AbstractAlticini genera from the Afrotropical region is reported. The paper includes the following for the flea beetle fauna occurring in Sub-Saharan Africa and Madagascar: a key to their identification; habitus photos of all the genera; microscope and scanning electron micrographs of many diagnostic morphological characters; and an updated annotated catalogue with biogeographical notes that include new distributional data. The following new synonymies are proposed: Aphthona Chevrolat, 1836 = Ethiopia Scherer, 1972 syn. n.; Sanckia Duvivier, 1891 = Eugonotes Jacoby, 1897 syn. n.; Eurylegna Weise, 1910a = Eurylegniella Scherer, 1972 syn. n.; Kimongona Bechyné, 1959a = Mesocrepis Scherer, 1963 syn. n.; Diphaulacosoma Jacoby, 1892a = Neoderina Bechyné, 1952 syn. n.; Sesquiphaera Bechyné, 1958a = Paropsiderma Bechyné, 1958a syn. n.; Podagrica Chevrolat, 1836 = Podagricina Csiki in syn. n.; Amphimela Chapuis, 1875 = Sphaerophysa Baly, 1876a syn. n. The following new combinations are proposed: Blepharida insignis Brancsik, 1897 = Xanthophysca insignis  comb. n.; Blepharida multiguttata Duvivier, 1891 = Xanthophysca multiguttata  comb. n.; Hemipyxis balyana  comb. n.; Hemipyxis brevicornis  = Pseudadorium brevicornis  comb. n.; Hemipyxis cyanea  = Pseudadorium cyaneum  comb. n.; Hemipyxis gynandromorpha Bechyné, 1958c = Pseudadorium gynandromorphum  comb. n.; Hemipyxis latiuscula Bechyné, 1958c = Pseudadorium latiusculum  comb. n.; Hemipyxis soror  = Pseudadorium soror  comb. n. The genera Buphonella Jacoby, 1903aand Halticopsis Fairmaire, 1883a are transferred to the tribe Galerucini; the genus Biodontocnema Biondi, 2000 stat. prom. is considered to be valid and reinstated at generic level. Finally, a zoogeographical analysis of the flea beetle fauna in the Afrotropical region is provided.A revision of the Csiki in  = Pseuda Chrysomelidae is one of the largest phytophagous insect families and includes approximately 37,000 to 40,000 species . In our opinion, some of the recently established groupings, based on DNA sequences, still need further in-depth analysis because they are phylogenetically and biogeographically incomplete , there were three respected entomologists working on this fauna: Léon Fairmaire (1820−1906), a French specialist on Coleoptera and Hemiptera; Julius Weise (1844−1925), a German coleopterist that, during his life, published a large number of scientific papers, not only on Chrysomelidae but also on Coccinellidae, Curculionoidea and others; and Martin Jacoby (1842−1907), a German musician and coleopterist, who published 150 articles on leaf beetles after moving to London.We recently published an annotated catalogue of the Afrotropical flea beetle genera, based largely on data from the literature . Subsequ ecology . The chrAlticinae, then published many monographs (see References) on the flea beetle fauna of Sub-Saharan Africa and, to a lesser extent, Madagascar. They described many new genera and species between 1950 and 1970. More recently, contributions on the Afrotropical flea beetle fauna were published by Gerhard Scherer, Maurizio Biondi, Paola D’Alessandro, Manfred Döberl, Serge Doguet, and Elizabeth Grobbelaar (see References).A decrease in the number of publications on the Afrotropical flea beetle fauna followed, until a revival in 1930−1940, initiated by the English coleopterist Gilbert Ernest Bryant (1878−1965) and the French chrysomelid specialist Victor Laboissière (1875−1942). Jan Bechyné (1920−1973) and Gerhard Scherer (1929-2012), specialists on the Galerucini; or genus-group names that are unavailable. The rules of the The catalogue is arranged alphabetically by generic names. Names in bold refer to flea beetle genera primarily occurring in the Afrotropical region; those in square brackets refer to: synonymies; genera incorrectly reported in the Afrotropical region; in some cases genera transferred to In addition to the author and date of publication, each genus-group name is accompanied by: a) synonymies, exclusively those for the Afrotropical region; b) bibliographic references, including the original description, other important taxonomic contributions, and distribution data; c) type species, including the method of species assignment; d) geographic distribution in the Afrotropical region cf.  and otheSpecimens were examined and dissected using WILD MZ12.5 and LEICA M205C binocular microscopes. Photomicrographs were taken using a Leica DFC500 camera and the Auto-Montage Pro 2006 software (license number: 15224*syn2459*153a2112_maurizio_266836). Scanning electron micrographs were taken using a PHILIPS SEM XL30 CP and HITACHI TM-1000. Morphometric measures were taken using the image analysis software Image-Pro Insight 8.0 (license number: 03080000-5385).PageBreaktional d’Histoire Naturelle, Paris, France; MCSN: Museo Civico di Storia Naturale ‘Giacomo Doria’, Genova, Italy; MRAC: Musée Royal de l’Afrique Centrale, Tervuren, Belgium; MUAF: Mendel University of Agriculture and Forestry, Brno, Czech Republic; MZHF: Finnish Museum of Natural History, University of Helsinki, Finland; MZLU: Lund University, Sweden; NHMB: Naturhistorisches Museum, Basel, Switzerland; NHRS: Naturhistoriska Riksmuseet, Stockholm, Sweden; NMPC: Entomologické Oddělení Národního Muzea, Praha-Kunratice, Czech Republic; SANC: South African National Collection, ARC-Plant Protection Research Institute, Pretoria, South Africa; SMNS: Staatliches Museum für Naturkunde, Stuttgart, Germany; TMSA: Ditsong: National Museum of Natural History , Pretoria, South Africa; ZMHB: Museum für Naturkunde der Humboldt-Universität, Berlin, Germany; ZSM: Zoologische Staatssammlung, Munich, Germany.The type material examined during this study is preserved in the following institutions: BAQ: collection of M. Biondi, University of L’Aquila, Italy; BMNH: The Natural History Museum, London, United Kingdom; ISNB: Institut Royal des Sciences Naturelles de Belgique, Brussels, Belgium; MNHN: Muséum NaAbbreviations.Morphology - LAN: length of antennae; LB: total length of body; LE: length of elytra; LHT: length of hind tibia; LHTS: length of hind tibial spur; LP: length of pronotum; WE: width of elytra; WP: width of pronotum. Regions - AFR: Afrotropical; AUR: Australian; CAF: Central Afrotropical; EAF: Eastern Afrotropical; ORR: Oriental; MAD: Madagascar; MAS: Mascarene Islands; NAR: Nearctic; NTR: Neotropical; PAR: Palaearctic; SAF: Southern Afrotropical; SEY: Seychelles Islands; SSA: Sub-Saharan Africa; WAF: Western Afrotropical. (?) record to be confirmed; (!) new record; (i) introduced.A new key for the identification of the Afrotropical flea beetle genera is proposed. In comparison with the key previously proposed by PageBreakFairmaire, 1902http://species-id.net/wiki/Abrarius=Entymosina Weise, 1910 (synonymized by Entymosina); 1958c: 9; Abrarius: Abrarius