PUB - Publikationen an der Universität Bielefeld

Ferns diversified in the shadow of angiosperms.
Schneider H, Schuettpelz E, Pryer KM, Cranfill R, Magallon S, Lupia R., Nature 428(6982), 2004
PMID: 15058303

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Arabidopsis Genome Initiative., Nature 408(6814), 2000
PMID: 11130711

Nuclear DNA C-values in 30 species double the familial representation in pteridophytes.
Obermayer R, Leitch IJ, Hanson L, Bennett MD., Ann. Bot. 90(2), 2002
PMID: 12197518

Is There an Upper Limit to Genome Size?
Hidalgo O, Pellicer J, Christenhusz M, Schneider H, Leitch AR, Leitch IJ., Trends Plant Sci. 22(7), 2017
PMID: 28506667

EB, Adv. Bot. Res. 78(), 2016

Episodic fresh surface waters in the Eocene Arctic Ocean.
Brinkhuis H, Schouten S, Collinson ME, Sluijs A, Sinninghe Damste JS, Dickens GR, Huber M, Cronin TM, Onodera J, Takahashi K, Bujak JP, Stein R, van der Burgh J, Eldrett JS, Harding IC, Lotter AF, Sangiorgi F, van Konijnenburg-van Cittert H, de Leeuw JW, Matthiessen J, Backman J, Moran K; Expedition 302 Scientists., Nature 441(7093), 2006
PMID: 16752440

The Eocene Arctic Azolla bloom: environmental conditions, productivity and carbon drawdown.
Speelman EN, Van Kempen MM, Barke J, Brinkhuis H, Reichart GJ, Smolders AJ, Roelofs JG, Sangiorgi F, de Leeuw JW, Lotter AF, Sinninghe Damste JS., Geobiology 7(2), 2009
PMID: 19323694

TA, Econ. Bot. 34(), 1980

Cellular responses in the cyanobacterial symbiont during its vertical transfer between plant generations in the Azolla microphylla symbiosis.
Zheng W, Bergman B, Chen B, Zheng S, Xiang G, Rasmussen U., New Phytol. 181(1), 2009
PMID: 19076717

Genome erosion in a nitrogen-fixing vertically transmitted endosymbiotic multicellular cyanobacterium.
Ran L, Larsson J, Vigil-Stenman T, Nylander JA, Ininbergs K, Zheng WW, Lapidus A, Lowry S, Haselkorn R, Bergman B., PLoS ONE 5(7), 2010
PMID: 20628610

JW, Am. J. Bot. 55(), 1968

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors.
Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB., Proc. Natl. Acad. Sci. U.S.A. 107(18), 2010
PMID: 20385809

Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae.
Wilhelmsson PKI, Muhlich C, Ullrich KK, Rensing SA., Genome Biol Evol 9(12), 2017
PMID: 29216360

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riano-Pachon DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sorensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loque D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV., Science 332(6032), 2011
PMID: 21551031

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.
Evkaikina AI, Berke L, Romanova MA, Proux-Wera E, Ivanova AN, Rydin C, Pawlowski K, Voitsekhovskaja OV., Genome Biol Evol 9(9), 2017
PMID: 28957460

AUTHOR UNKNOWN, 0

DJ, Phytochemistry 42(), 1996

A combinatorial interplay among the 1-aminocyclopropane-1-carboxylate isoforms regulates ethylene biosynthesis in Arabidopsis thaliana.
Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A., Genetics 183(3), 2009
PMID: 19752216

Early genome duplications in conifers and other seed plants.
Li Z, Baniaga AE, Sessa EB, Scascitelli M, Graham SW, Rieseberg LH, Barker MS., Sci Adv 1(10), 2015
PMID: 26702445

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences
Pryer KM, Schuettpelz E, Wolf PG, Schneider H, Smith AR, Cranfill R., Am. J. Bot. 91(10), 2004
PMID: IND43664159

The Chromosome Counts Database (CCDB) - a community resource of plant chromosome numbers.
Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose I., New Phytol. 206(1), 2014
PMID: 25423910

