Natl Acad Sci U S A. 2022. PMID: 35042801 Free PMC article.
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Carneiro M, et al. Among authors: di palma f. Science. 2014 Aug 29;345(6200):1074-1079. doi: 10.1126/science.1253714. Science. 2014. PMID: 25170157 Free PMC article.
The Earth BioGenome Project 2020: Starting the clock.
Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. Lewin HA, et al. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118. Proc Natl Acad Sci U S A. 2022. PMID: 35042800 Free PMC article. No abstract available.
An Improved microRNA Annotation of the Canine Genome.
Penso-Dolfin L, Swofford R, Johnson J, Alföldi J, Lindblad-Toh K, Swarbreck D, Moxon S, Di Palma F. Penso-Dolfin L, et al. Among authors: di palma f. PLoS One. 2016 Apr 27;11(4):e0153453. doi: 10.1371/journal.pone.0153453. eCollection 2016. PLoS One. 2016. PMID: 27119849 Free PMC article.
Unsupervised genome-wide recognition of local relationship patterns.
Zamani N, Russell P, Lantz H, Hoeppner MP, Meadows JR, Vijay N, Mauceli E, di Palma F, Lindblad-Toh K, Jern P, Grabherr MG. Zamani N, et al. Among authors: di palma f. BMC Genomics. 2013 May 24;14:347. doi: 10.1186/1471-2164-14-347. BMC Genomics. 2013. PMID: 23706020 Free PMC article.
Genomic architecture and introgression shape a butterfly radiation.
Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE, Challis R, Kumar S, Moreira GRP, Salazar C, Chouteau M, Counterman BA, Papa R, Blaxter M, Reed RD, Dasmahapatra KK, Kronforst M, Joron M, Jiggins CD, McMillan WO, Di Palma F, Blumberg AJ, Wakeley J, Jaffe D, Mallet J. Edelman NB, et al. Among authors: di palma f. Science. 2019 Nov 1;366(6465):594-599. doi: 10.1126/science.aaw2090. Science. 2019. PMID: 31672890 Free PMC article.
154 results