cribrosus Fairmaire, 1902: 261 (Madagascar: Plateau de l’Ankara), designation by monotypy; Entymosina: Entymosina parvula Weise, 1910b: 439 (Madagascar: Nossibé), by present designation.Madagascar .No information.Gioia Bechyné (1955d: 77) is very similar to Abrarius, and may well be a synonym.Endemic to Madagascar and comprises about ten known species. The Neotropical genus Biondi & D’Alessandro, 2007http://species-id.net/wiki/AfroalticaAfroaltica subaptera Biondi & D’Alessandro, 2007: 100 , by original designation.Republic of South Africa  .Afroaltica subaptera was collected in an open field on Poaceae  (amineae) .Two species have been described.Afroalytus Scherer, 1961] and the Republic of South Africa .No information.Crepidodera betiokyensis Bechyné (1954a: 46) from Madagascar, erroneously attributed to this genus by Afrorestia Bechyné .Some species of this genus have been collected from plants in the family Crepidodera betiokyensis Bechyné (1954a: 46) from Madagascar, erroneously attributed to Afrocrepis Bechyné by Crepidodera sjostedti Weise (1910a: 221) from Kilimanjaro was incorrectly attributed to Asiorestia Jacobson, 1925  by Afrorestia Bechyné by PageBreakAbout twenty described species. Allomorpha Jacoby, 1892b] and Halticova rufoguttata Fairmaire, 1898; while Sphaerophysa Baly and Dibolosoma Jacoby. Moreover, there are no important diagnostic characters distinguishing Sphaerophysa from Amphimela, this latter characterized by a wide variability in the Afrotropical region. Therefore, the following new synonymy is proposed: Amphimela Chapuis, 1875 = Sphaerophysa Baly, 1876b syn. n. Material examined: Sphaerophysa clavicornis Baly (det. J. Bechyné), “Madagascar, Tananarive”, 2 specimens (NMPC).PageBreakAbout thirty-five species have been described in the Afrotropical region. Fairmaire, 1902http://species-id.net/wiki/AnaxertaAnaxerta castanea Fairmaire, 1902: 268 (Madagascar: Ankarahitra), designation by monotypy.Madagascar .No information.A single species has been described.Bechyné, 1960bhttp://species-id.net/wiki/AngulaphthonaAphthona heteromorpha Bechyné, 1955c: 62 (Madagascar: Bas Mangoky), by original designation.Egypt, Tchad, Sudan, Somaliland, Sierra Leone, Nigeria, Democratic Republic of Congo, Uganda, Zambia (!) [50 km W Kasama (BAQ)], Malawi (!) [Dedza (BAQ)], Mozambique, Republic of South Africa (!) [KwaZulu-Natal: Durban (SANC)], Madagascar, and Arabian Peninsula (Saudi Arabia and North Yemen) .Angulaphthona heteromorpha collected on cotton plants, Gossypium sp.  (Aphthona).Five species are known from the Afrotropical region.Bechyné, 1964http://species-id.net/wiki/AntanemoraLactica Erichson, 1847 (pars)Lactica); 1964: 145; .Lactica carbonaria Bechyné, 1948a: 7 , by original designation.Madagascar .No information.There are about twenty known species .Chevrolat, 1836http://species-id.net/wiki/Aphthona=Ethiopia Scherer, 1972 syn. n.=Pseudeugonotes Jacoby, 1899 (synonymized by Ethiopia); Ethiopia).Aphthona: Altica cyparissiae Koch, 1803: 80 (Europe), by subsequent designation by Ethiopia: Ethiopia tricolor Scherer, 1972: 7 , by original designation; Pseudeugonotes: Pseudeugonotes vannutellii Jacoby, 1899a: 531 (Ethiopia: Sancurar-Amarr Burgi), designation by monotypy.Aphthona should be attributed to different genera , Australian, Nearctic, Oriental and Palaearctic regions . All thenera cf. .Euphorbiaceae, but also with Geraniaceae, Cistaceae, Rosaceae, Linaceae, Iridaceae, Malvaceae and Lythraceae .About one hundred species are described from Madagascar and Sub-Saharan Africa. There are no important diagnostic characters distinguishing Motschulsky, 1860http://species-id.net/wiki/ArgopistesArgopistes biplagiata Motschulsky, 1860: 236 (Siberia), designation by monotypy.Central, Eastern and Southern Africa, and Madagascar; Australian, Eastern Palaearctic, Nearctic, Northern Neotropical and Oriental regions .Oleaceae in Sub-Saharan Africa, especially with Olive trees [Olea europaea var. africana (Mill.)], on which the larvae are leaf miners and adults defoliators .Jacoby, 1892bhttp://species-id.net/wiki/Argopistoides=Torodera Weise, 1902a (synonymized by Torodera); Torodera): 437; Torodera).Argopistoides septempunctata Jacoby, 1892b: 932 [Burma (=Myanmar): Carin Chebà], designation by monotypy; Torodera: Torodera octomaculata Weise, 1902a: 164 (Kwai), by subsequent designation by Scherer (1987:67).Republic of the Congo, Democratic Republic of the Congo, Guinea, Kenya, Rwanda (!) , Republic of South Africa , Sierra Leone, Sudan, Tanzania, Uganda, Zimbabwe, and Oriental region .Poaceae  (Oryza) in Kenya [cf. Torodera)].Genus reported from The Afrotropical region has four described species.Argopus Fischer, 1824], Rwanda (!) ; Seychelles, Sierra Leone (!) , Eastern Palaearctic and Oriental regions (Burundi (!) [Kibira National Park (BAQ)], Democratic Republic of the Congo (!) , Kenya (!) , Madagascar (!) , Malawi (!) [Dedza (BAQ)], Republic of South Africa (!)  were collected in forest, and Bikasha minor Maulik (1931: 259) in wet coastal meadows.In Seychelles, About ten species are known from the Afrotropical region .Biondi, 2000 stat. prom.http://species-id.net/wiki/BiodontocnemaBiodontocnema brunnea Biondi, 2000: 348 , designation by monotypy.Namibia .Biodontocnema brunnea is the only species in this genus, and it is associated with moist habitats (habitats .Chaetocnema Stephens by Biodontocnema and based their synonymy only on the examination of some photos and figures. Chaetocnema schlaeflii (Chaetocnema major (Biodontocnema (Biodontocnema (Biodontocnema (Biodontocnema (Biodontocnema (Biodontocnema); longer antennae that reach at least the middle of the elytra  in Sulawesi (Indonesia)   and in pdonesia) .Four species are known from Afrotropical region, one from Sub-Saharan Africa, probably introduced, and three from Madagascar.Stephens, 1831http://species-id.net/wiki/Chaetocnema=Brinckaltica Bechyné, 1959b , by subsequent designation by Exorhina: Haltica chlorophana Duftschmid, 1825: 286 (Austria), by subsequent designation by Brinckaltica: Chaetocnema subaterrima Jacoby, 1900: 254 , by original designation.All zoogeographical regions .Chenopodiaceae, Cyperaceae, Juncaceae, Poaceae , and Polygonaceae  [N’Kongsamba (MCSN)] and Republic of Congo .No information.A single species has been described.Chaloenus Westwood, 1862].Weise, 1895http://species-id.net/wiki/Decaria=Embolimus Weise, 1902Decaria: Decaria tricolor Weise, 1895: 344 , designation by monotypy; Embolimus: Embolimus pauli Weise, 1902b: 304 (Kwai), designation by monotypy.Afrotropical region (excluding Madagascar) .Decaria is associated mainly with plans from the genera Heliotropium (Boraginaceae), Cola (Sterculiaceae) and Ocimum (Lamiaceae) (cf. eae) cf. .About twenty species have been described.Decarthrocera Laboissière, 1937] .No information.Gabonia miraculosa