The frequency of polyploid speciation in vascular plants.
Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH., Proc. Natl. Acad. Sci. U.S.A. 106(33), 2009
PMID: 19667210

Modeling gene and genome duplications in eukaryotes.
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y., Proc. Natl. Acad. Sci. U.S.A. 102(15), 2005
PMID: 15800040

Pentatricopeptide repeat proteins in plants.
Barkan A, Small I., Annu Rev Plant Biol 65(), 2014
PMID: 24471833

RNA editing in plants and its evolution.
Takenaka M, Zehrmann A, Verbitskiy D, Hartel B, Brennicke A., Annu. Rev. Genet. 47(), 2013
PMID: 24274753

Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants.
Cheng S, Gutmann B, Zhong X, Ye Y, Fisher MF, Bai F, Castleden I, Song Y, Song B, Huang J, Liu X, Xu X, Lim BL, Bond CS, Yiu SM, Small I., Plant J. 85(4), 2016
PMID: 26764122

Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata.
Oldenkott B, Yamaguchi K, Tsuji-Tsukinoki S, Knie N, Knoop V., RNA 20(10), 2014
PMID: 25142065

Evolutionary origin of RNA editing.
Gray MW., Biochemistry 51(26), 2012
PMID: 22708551

SD, Am. Nat. 115(), 1980

Expression of an insecticidal fern protein in cotton protects against whitefly.
Shukla AK, Upadhyay SK, Mishra M, Saurabh S, Singh R, Singh H, Thakur N, Rai P, Pandey P, Hans AL, Srivastava S, Rajapure V, Yadav SK, Singh MK, Kumar J, Chandrashekar K, Verma PC, Singh AP, Nair KN, Bhadauria S, Wahajuddin M, Singh S, Sharma S, Omkar , Upadhyay RS, Ranade SA, Tuli R, Singh PK., Nat. Biotechnol. 34(10), 2016
PMID: 27598229

Data access for the 1,000 Plants (1KP) project.
Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK., Gigascience 3(), 2014
PMID: 25625010

Endosymbiotic origin and differential loss of eukaryotic genes.
Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF., Nature 524(7566), 2015
PMID: 26287458

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns.
Li FW, Villarreal JC, Kelly S, Rothfels CJ, Melkonian M, Frangedakis E, Ruhsam M, Sigel EM, Der JP, Pittermann J, Burge DO, Pokorny L, Larsson A, Chen T, Weststrand S, Thomas P, Carpenter E, Zhang Y, Tian Z, Chen L, Yan Z, Zhu Y, Sun X, Wang J, Stevenson DW, Crandall-Stotler BJ, Shaw AJ, Deyholos MK, Soltis DE, Graham SW, Windham MD, Langdale JA, Wong GK, Mathews S, Pryer KM., Proc. Natl. Acad. Sci. U.S.A. 111(18), 2014
PMID: 24733898

Functional horizontal gene transfer from bacteria to eukaryotes.
Husnik F, McCutcheon JP., Nat. Rev. Microbiol. 16(2), 2017
PMID: 29176581

Genetic diversity and phylogeny analysis of Anabaena azollae based on RFLPs detected in Azolla-Anabaena azollae DNA complexes using nif gene probes.
Coppenolle Bvan, McCouch SR, Watanabe I, Huang N, Hove Cvan., Theor. Appl. Genet. 91(4), 1995
PMID: IND20486774

Genetic diversity and classification of cyanobacteria in different Azolla species by the use of PCR fingerprinting.
Zheng WW, Nilsson M, Bergman B, Rasmussen U., Theor. Appl. Genet. 99(7/8), 1999
PMID: IND22055288

Arbuscular mycorrhiza: the mother of plant root endosymbioses.
Parniske M., Nat. Rev. Microbiol. 6(10), 2008
PMID: 18794914

Algal ancestor of land plants was preadapted for symbiosis.
Delaux PM, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels CJ, Sederoff HW, Stevenson DW, Surek B, Zhang Y, Sussman MR, Dunand C, Morris RJ, Roux C, Wong GK, Oldroyd GE, Ane JM., Proc. Natl. Acad. Sci. U.S.A. 112(43), 2015
PMID: 26438870

Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution.
Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ane JM., PLoS Genet. 10(7), 2014
PMID: 25032823

Genes conserved for arbuscular mycorrhizal symbiosis identified through phylogenomics.
Bravo A, York T, Pumplin N, Mueller LA, Harrison MJ., Nat Plants 2(), 2016
PMID: 27249190

Metabolic Adaptation, a Specialized Leaf Organ Structure and Vascular Responses to Diurnal N2 Fixation by Nostoc azollae Sustain the Astonishing Productivity of Azolla Ferns without Nitrogen Fertilizer.
Brouwer P, Brautigam A, Buijs VA, Tazelaar AO, van der Werf A, Schluter U, Reichart GJ, Bolger A, Usadel B, Weber AP, Schluepmann H., Front Plant Sci 8(), 2017
PMID: 28408911

Suppression of Arbuscule Degeneration in Medicago truncatula phosphate transporter4 Mutants is Dependent on the Ammonium Transporter 2 Family Protein AMT2;3.
Breuillin-Sessoms F, Floss DS, Gomez SK, Pumplin N, Ding Y, Levesque-Tremblay V, Noar RD, Daniels DA, Bravo A, Eaglesham JB, Benedito VA, Udvardi MK, Harrison MJ., Plant Cell 27(4), 2015
PMID: 25841038

Characterization of three functional high-affinity ammonium transporters in Lotus japonicus with differential transcriptional regulation and spatial expression.
D'Apuzzo E, Rogato A, Simon-Rosin U, El Alaoui H, Barbulova A, Betti M, Dimou M, Katinakis P, Marquez A, Marini AM, Udvardi MK, Chiurazzi M., Plant Physiol. 134(4), 2004
PMID: 15075393

Medicago truncatula Molybdate Transporter type 1 (MtMOT1.3) is a plasma membrane molybdenum transporter required for nitrogenase activity in root nodules under molybdenum deficiency.
Tejada-Jimenez M, Gil-Diez P, Leon-Mediavilla J, Wen J, Mysore KS, Imperial J, Gonzalez-Guerrero M., New Phytol. 216(4), 2017
PMID: 28805962

Modulation of the growth and metabolic response of cyanobacteria by the multifaceted activity of naringenin.
Zyszka B, Aniol M, Lipok J., PLoS ONE 12(5), 2017
PMID: 28498848

Flavonoid-induced expression of a symbiosis-related gene in the cyanobacterium Nostoc punctiforme.
Cohen MF, Yamasaki H., J. Bacteriol. 182(16), 2000
PMID: 10913102

Automation and Evaluation of the SOWH Test with SOWHAT.
Church SH, Ryan JF, Dunn CW., Syst. Biol. 64(6), 2015
PMID: 26231182

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T, Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A, Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA, Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B, Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ, Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL., Science 319(5859), 2007
PMID: 18079367

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.
Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS, Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B, Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN, Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J, Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y, Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U, Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I, Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A, Rovekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y, Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y, Yotsui I, Zachgo S, Schmutz J., Cell 171(2), 2017
PMID: 28985561

H, Tetrahedron Lett. 22(), 1963

Squalene cyclase and oxidosqualene cyclase from a fern.
Shinozaki J, Shibuya M, Masuda K, Ebizuka Y., FEBS Lett. 582(2), 2007
PMID: 18154734

A, Phytochemistry 7(), 1968

Hopanoids as functional analogues of cholesterol in bacterial membranes.
Saenz JP, Grosser D, Bradley AS, Lagny TJ, Lavrynenko O, Broda M, Simons K., Proc. Natl. Acad. Sci. U.S.A. 112(38), 2015
PMID: 26351677

LY, Bio Protoc. 7(), 2017

C-value reassessment of plant standards: an image cytometry approach.
Praca-Fontes MM, Carvalho CR, Clarindo WR., Plant Cell Rep. 30(12), 2011
PMID: 21850594

Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify.
Dijkhuizen LW, Brouwer P, Bolhuis H, Reichart GJ, Koppers N, Huettel B, Bolger AM, Li FW, Cheng S, Liu X, Wong GK, Pryer K, Weber A, Brautigam A, Schluepmann H., New Phytol. 217(1), 2017
PMID: 29084347

