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Items: 33

1.

Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon.

Magain N, Miadlikowska J, Mueller O, Gajdeczka M, Truong C, Salamov AA, Dubchak I, Grigoriev IV, Goffinet B, Sérusiaux E, Lutzoni F.

Mol Phylogenet Evol. 2017 Dec;117:10-29. doi: 10.1016/j.ympev.2017.08.013. Epub 2017 Aug 30.

PMID:
28860010
2.

The transcription factor PDR-1 is a multi-functional regulator and key component of pectin deconstruction and catabolism in Neurospora crassa.

Thieme N, Wu VW, Dietschmann A, Salamov AA, Wang M, Johnson J, Singan VR, Grigoriev IV, Glass NL, Somerville CR, Benz JP.

Biotechnol Biofuels. 2017 Jun 12;10:149. doi: 10.1186/s13068-017-0807-z. eCollection 2017.

3.

A parts list for fungal cellulosomes revealed by comparative genomics.

Haitjema CH, Gilmore SP, Henske JK, Solomon KV, de Groot R, Kuo A, Mondo SJ, Salamov AA, LaButti K, Zhao Z, Chiniquy J, Barry K, Brewer HM, Purvine SO, Wright AT, Hainaut M, Boxma B, van Alen T, Hackstein JHP, Henrissat B, Baker SE, Grigoriev IV, O'Malley MA.

Nat Microbiol. 2017 May 30;2:17087. doi: 10.1038/nmicrobiol.2017.87.

PMID:
28555641
4.

Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.

5.

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants.

Chang Y, Wang S, Sekimoto S, Aerts AL, Choi C, Clum A, LaButti KM, Lindquist EA, Yee Ngan C, Ohm RA, Salamov AA, Grigoriev IV, Spatafora JW, Berbee ML.

Genome Biol Evol. 2015 May 14;7(6):1590-601. doi: 10.1093/gbe/evv090.

6.

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.

Riley R, Salamov AA, Brown DW, Nagy LG, Floudas D, Held BW, Levasseur A, Lombard V, Morin E, Otillar R, Lindquist EA, Sun H, LaButti KM, Schmutz J, Jabbour D, Luo H, Baker SE, Pisabarro AG, Walton JD, Blanchette RA, Henrissat B, Martin F, Cullen D, Hibbett DS, Grigoriev IV.

Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9923-8. doi: 10.1073/pnas.1400592111. Epub 2014 Jun 23. Erratum in: Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14959.

7.

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.

Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, Barry KW, Condon BJ, Copeland AC, Dhillon B, Glaser F, Hesse CN, Kosti I, LaButti K, Lindquist EA, Lucas S, Salamov AA, Bradshaw RE, Ciuffetti L, Hamelin RC, Kema GH, Lawrence C, Scott JA, Spatafora JW, Turgeon BG, de Wit PJ, Zhong S, Goodwin SB, Grigoriev IV.

PLoS Pathog. 2012;8(12):e1003037. doi: 10.1371/journal.ppat.1003037. Epub 2012 Dec 6. Erratum in: PLoS Pathog. 2013 Mar 5;9(3):.

8.

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.

Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17501-6. doi: 10.1073/pnas.1206847109. Epub 2012 Oct 8. Erratum in: Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):4146.

9.

Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis.

Fernandez-Fueyo E, Ruiz-Dueñas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavín JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kües U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5458-63. doi: 10.1073/pnas.1119912109. Epub 2012 Mar 20. Erratum in: Proc Natl Acad Sci U S A. 2012 May 22;109(21):8352. San, Ryu Jae [corrected to Ryu, Jae San].

10.

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production.

Wohlbach DJ, Kuo A, Sato TK, Potts KM, Salamov AA, Labutti KM, Sun H, Clum A, Pangilinan JL, Lindquist EA, Lucas S, Lapidus A, Jin M, Gunawan C, Balan V, Dale BE, Jeffries TW, Zinkel R, Barry KW, Grigoriev IV, Gasch AP.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13212-7. doi: 10.1073/pnas.1103039108. Epub 2011 Jul 25.

11.

Obligate biotrophy features unraveled by the genomic analysis of rust fungi.