Scherer (1963: 652) in this genus  syn. n. Bechyné, 1952 , designation by monotypy; Neoderina: Neodera (Neoderina) crassicornis Bechyné, 1952: 251 , designation by monotypy.Madagascar .No information.Neoderina Bechyné from Diphaulacosoma. Therefore, the following new synonymy is proposed: Diphaulacosoma Jacoby, 1892a = Neoderina Bechyné, 1952 syn. n. Material examined: Neodera (Neoderina) crassicornis Bechyné, “Madagascar, Ambohitsitondrona, x-xii.47, Michel leg.”, “typus” ♂ and “cotypus” ♀ (MNHN).Four species . No diagnostic characters distinguish Bechyné, 1955bhttp://species-id.net/wiki/DjalloniaDjallonia maindra Bechyné, 1955b: 534 , designation by monotypy.Democratic Republic of the Congo and Guinea .No information.PageBreakOnly one species is known.Biondi & D’Alessandro, 2003http://species-id.net/wiki/DrakensbergianellaDrakensbergianella rudebecki Biondi and D’Alessandro, 2003: 100 , designation by monotypy.Distribution. Republic of South Africa   .Drakensbergianella rudebecki is the only species in this genus. It lives in alpine meadows  on the Drakensberg and was collected on the inflorescences of Senecio and Helichrysum (Asteraceae) (eraceae) .A single species has been described.Jacoby, 1906http://species-id.net/wiki/DunbrodyaDunbrodya nitida Jacoby, 1906: 20 (Cape Colony), designation by monotypy.Ethiopia (!) [Sidamo (BAQ)] and the Republic of South Africa  .Dunbrodya nitida was collected on an Asparagus sp. (Asparagaceae) (agaceae) .Two species are known .Embolimus Weise, 1902b], Malawi, Mozambique, Tanzania and Socotra Island (Yemen) .No information.PageBreakSeven species are known.Escaleriella Weise, 1907a], Rwanda, and Malawi (!) [Dedza (BAQ)] .No information.Eurylegniella Scherer from Eurylegna. The following synonymy is therefore proposed: Eurylegna Weise, 1910 = Eurylegniella Scherer, 1972 syn. n. Material examined: Eurylegniella guineensis (Bechyné) (det. G. Scherer), “Imperial College, Expdn. Ghana 1960, 24.8.60, Bobiri Forest, Kumasi, Ashanti”, 1 specimen (ZSM); “Congo Belge, P.N.G., Miss. H. De Saeger, Mt Embe, 20-iv-1952, H. De Saeger, 3347”, 1 specimen (MRAC).Six species have been described. There are no important diagnostic characters distinguishing Eurylegniella Scherer, 1972], designation by monotypy.Afrotropical (excluding Madagascar), Eastern Palaeartic, and Oriental regions .Anacardiaceae and Ericaceae , by original designation.Madagascar .No information.Galerucinae to the Alticinae (currently the tribe Alticini) by Mandarella Duvivier (1892b: 433)  cf. .Weise, 1902ahttp://species-id.net/wiki/Homichloda=Weiseana Jacoby, 1903a (synonymized by Weiseana); Homichloda: Homichloda pauli Weise, 1902a: 166 (Kwai), designation by monotypy; Weiseana: Weiseana barkeri Jacoby, 1903: 16 , by original designation.Kenya, Republic of South Africa , Tanzania and Zambia .Acacia species, trees in the family Fabaceae Hyphasoma); .Hyphasis: Oedionychis magica Harold, 1877b: 434 (India), by original designation. Hyphasoma: Hyphasoma inconspicua Jacoby, 1903b: 111 (India), by subsequent designation of Maulik (1926: 156).Mascarene Islands (probably introduced), Oriental region and South-Eastern part of the Palaearctic region .Verbenaceae and Lamiaceae (cf. This genus is associated with plants in the families ceae cf. .Hyphasoma Jacoby (Physoma Clark (Hyphasis (as Hyphasoma) sita  sita : 158, deMaulik, 1926http://species-id.net/wiki/JacobyanaSphaerophysa piceicollis Jacoby, 1889c: 195 (Burma), by original designation.Democratic Republic of the Congo, Malawi, Republic of South Africa (Eastern Cape Province), Zimbabwe (!) , and the Oriental region .No information for Afrotropical region.Three species have been described.Jamesonia Jacoby, 1895] .No information.Seven species have been described.Bechyné, 1959ahttp://species-id.net/wiki/Kimongona=Mesocrepis Scherer, 1963 syn. n.Kimongona: Kimongona callifera Bechyné, 1959a: 19 , by original designation. Mesocrepis: Mesocrepis lindemannae Scherer, 1963: 669 (Tanzania: Njombe), by original designation.Democratic Republic of the Congo, Republic of South Africa , Rwanda, and Tanzania .No information.Mesocrepis Scherer from Kimongona. Therefore, the following new synonymy is proposed: Kimongona Bechyné, 1959 = Mesocrepis Scherer, 1963 syn. n.Type material examined: Mesocrepis lindemannae Scherer, “Tanganjika, Uwemba b. Njombe, 2000 m, 8–11.XI.1958, leg. C. Lindemann”, paratypes 1♂ and 1♀ (NHMB).Three species are known.There are no significant diagnostic characters distinguishing Lactica Erichson, 1847] and Zambia (!) [35 km S of Kasama (BAQ)] .No information.Four species are known .Livolia Jacoby, 1903],Nigeria, and Saudi Arabia, Socotra Island (Yemen) and the Australian, Eastern Palaearctic and Oriental regions .Luperomorpha biondii Döberl (2012: 439) was collected in Socotra on Cephalocroton socotranus (Euphorbiaceae).Polyphagous cf. . There iLuperomorpha vittula  , by present designation; Poephila: Poephila lacessita Weise, 1895: 342 (Addah), designation by monotypy.Afrotropical (including Madagascar), Australian, Eastern Palaearctic, and Oriental regions .Lypnea flaveola  collected on Oncoba echinata Oliver (Flacourtiaceae) (Poephila).Escaleriella Weise and Lypnea Baly to be separate genera because of the difference in the shape of their elytral epipleura: expanded in Lypnea, but straight and narrow in Escaleriella.About ten species are known from Madagascar and Sub-Saharan Africa . Bechyné (1968: 1718) considered Macroorthocrepis Pic, 1921] and Western Africa; Australian, Eastern Palaearctic, and Oriental regions .Epacridaceae, Urticaceae, Cyatheaceae, Asteraceae and Arecaceae  transferred to Podagrica Chevrolat by Balanomorpha aethiopica Chapuis (1879: 13) transferred to Neumannia Weise nom. preocc. by Weise (1907).Mediafra Scherer, 1961], Rwanda, Tanzania and Uganda The species of this genus generally live at altitudes above 2,500 m in mixed bamboo forests.Six species have been described.Musaka Bechyné, 1958a], Nigeria and Uganda .No information.Nine species are known.Ochrosis Foudras, 1860], Republic of South Africa, Sierra Leone, Australian and Oriental regions .Lamiaceae in South Africa .Species in this genus are associated with plants from the family Three species are known.Sesquiphaera Bechyné, 1958a= Weise, 1919http://species-id.net/wiki/PerichilonaPerichilona rufa Weise, 1919: 203 , by present designation.Tanzania .No information.Two species have been described.Weise, 1903http://species-id.net/wiki/PhiloponaOedionychus Berthold, 1827 (pars)Oedionychis (?) vernicata Gerstaecker, 1871: 84 (Zanzibar), by original designation.Afrotropical (excluding Madagascar), Australian, Oriental and Southern-Eastern Palaearctic regions .Philopona usambarica Csiki  in Kenya Phygasia: Altica unicolor Olivier, 1808: 699 (India), by original designation; Macroorthocrepis: Macroorthocrepis