Azolla domestication towards a biobased economy?
Brouwer P, Brautigam A, Kulahoglu C, Tazelaar AO, Kurz S, Nierop KG, van der Werf A, Weber AP, Schluepmann H., New Phytol. 202(3), 2014
PMID: 24494738

Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots.
de Vries J, Fischer AM, Roettger M, Rommel S, Schluepmann H, Brautigam A, Carlsbecker A, Gould SB., New Phytol. 209(2), 2015
PMID: 26358624

Does hybridization drive the transition to asexuality in diploid Boechera?
Beck JB, Alexander PJ, Allphin L, Al-Shehbaz IA, Rushworth C, Bailey CD, Windham MD., Evolution 66(4), 2011
PMID: 22486684

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.
Berlin K, Koren S, Chin CS, Drake JP, Landolin JM, Phillippy AM., Nat. Biotechnol. 33(6), 2015
PMID: 26006009

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J., Nat. Methods 10(6), 2013
PMID: 23644548

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM., PLoS ONE 9(11), 2014
PMID: 25409509

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.
Hahn C, Bachmann L, Chevreux B., Nucleic Acids Res. 41(13), 2013
PMID: 23661685

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A., Bioinformatics 28(12), 2012
PMID: 22543367

BlobTools: Interrogation of genome assemblies
Laetsch DR, Blaxter ML., 2017
PMID: PPR41137

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner FO., Nucleic Acids Res. 41(Database issue), 2012
PMID: 23193283

UniProt: the universal protein knowledgebase.
The UniProt Consortium., Nucleic Acids Res. 45(D1), 2016
PMID: 27899622

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM., Bioinformatics 31(19), 2015
PMID: 26059717

Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168

HISAT: a fast spliced aligner with low memory requirements.
Kim D, Langmead B, Salzberg SL., Nat. Methods 12(4), 2015
PMID: 25751142

AUTHOR UNKNOWN, 0

BLAST+: architecture and applications.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL., BMC Bioinformatics 10(), 2009
PMID: 20003500

PlantTribes: a gene and gene family resource for comparative genomics in plants.
Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS, dePamphilis CW., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18073194

Repbase Update, a database of repetitive elements in eukaryotic genomes.
Bao W, Kojima KK, Kohany O., Mob DNA 6(), 2015
PMID: 26045719

The Dfam database of repetitive DNA families.
Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, Smit AF, Wheeler TJ., Nucleic Acids Res. 44(D1), 2015
PMID: 26612867

Accelerated Profile HMM Searches.
Eddy SR., PLoS Comput. Biol. 7(10), 2011
PMID: 22039361

GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.
Gremme G, Steinbiss S, Kurtz S., IEEE/ACM Trans Comput Biol Bioinform 10(3), 2013
PMID: 24091398

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons.
Ellinghaus D, Kurtz S, Willhoeft U., BMC Bioinformatics 9(), 2008
PMID: 18194517

Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
Steinbiss S, Willhoeft U, Gremme G, Kurtz S., Nucleic Acids Res. 37(21), 2009
PMID: 19786494

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts.
Cheng B, Furtado A, Henry RJ., Gigascience 6(11), 2017
PMID: 29048540

AUTHOR UNKNOWN, 0

Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A., Nat. Biotechnol. 29(7), 2011
PMID: 21572440

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL., Nat. Biotechnol. 33(3), 2015
PMID: 25690850

Tandem repeats finder: a program to analyze DNA sequences.
Benson G., Nucleic Acids Res. 27(2), 1999
PMID: 9862982

Search and clustering orders of magnitude faster than BLAST.
Edgar RC., Bioinformatics 26(19), 2010
PMID: 20709691

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.
Katoh K, Misawa K, Kuma K, Miyata T., Nucleic Acids Res. 30(14), 2002
PMID: 12136088

MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.
Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M., Plant Physiol. 164(2), 2013
PMID: 24306534

Gene finding in novel genomes.
Korf I., BMC Bioinformatics 5(), 2004
PMID: 15144565