Duplessis S, Cuomo CA, Lin YC, Aerts A, Tisserant E, Veneault-Fourrey C, Joly DL, Hacquard S, Amselem J, Cantarel BL, Chiu R, Coutinho PM, Feau N, Field M, Frey P, Gelhaye E, Goldberg J, Grabherr MG, Kodira CD, Kohler A, Kües U, Lindquist EA, Lucas SM, Mago R, Mauceli E, Morin E, Murat C, Pangilinan JL, Park R, Pearson M, Quesneville H, Rouhier N, Sakthikumar S, Salamov AA, Schmutz J, Selles B, Shapiro H, Tanguay P, Tuskan GA, Henrissat B, Van de Peer Y, Rouzé P, Ellis JG, Dodds PN, Schein JE, Zhong S, Hamelin RC, Grigoriev IV, Szabo LJ, Martin F.

Proc Natl Acad Sci U S A. 2011 May 31;108(22):9166-71. doi: 10.1073/pnas.1019315108. Epub 2011 May 2.

12.

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.

Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL.

Nat Genet. 2011 May;43(5):476-81. doi: 10.1038/ng.807. Epub 2011 Apr 10.

13.

Identification of promoter regions and regulatory sites.

Solovyev VV, Shahmuradov IA, Salamov AA.

Methods Mol Biol. 2010;674:57-83. doi: 10.1007/978-1-60761-854-6_5.

PMID:
20827586
14.

The Sorghum bicolor genome and the diversification of grasses.

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS.

Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.

PMID:
19189423
15.

The amphioxus genome and the evolution of the chordate karyotype.

Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS.

Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967.

PMID:
18563158
16.

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina).

Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS.

Nat Biotechnol. 2008 May;26(5):553-60. doi: 10.1038/nbt1403. Epub 2008 May 4. Erratum in: Nat Biotechnol. 2008 Oct;26(10):1193.. Barbote, Ravi [corrected to Barabote, Ravi].

PMID:
18454138
17.

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities.

García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD, Hugenholtz P.

Nat Biotechnol. 2006 Oct;24(10):1263-9. Epub 2006 Sep 24.

PMID:
16998472
18.

Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis.

Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL.

Science. 2006 Sep 1;313(5791):1261-6.

19.

Comparative metagenomics of microbial communities.

Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM.

Science. 2005 Apr 22;308(5721):554-7.

20.

Using the CATH domain database to assign structures and functions to the genome sequences.

Pearl F, Todd AE, Bray JE, Martin AC, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA.

Biochem Soc Trans. 2000 Feb;28(2):269-75.

PMID:
10816141
21.

Ab initio gene finding in Drosophila genomic DNA.

Salamov AA, Solovyev VV.

Genome Res. 2000 Apr;10(4):516-22.

22.

Genome analysis: Assigning protein coding regions to three-dimensional structures.

Salamov AA, Suwa M, Orengo CA, Swindells MB.

Protein Sci. 1999 Apr;8(4):771-7.

23.

Combining sensitive database searches with multiple intermediates to detect distant homologues.

Salamov AA, Suwa M, Orengo CA, Swindells MB.

Protein Eng. 1999 Feb;12(2):95-100.

PMID:
10195280
24.
25.

Assessing protein coding region integrity in cDNA sequencing projects.

Salamov AA, Nishikawa T, Swindells MB.

Bioinformatics. 1998 Jun;14(5):384-90.

PMID:
9682051
26.

Protein secondary structure prediction using local alignments.

Salamov AA, Solovyev VV.

J Mol Biol. 1997 Apr 25;268(1):31-6.

PMID:
9149139
27.

Recognition of 3'-processing sites of human mRNA precursors.

Salamov AA, Solovyev VV.

Comput Appl Biosci. 1997 Feb;13(1):23-8.

PMID:
9088705
28.
29.

Identification of human gene structure using linear discriminant functions and dynamic programming.

Solovyev VV, Salamov AA, Lawrence CB.

Proc Int Conf Intell Syst Mol Biol. 1995;3:367-75.

PMID:
7584460
30.
31.

Predicting alpha-helix and beta-strand segments of globular proteins.

Solovyev VV, Salamov AA.

Comput Appl Biosci. 1994 Dec;10(6):661-9.

PMID:
7704665
32.

The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames.

Solovyev VV, Salamov AA, Lawrence CB.

Proc Int Conf Intell Syst Mol Biol. 1994;2:354-62.

PMID:
7584412
33.

[Factors determining the formation of secondary structures of globular proteins].

Solov'ev VV, Salamov AA, Kapitonov VV.

Mol Biol (Mosk). 1991 May-Jun;25(3):795-809. Russian. No abstract available.

PMID:
1944261

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