pallidicolor Pic, 1921: 14 (Abyssinia), designation by monotypy.Afrotropical (excluding Madagascar), Oriental and Palaearctic regions .Asclepiadaceae , by subsequent designation by All zoogeographical regions .Brassicaceae), Resedaceae, and Capparidaceae Physonychis africana Chapuis, 1875: 89 (East Africa), by original designation.Democratic Republic of the Congo, Kenya, Republic of South Africa , Sudan and Tanzania .Physodactyla rubiginosa  in Kenya (Physodactyla africana (Chapuis) from Digera arvensis Forssk. (Amaranthaceae) in Sudan (Physonychis).biginosa : 84 was in Kenya ; PhysodaSix described species.Clark, 1863http://species-id.net/wiki/Physoma=Tropidophora Thomson, 1858: 217 Hyphasoma Jacoby, 1903 (pars)Oedionychus Berthold, 1827 (pars)Physonychis); Physoma:Physoma tripartitum  (Gabon), by subsequent designation by Tropidophora: Tropidophora tripartita Thomson, 1858: 217 (Gabon), designation by monotypy.Central and Western Africa, and Madagascar No information.Tropidophora Thomson is not available because it was ambiguously applied .Two species known from Sub-Saharan Africa and about twenty from Madagascar.The genus-nameBechyné, 1959http://species-id.net/wiki/PhysomandroyaAsphaera Chevrolat, 1843 (pars)Oedionychus Berthold, 1827 (pars)Physomandroya decorsei Bechyné, 1959c: 319 (Madagascar: Ambowombé), by original designation.Madagascar .No information.Asphaera melanarthra Fairmaire, 1886: 94  to this genus.Seven described species. Clark, 1860http://species-id.net/wiki/PhysonychisPhysonychis smaragdina Clark, 1860: 31 (Western Africa), by original designation.Physonychis varicornis Duvivier, 1891 from Madagascar was transferred to the genus Physoma Clark by Sub-Saharan Africa (absent in the southern-western part of SAF and Madagascar). No information.About thirty known species.Plectroscelis Chevrolat, 1836], Oriental , and Palaearctic regions .Malvaceae .The species in this genus are mainly associated with plants in the family ceae cf. : 128; soPodagricina Csiki from Podagrica. Therefore, the following new synonymy is proposed: Podagrica Chevrolat, 1836 = Podagricina Csiki in Heikertinger and Csiki, 1940 syn. n. Type material examined: Balanomorpha aethiopica Chapuis, “Bogos, 1870, Keren, O. Beccari”, 4 syntypes (MCSN).About fifty species are known from Sub-Saharan Africa, with one having been recorded from Madagascar. There are no significant diagnostic characters distinguishing Podagricina Csiki in ; frons emipyxis  in Pseudemipyxis ]; elytraanterior  in Pseudemipyxis ]; hind tdadorium  [broadlyemipyxis ]. The foCsiki in : 461 = PCsiki in  comb. n.Pseudonisotra Bechyné, 1968], Democratic Republic of the Congo, Ethiopia, Guinea, Kenya, Madagascar, Rwanda, Senegal, Uganda, and the Oriental region .No information.Eugonotes Jacoby from Sanckia. The following new synonymy is therefore proposed: Sanckia Duvivier, 1891 = Eugonotes Jacoby, 1897 syn. n. Type material examined: Eugonotes longicornis Jacoby, “Madagascar, Diego Suarez”, syntype ♀ (BMNH).About twenty species are known from the Afrotropical region, most of these are from Madagascar. There are no significant diagnostic characters distinguishing Jacoby, 1897http://species-id.net/wiki/SerraphulaSerraphula aenea Jacoby, 1897: 557 , designation by monotypy.Republic of South Africa  and Zimbabwe .Species in this genus are known to be associated with plants in the family Asteraceae .Nineteen species have been described.Bechyné, 1958ahttp://species-id.net/wiki/Sesquiphaera=Paropsiderma Bechyné, 1958a syn. n.Sesquiphaera: Sphaeroderma mashonanum Jacoby, 1900: 252 , by original designation; Paropsiderma: Sphaeroderma anthrax Brancsik, 1910: 185 (Madagascar), designation by monotypy.Democratic Republic of the Congo, Guinea, Guinea Bissau, Madagascar, Namibia, Republic of South Africa , Rwanda, Tanzania, and Zimbabwe .No information.Paropsiderma Bechyné from Sesquiphaera. The following new synonymy is therefore proposed: Sesquiphaera Bechyné, 1958 = Paropsiderma Bechyné, 1958 syn. n. Material examined: Paropsiderma anthrax (Brancsik) (det. J. Bechyné), “Madagascar, Joffreville, 13.V.1953, F. Kaiser”, 1 specimen (NHMB).There are about ten described species. No significant diagnostic characters distinguish Biondi, 2002bhttp://species-id.net/wiki/SeychellalticaChaetocnema mahensis Maulik, 1931: 250 (Seychelles: Mahé), by original designation.Indian Ocean (Seychelles) .The species in this genus are associated with indigenous forests in the Seychelles.Four species have been described.Weise, 1910ahttp://species-id.net/wiki/SjostedtiniaSjostedtinia montivaga Weise, 1910a: 206 (Kilimanjaro: Kibocho), by original designation.PageBreakKenya, Tanzania, and Uganda, .Sjostedtinia montivaga has been collected from Lobelia deckeni (Asch.) Hemsl. (Lobeliaceae) , and Sjostedtinia fordi Bryant, 1953 from a Senecio sp. (Asteraceae) in Uganda , and from a Lobelia sp. in Kenya .This genus lives at high altitudes on Kilimanjaro and Mount Elgon. Two species are known.Stephens, 1831http://species-id.net/wiki/Sphaeroderma=Argosomus Wollaston, 1867 , by subsequent designation by Maulik, (1926: 316); Argosomus: Argosomus epilachnoides Wollaston, 1867: 152 (Cape Verde Islands: Brava), by subsequent designation by Musaka: Sphaeroderma freyi Bechyné, 1955b: 563 (Cameroon), by original designation.Sphaeroderma reported from the Neotropical and Nearctic regions should be attributed to different genera  and Australian, Oriental, and Palaearctic regions. The species of nera cf.  , designation by monotypy.Republic of South Africa (Western Cape Province) and Tristan da Cunha .Stegnaspea trimeni collected from Poaceae  in meadows .Six species are known.Scherer, 1963http://species-id.net/wiki/StuckenbergianaPodagrica glabrata Jacoby, 1899b: 349 , by original designation.Republic of South Africa  .No information.Only one species is known.Fairmaire, 1904http://species-id.net/wiki/TerpnochlorusChaloenus Westwood, 1862 (pars)Chaloenus); Terpnochlorus perrieri Fairmaire, 1904: 269 , designation by monotypy.Botswana, Democratic Republic of the Congo, Gambia, Guinea Bissau, Madagascar, Mali, Namibia, Sierra Leone, and South America (Venezuela and Mexico) .Juncaceae  synonymised s Bryant  with Ters Bryant ].Torodera Weise, 19082a] because of the occurrence of a high percentage of widespread genera that characterize the flea beetle fauna of these two archipeligoes. Moreover, faunistic similarity based on the widespread flea beetle genera also clusters the other zoogeographical regions together in two distinct groups, namely the Palaearctic-Oriental-Australian regions [(PAR-ORR)AUR] and Nearctic-Neotropical regions (NAR-NTR).The geographic distribution of Afrotropical flea beetle genera is therefore well characterized and it has distinct Malagasy and Sub-Saharan African components .Alticini genera endemic to the Afrotropical