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
Stanke M, Morgenstern B., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980513

AUTHOR UNKNOWN, 0

GSC, BMC Bioinformatics 6(), 2005

Phytozome: a comparative platform for green plant genomics.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22110026

EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
Barker MS, Dlugosch KM, Dinh L, Challa RS, Kane NC, King MG, Rieseberg LH., Evol. Bioinform. Online 6(), 2010
PMID: 21079755

DM, Genome Biol. 16(), 2015

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.
Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T., J. Comput. Biol. 22(5), 2014
PMID: 25549288

MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res. 32(5), 2004
PMID: 15034147

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
Stamatakis A., Bioinformatics 22(21), 2006
PMID: 16928733

Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach.
Rabier CE, Ta T, Ane C., Mol. Biol. Evol. 31(3), 2013
PMID: 24361993

GenPhyloData: realistic simulation of gene family evolution.
Sjostrand J, Arvestad L, Lagergren J, Sennblad B., BMC Bioinformatics 14(), 2013
PMID: 23803001

TimeTree2: species divergence times on the iPhone.
Kumar S, Hedges SB., Bioinformatics 27(14), 2011
PMID: 21622662

E, Trop. Plant Biol. 1(), 2008

How to usefully compare homologous plant genes and chromosomes as DNA sequences.
Lyons E, Freeling M., Plant J. 53(4), 2008
PMID: 18269575

A codon-based model of nucleotide substitution for protein-coding DNA sequences.
Goldman N, Yang Z., Mol. Biol. Evol. 11(5), 1994
PMID: 7968486

PAML 4: phylogenetic analysis by maximum likelihood.
Yang Z., Mol. Biol. Evol. 24(8), 2007
PMID: 17483113

An empirical codon model for protein sequence evolution.
Kosiol C, Holmes I, Goldman N., Mol. Biol. Evol. 24(7), 2007
PMID: 17400572

L, R J. 8(), 2016

An efficient algorithm for large-scale detection of protein families.
Enright AJ, Van Dongen S, Ouzounis CA., Nucleic Acids Res. 30(7), 2002
PMID: 11917018

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.
Csuros M., Bioinformatics 26(15), 2010
PMID: 20551134

Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity.
Lang D, Weiche B, Timmerhaus G, Richardt S, Riano-Pachon DM, Correa LG, Reski R, Mueller-Roeber B, Rensing SA., Genome Biol Evol 2(), 2010
PMID: 20644220

EMBOSS: the European Molecular Biology Open Software Suite.
Rice P, Longden I, Bleasby A., Trends Genet. 16(6), 2000
PMID: 10827456

D, Genome Biol. 14(), 2013

The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ., Mol. Biol. Evol. 32(1), 2014
PMID: 25371430

Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
Lanfear R, Calcott B, Ho SY, Guindon S., Mol. Biol. Evol. 29(6), 2012
PMID: 22319168

HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment.
Johnson MG, Gardner EM, Liu Y, Medina R, Goffinet B, Shaw AJ, Zerega NJ, Wickett NJ., Appl Plant Sci 4(7), 2016
PMID: 27437175

C, BMC Evol. Biol. 19(), 2018

Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Lowe TM, Eddy SR., Nucleic Acids Res. 25(5), 1997
PMID: 9023104

Mugsy: fast multiple alignment of closely related whole genomes.
Angiuoli SV, Salzberg SL., Bioinformatics 27(3), 2010
PMID: 21148543

STRIDE: Species Tree Root Inference from Gene Duplication Events.
Emms DM, Kelly S., Mol. Biol. Evol. 34(12), 2017
PMID: 29029342

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S., Mol. Biol. Evol. 30(12), 2013
PMID: 24132122

AUTHOR UNKNOWN, 0

HTSeq--a Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W., Bioinformatics 31(2), 2014
PMID: 25260700

Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621

Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH., Nat. Methods 12(1), 2014
PMID: 25402007

A 4000-species dataset provides new insight into the evolution of ferns.
Testo W, Sundue M., Mol. Phylogenet. Evol. 105(), 2016
PMID: 27621129