region is very high (71.0%), with the following distribution: Sub-Saharan Africa, 52 genera; Madagascar, 12; Seychelles Islands, 1; Sub-Saharan Africa-Madagascar, 4; Madagascar-Mascarene Islands, 1; Seychelles-Mascarene Islands, 1 , Oriental and, generally Australian regions, but also in the eastern part of the Palaearctic region. More specifically, the Palaeartic region shares 27 flea beetle genera with the Afrotropical region  occur in both the Afrotropical and Australian regions, although all of these can also be found throughout the Oriental region.The percentage of genera occurring in both the Afrotropical and another zoogeographical region is 32.0%, with the cosmopolitan component significant and well represented [8.0% of the total of 99] . The Afrl region , includiscar cf. . A signiTerpnochlorus, which only occurs in the Afrotropical region, Venezuela and Mexico (cf. Abrarius from Madagascar and Gioia from South America (see above), if confirmed, could indicate an interesting zoogeographical connection among the ancient regions of Gondwana  and Afrotropical/Neotropical regions (10.0%). All genera common to the Afrotropical, Nearctic and Neotropical regions are also found in all other zoogeographical regions with the exception of the genus xico cf. . MoreoveGondwana .As reported in Zomba belonging to the tribe Monoplatini, which mainly occurs in the Neotropical region with a few species found in the Nearctic region. The genus Opisthopygme, also from the Monoplatini, is also present in Australia (see above).The unique Afrotropical genus Bubiscus Savini, Furth and Joly (2009: 53), a recently described Costa Rican genus (1 species); NormalticaClavicornaltica Scherer (1974: 58), a genus occurring in the Oriental (18 species) and Australian regions (1 species) (cf. Kiskeya Konstantinov and Chamorro-Lacayo (2006: 276), which has nine-segmented clavate antennae - 2 species in the Dominican Republic; and Monotalla Bechyné (1956: 588), which has ten-segmented clavate antennae, with 1 species in Guadalupe . Both these genera have clavate or subclavate antennae with 11 segments, are subsphaerical in shape and very small, characteristics they share with related genera in Central America, such as: ies) cf. . Other vlupe cf. : 907.Metroserrapha Bechyné, also occurs in the Mascarene Islands (Neodera, Physomandroya, Pseudadorium, Pseudophygasia, and Xanthophysca, show clear African affinities, but Antanemora, Ntaolaltica, and Metroserrapha are more closely related to Oriental genera (Anaxerta, Diphaulacosoma, Halticotropis, and Hildebrandtina, are probably all very ancient. Establishing their affinities with certainty, whether African or Oriental, is very difficult using only a comparative morphological approach.There are 39 flea beetle genera known from Madagascar, 13 of which are endemic. One of them,


In the Author Byline, the name of the fifth author was misspelled.It should be: Hector Hernandez-Vargas.The correct Citation is: Rakosy Z, Ecsedi S, Toth R, Vizkeleti L, Hernandez-Vargas H, et al. (2013) Integrative Genomics Identifies Gene Signature Associated with Melanoma Ulceration. PLoS ONE 8(1): e54958. doi:10.1371/journal.pone.0054958In Table 1, in the second column and the '20-50' row, the correct value is 7.


Reference 31 is incomplete. The corrected reference is:Pan, S., Cheung, X. and Sifers, R.N. (2013) Golgi-situated ERManI contributes to the retrieval of ERAD substrates through a direct interaction with γ-COP. Molecular Biology of the Cell 24, 1111-1121.


The name of the second author was spelled incorrectly. The correct name is: Felix Luessi. The correct Citation is: Trinschek B, Luessi F, Haas J, Wildemann B, Zipp F, et al. (2013) Kinetics of IL-6 Production Defines T Effector Cell Responsiveness to Regulatory T Cells in Multiple Sclerosis. PLoS ONE 8(10): e77634. doi:10.1371/journal.pone.0077634.


There was an error in the article title.The correct title is: Resveratrol as a Pan-HDAC Inhibitor Alters the Acetylation Status of Histone Proteins in Human-Derived Hepatoblastoma CellsThe correct citation is: Venturelli S, Berger A, Böcker A, Busch C, Weiland T, et al. (2013) Resveratrol as a Pan-HDAC Inhibitor Alters the Acetylation Status of Histone Proteins in Human-Derived Hepatoblastoma Cells. PLoS ONE 8(8): e73097. doi:10.1371/journal.pone.0073097


The 5th author's last name was misspelled. The correct spelling of the author's name is: Adi Gundlapalli. The correct citation is: DeLisle S, South B, Anthony JA, Kalp E, Gundlapalli A, et al. (2010) Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections. PLoS ONE 5(10): e13377. doi:10.1371/journal.pone.0013377.


An impact of the gut flora, the microbiota, on the modulation of allergies has been suspected for many years. Among non-pathogenic, colonizing organisms of the gut, probiotics play a special role in this regard and many experimental and clinical studies have focused on these micro-organisms. The presentation will first address immunologic concepts which are the basis of a potential action of probiotics, by presenting mostly experimental studies in animals. In the second part, clinical studies will be presented and will address mostly the timing of administration of probiotics, as well as specific effect on atopic disease prevention that have been studied. Finally, a critical review and interpretation based on the clinical studies available will be provided. The presentation should allow the attendance to understand which effect might be obtained by probiotics for prevention of atopic diseases. Selected references: 1 Sudo N, Sawamura S, Tanaka K, Aiba Y, Kubo C, Koga Y. The requirement of intestinal bacterial flora for the development of an ige production system fully susceptible to oral tolerance induction. J Immunol 1997; 159(4):1739-1745. 2 Majamaa H, Isolauri E. Probiotics: a novel approach in the management of food allergy. J Allergy Clin Immunol 1997; 99(2):179-185. 3 Kalliomaki M, Salminen S, Poussa T, Arvilommi H, Isolauri E. Probiotics and prevention of atopic disease: 4-year follow-up of a randomised placebo-controlled trial. Lancet 2003; 361(9372):1869-1871. 4 Viljanen M, Savilahti E, Haahtela T, Juntunen-Backman K, Korpela R, Poussa T et al. Probiotics in the treatment of atopic eczema/dermatitis syndrome in infants: a double-blind placebo-controlled trial. Allergy 2005; 60(4):494-500. 5 Kopp MV, Hennemuth I, Heinzmann A, Urbanek R. Randomized, Double-Blind, Placebo-Controlled Trial of Probiotics for Primary Prevention: No Clinical Effects of Lactobacillus GG Supplementation. Pediatrics 2008; 121(4):e850-e856. 6 Boyle RJ, Ismail IH, Kivivuori S, Licciardi PV, Robins-Browne RM, Mah LJ et al. Lactobacillus GG treatment during pregnancy for the prevention of eczema: a randomized controlled trial. Allergy 2010; doi: 10.1111/j.1398-9995.2010.02507.x.


Pongo pygmaeus wurmbii) Indicates Functional ArbitrarinessThe correct version of the title is: Population-Specific Use of the Same Tool-Assisted Alarm Call between Two Wild Orangutan Populations (Pongo pygmaeus wurmbii) Indicates Functional Arbitrariness. PLoS ONE 8(7): e69749. doi:10.1371/journal.pone.0069749 The correct citation is: Lameira AR, Hardus ME, Nouwen KJJM, Topelberg E, Delgado RA, et al. (2013) Population-Specific Use of the Same Tool-Assisted Alarm Call between Two Wild Orangutan Populations (


An initial is missing in the fifth author's name. The correct name is: Carlo MT Marobbio. The correct citation is: Dolezal P, Aili M, Tong J, Jiang J-H, Marobbio CMT, et al. (2012) Legionella pneumophila Secretes a Mitochondrial Carrier Protein during Infection. PLoS Pathog 8(1): e1002459. doi:10.1371/journal.ppat.1002459


There was an error in the citation. The correct citation is: Iglesias MJ, Reilly S-J, Emanuelsson O, Sennblad B, Pirmoradian Najafabadi M, et al. (2012) Combined Chromatin and Expression Analysis Reveals Specific Regulatory Mechanisms within Cytokine Genes in the Macrophage Early Immune Response. PLoS ONE 7(2): e32306. doi:10.1371/journal.pone.0032306


Recent positive clinical results in cancer immunotherapy point to the potential of immune-based strategies to provide effective treatment of a variety of cancers. In some patients, the responses to cancer immunotherapy are durable, dramatically extending survival. Extensive research efforts are being made to identify and validate biomarkers that can help identify subsets of cancer patients that will benefit most from these novel immunotherapies. In addition to the clear advantage of such predictive biomarkers, immune biomarkers are playing an important role in the development, clinical evaluation and monitoring of cancer immunotherapies. This Cancer Immunotherapy Resource Document, prepared by the Society for Immunotherapy of Cancer , provides key references and online resources relevant to the discovery, evaluation and clinical application of immune biomarkers. These key resources were identified by experts in the field who are actively pursuing research in biomarker identification and validation. This organized collection of the most useful references, online resources and tools serves as a compass to guide discovery of biomarkers essential to advancing novel cancer immunotherapies. Immunotherapy has emerged as an important treatment strategy for patients with cancer. With several recent approvals by the U.S. Food and Drug Administration (FDA), cancer immunotherapy has become the latest addition to the toolbox of effective cancer treatments that includes chemotherapy, signal transduction inhibitors, anti-angiogenic agents, radiotherapy, and surgery.Successful development and testing, regulatory approval and clinical application of cancer immunotherapies require the identification and validation of biomarkers of efficacy. The importance of reliable biomarkers to guide immune-based and personalized cancer therapies is clear. Biomarkers can aid in early disease diagnosis, help clinicians identify patients most likely to benefit from these expensive treatments, and facilitate drug discovery, development and biological/clinical evaluation of cancer immunotherapies.For over twenty-five years the Society for Immunotherapy of Cancer  has advanced the science, development and application of biological therapy/immunotherapy of cancer. The society has long recognized the importance of biomarkers for cancer immunotherapy, which has been the focus of a number of SITC/iSBTc symposia and workshops -5, and hTo support the efforts of investigators involved in research to identify and validate biomarkers for cancer immunotherapy, the authors and members of the SITC Biomarkers Taskforce have identified key biomarker references and online resources and organized these into this SITC/iSBTc Cancer Immunotherapy Biomarkers Resource Document. This document provides an overview of suggested publications and resources for studies on biomarkers for cancer immunotherapy. This resource document is divided into two sections: Part I: Immunotherapy Biomarker References; and Part II: High Throughput and New Technologies for Biomarker Discovery: Arrays, Platforms, Tools for The Bench and Online Resources. While many important references and resources in the field are included in this document, it does not intend to represent an exhaustive list of all relevant publications, products or resources in the growing, and important field of immune biomarkers. A comprehensive list of online tools for bioinformatics and molecular biology research is available from the Bioinformatics Links Directory ,12.A draft of the present document was originally provided to attendees of the SITC/iSBTc Symposium on Immuno-Oncology Biomarkers, 2010 and Beyond: Perspectives from the iSBTc Biomarker Task Force Kirkwood JM, Butterfield LH, Tarhini AA, Zarour H, Kalinski P, Ferrone S: Immunotherapy of Cancer in 2011 CA: A Cancer Journal for Clinicians [in press]Ascierto ML, De Giorgi V, Liu Q et al.: An immunologic portrait of cancer. Journal of Translational Medicine, .Gajewski TF, Fuertes M, Spaapen R, et al.: Molecular profiling to identify relevant immune resistance mechanisms in the tumor microenvironment. Curr Opin Immunol 23:286-92, 2011Disis ML: Immunologic biomarkers as correlates of clinical response to cancer immunotherapy. Cancer Immunol Immunother. 60:433-42, 2011Sznol M: Molecular markers of response to treatment for melanoma Cancer J 17:127-33, 2011Bedognetti D, Wang E, Sertoli MR, Marincola FM. Gene-expression profiling in vaccine therapy and immunotherapy for cancer. Expert Rev Vaccines 6:555-65, 2010Slota M, Lim JB, Dang Y, Disis ML: ELISpot for measuring human immune responses to vaccines. Expert Rev Vaccines 10:299-306, 2011Gogas H, Eggermont AM, Hauschild et al: Biomarkers in melanoma. Ann Oncol. 20 Suppl 6:vi8-13, 2009Simon R: Translational research in oncology: key bottlenecks and new paradigms. Expert Rev Mol Med 12:e32, 2010Kirkwood JM, Tarhini AA, Panelli MC, Moschos SJ, Zarour HM, Butterfield LH,Gogas HJ: Next generation of immunotherapy for melanoma. J Clin Oncol 26:3445-55, 2008Freidlin B, McShane LM, Korn EL: Randomized clinical trials with biomarkers:design issues. 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J Immunol Methods 308:13-18, 2006Bull M, Lee D, Stucky J, et al.: Defining blood processing parameters for optimal detection of cryopreserved antigen-specific responses for HIV vaccine trials. J Immunol Methods 322:57-69, 2007Kierstead LS, Dubey S, Meyer B, et al.: Enhanced rates and magnitude of immune responses detected against an HIV vaccine: effect of using an optimized process for isolating PBMC. AIDS Res Human Retroviruses 23:86-92, 2007Ruitenberg JJ, Mulder CB, Maino VC, et al.: VACUTAINER CPT and Ficoll density gradient separation perform equivalently in maintaining the quality and function of PBMC from HIV seropositive blood samples. BMC Immunol 7:11, 2006Tree TI, Roep BO, Peakman M.: Enhancing the sensitivity of assays to detect T cell reactivity: the effect of cell separation and cryopreservation media. Ann N Y Acad Sci 1037:26-32, 2004Smith JG, Joseph HR, Green T, et al.: Establishing acceptance criteria for cell-mediated immunity assays using frozen peripheral blood mononuclear cells stored under optimal and suboptimal conditions. Clin Vaccine Immunol 14:527-37, 2007McKenna KC, Beatty KM, Vicetti Miguel R, Bilonick RA: Delayed processing of blood increases the frequency of activated CD11b+ CD15+ granulocytes which inhibit T cell function. J Immunol Method 341:68-75, 2009ExamplesJin P, Han TH, Ren J, Saunders S, et al.: Molecular signatures of maturing dendritic cells: implications for testing the quality of dendritic cell therapies. J Transl Med 8:4, 2010Sheikh NA, Jones LA: CD54 is a surrogate marker of antigen presenting cell activation. Immunol Immunother 57:1381-1390, 2008Higano CS, Schellhammer PF, Small EJ, et al.: Integrated data from 2 randomized, double-blind, placebo-controlled, phase 3 trials of active cellular immunotherapy with Sipuleucel-T in advanced prostate cancer. Cancer 115:3670-3679, 2009Butterfield LH, Gooding W, Whiteside TL: Development of a potency assay for human dendritic cells: IL-12p70 production. J Immunother 31:89-100, 2008Ayache S, Panelli M, Marincola FM, et al.: Effects of storage time and exogenous protease inhibitors on plasma protein levels. American Journal of Clinical Pathology 126:174-184, 2006Exampleshttp://www.cms.hhs.gov/CLIA/:Clinical Laboratory Improvement Amendments (CLIA) Guideline: http://www.ich.org/products/guidelines.htmlInternational Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) - common platform of Europe, Japan and United States authorities: Attig S, Price L, Janetzki S, Kalos M, Pride M, McNeil L, Clay T, Yuan J, Odunsi K, Hoos A, Romero P, Britten CM, Assay Working Group CC. A critical assessment for the value of markers to gate-out undesired events in HLA-peptide multimer staining protocols. J Transl Med, 9:108, 2011Maecker HT, Hassler J, Payne JK, et al.: Precision and linearity targets for validation of an IFNgamma ELISPOT, cytokine flow cytometry, and tetramer assay using CMV peptides. BMC Immunol 9:9, 2008Nomura L, Maino VC, Maecker HT: Standardization and optimization of multiparameter intracellular cytokine staining. Cytometry A 73:984-991, 2008Afonso G, Scotto M, Renand A, et al.: Critical parameters in blood processing for T-cell assays: validation on ELISpot and tetramer platforms. J Immunol Methods 359:28-36, 2010Britten CM, Gouttefangeas C, Welters MJ, et al.: The CIMT-monitoring panel: a two-step approach to harmonize the enumeration of antigen-specific CD8+ T lymphocytes by structural and functional assays. Cancer Immunol Immunother 57:289-302, 2008Britten CM, Janetzki S, Ben Porat L, et al.: Harmonization guidelines for HLA-peptide multimer assays derived from results of a large scale international proficiency panel of the Cancer Vaccine Consortium. 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Cytometry B Clin Cytom 74 Suppl 1: S52-S64, 2008Boaz MJ, Hayes P, Tarragona T, et al.: Concordant proficiency in measurement of T-cell immunity in human immunodeficiency virus vaccine clinical trials by peripheral blood mononuclear cell and enzyme-linked immunospot assays in laboratories from three continents. Clin Vaccine Immunol 16:147-155, 2009Smith SG, Joosten SA, Verscheure V, et al.: Identification of major factors influencing ELISpot-based monitoring of cellular responses to antigens from Mycobacterium tuberculosis. PLoS One 4:e7972, 2009Hanekom WA, Dockrell HM, Ottenhoff TH, et al.: Immunological outcomes of new tuberculosis vaccine trials: WHO panel recommendations. PLoS Med 5:e145, 2008Schloot NC, Meierhoff G, Karlsson Faresjö M, et al.: Comparison of cytokine ELISpot assay formats for the detection of islet antigen autoreactive T cells. Report of the third immunology of diabetes society T-cell workshop. J Autoimmun 21:365-76, 2003Moodie Z, Price L, Gouttefangeas C, et al.: Response definition criteria for ELISPOT assays revisited. Cancer Immunol Immunother 59:1489-501, 2010ExamplesQuast S, Zhang W, Shive C, et al.: IL-2 absorption affects IFN-gamma and IL-5, but not IL-4 producing memory T cells in double color cytokine ELISPOT assays. Cell Immunol 237:28-36, 2005Shafer-Weaver K, Rosenberg S, Strobl S, et al.: Application of the granzyme B ELISPOT assay for monitoring cancer vaccine trials. J Immunother 29:328-335, 2006Malyguine A, Strobl SL, Shafer-Weaver KA, et al.: A modified human ELISPOT assay to detect specific responses to primary tumor cell targets. J Trans Med 2:9, 2004Kim GG, Donnenberg VS, Donnenberg AD, et al.: A novel multiparametric flow cytometry-based cytotoxicity assay simultaneously immunophenotypes effector cells: comparisons to a 4 h 51Cr-release assay. J Immunol Methods 325:51-66, 2007Devevre E, Romero P, Mahnke YD: LiveCount Assay: concomitant measurement of cytolytic activity and phenotypic characterisation of CD8(+) T-cells by flow cytometry. J Immunol Methods 311:31-46, 2006Zaritskaya L, Shafer-Weaver KA, Gregory MK, et al.: Application of a flow cytometric cytotoxicity assay for monitoring cancer vaccine trials. J Immunother 32:186-194, 2009Maecker HT, Dunn HS, Suni MA, et al.: Use of overlapping peptide mixtures as antigens for cytokine flow cytometry. J Immunol Methods 255:27-40, 2001Whiteside TL, Zhao Y, Tsukishiro T, Elder EM, Gooding W, Baar J: Enzyme-linked immunospot, cytokine flow cytometry, and tetramers in the detection of T-cell responses to a dendritic cell-based multipeptide vaccine in patients with melanoma. Clin Cancer Res, 2003ExamplesMcShane LM, Altman DG, Sauerbrei W, et al.: Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Canc Inst 97:1180-1184, 2005http://www.mibbi.orgTaylor CF, Field D, Sansone SA, et al.: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechn 26:889-896, 2008Brazma A, Hingamp P, Quackenbush J, et al.: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365-371, 2001http://www.miataproject.orgJanetzki S, Britten CM, Kalos M, et al.: "MIATA"-minimal information about T cell assays. Immunity 31:527-528, 2009Britten CM, Janetzki S, van der Burg SH, et al: Minimal information about T cell assays: the process of reaching the community of T cell immunologists in cancer and beyond. Cancer Immunol Immunother 60:15-22, 2011Lee JA, Spidlen J, Boyce K, et al.: MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A 73:926-930, 2008Spidlen J, Moore W, Parks D, et al.: Data file standard for flow cytometry, version FCS 3.1. Cytometry A 77:97-100, 2010ExamplesName: Affymetrix Genome-Wide Human SNP Array 6.0Comment:1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variationWebsite:http://www.affymetrix.com/browse/products.jsp?productId=131533&navMode=34000&navAction=jump&aId=productsNav#1_1Name: Affymetrix DMET Plus Premier PackComment:Drug metabolism studies. Coverage of a wide range of genetic variations, including common and rare SNPs, insertions, deletions, tri-alleles, and copy number. 1,936 drug metabolism markers in 225 genesWebsite:http://www.affymetrix.com/browse/products.jsp?productId=131412&navMode=34000&navAction=jump&aId=productsNav#1_1Name: Illumina Omni MicroarrayComment:Next generation genome-wide association studies. The Omni family of microarrays will soon allow researchers to assay up to 5 million markers per sample, including comprehensive coverage of both common and rare variants identified by 1000 Genomes Project. As novel SNP sets are released into the public database, researchers using Omni products will have exclusive access to supplemental arrays that build up to the full 5 million variantsWebsite:http://www.illumina.com/landing/click/gwas.ilmn?scid=2011110PPC1&gclid=CJij6ffe26kCFQPc4AodcmxEZQName: Fluidigm Dynamic Array for SNP GenotypingComment:The Fluidigm Dynamic Arrays allow you to use your existing TaqMan® SNP Genotyping assays in a flexible and cost effective fashion. Each dynamic array allows you to setup up to 9,216 individual TaqMan reactions in a single experimentWebsite:http://www.expressionanalysis.com/services/category/fluidigm_dna_focused_set_snpName: TaqMan® Pre-Designed SNP Genotyping AssaysComment:Includes over 4.5 million SNP assays, including 3.5 million HapMap, and ~70,000 coding SNP assays. This collection now includes ~160,000 validated assays with associated minor allele frequency data availableWebsite:https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600769&tab=TechSpecExamplesName:Agilent Human Genome CGH MicroarraysComment: High-resolution tool for genome-wide DNA copy number variation profiling. Comprehensive probe coverage is enhanced with emphasis on known genes, promoters, miRNAs, pseudoautosomal, and telomeric regionsWebsite:http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID=1463Name: Nimblegen Cytogenetics (CGX) ArraysComment: Genome-wide analysis of DNA copy number changes with a subset of probes focused in disease-associated regionsWebsite: http://www.nimblegen.com/products/cgh/human.html#cytoExampleName: Affymetrix GeneChip® Human Mitochondrial Resequencing Array 2.0Comment:Detection of germ line and heteroplasmic mutations by delivering the complete mitochondrial genome with minimal PCR in only 48 hoursWebsite:http://www.affymetrix.com/support/technical/byproduct.affx?product=humitoreseqExamplesName: Agilent Human DNA Methylation MicroarraysComment:The array is specifically designed for analysis of methylated DNA derived from affinity-based isolation methods such as methylated DNA immunoprecipitation (MDIP)Website:http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID=2157Name: Nimblegen 2.1 M Whole-Genome Tiling SetComment:Whole-genome formats are available in two versions: a 10-array set at 100 bp probe interval or a 4-array set at > 200 bp probe intervalWebsite:http://www.nimblegen.com/products/methylation/whole_genome.htmlName: Illumina 450 K Infinium Methylation BeadChip KitComment:This assay allow to interrogate > 450,000 methylation sites per sample at single-nucleotide resolutionWebsite:http://www.illumina.com/products/methylation_450_beadchip_kits.ilmnExamplesName: Illumina MicroRNA Universal Array MatrixComment:miRNA analysisWebsite:http://www.illumina.com/products/microrna_universal_array_matrix.ilmnName: Affymetrix GeneChip miRNA ArrayComment:miRNA analysisWebsite:http://www.affymetrix.com/estore/browse/products.jsp;jsessionid=7386716AB0BD679701B518044ADA58F5?navMode=34000&productId=131473&navAction=jump&aId=productsNavName: Exiqon's miRCURY LNA microRNA ArrayComment:miRNA analysisWebsite:http://www.exiqon.com/microrna-microarray-analysisExamplesName: Nimblegen 2.1 M ChIP-Chip ArrayComment:ChIP-chip analysisWebsite:http://www.nimblegen.com/products/chip/index.htmlName: Agilent SurePrint G3 Human Promoter MicroarrayComment:ChIP-chip analysisWebsite:http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID=1487Name: Affymetrix GeneChip Tiling ArraysComment:ChIP-chip analysisWebsite:http://www.affymetrix.com/estore/browse/level_three_category_and_children.jsp?parent=35808&expand=true&category=35818&fromAccordionMenu=true&subCategory=35818ExamplesName: Affymetrix Gene Chip Human Exon 1.0 ST ArrayComment:Whole genome microarray. With approximately four probes per exon and roughly 40 probes per gene, the GeneChip Human Exon 1.0 ST Array enables two complementary levels of analysis--gene expression and alternative splicingWebsite:http://www.affymetrix.com/estore/browse/products.jsp?navMode=34000&productId=131453&navAction=jump&aId=productsNav#1_1Name: Agilent SurePrint G3 Human GE 8 × 60 K KitComment:Whole genome microarray. The SurePrint G3 Human GE 8 × 60 K Microarrays and Human GE 4 × 44 K v2 Microarrays are based on updated transcriptome databases for mRNA targets, while the SurePrint G3 arrays also include probes for lincRNAs (long intergenic non-coding RNAs). With the combination of mRNA and lincRNAs, it is possible to perform two experiments on a single microarray, confidently predicting lincRNA functionWebsite:http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductDetail&PageID=1515Name: Illumina HumanHT-12 v4 Expression BeadChip KitsComment:The HumanHT-12 v4 Expression BeadChip provides high throughput processing of 12 samples per BeadChip. Each array on the HumanHT-12 v4 Expression BeadChip targets more than 31,000 annotated genes with more than 47,000 probesWebsite:http://www.illumina.com/products/humanht_12_expression_beadchip_kits_v4.ilmnExamplesName: QuantiGene® Plex 2.0 Reagent System (Luminex Assay)Comment:Quantitatively measure 3-36 RNA targets simultaneouslyWebsite:http://www.panomics.com/index.php?id=product_6Name: Procarta Transcription Factor Profiling Kits (Luminex Assay)Comment:Quantitate the DNA binding activity of up to 44 different transcription factors (TFs) in a single well using nuclear extracts or whole cell lysatesWebsite:http://www.panomics.com/index.php?id=product_17Name: TaqMan® Probe-Based Gene Expression AnalysisComment:Quantitatively measure 1-384 RNA targets simultaneouslyWebsite:http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/qpcr-real-time-pcr/taqman-probe-based-gene-expression-analysis.htmlName: Fluidigm Dynamic Array for Single Cell Gene ExpressionComment:The Fluidigm Dynamic Array enables you to test up to 96 individual cells against 96 genes in a single experiment. The dynamic array assembles the cDNA material from individual cells and reagents to create individual qPCR reactionsWebsite:http://www.fluidigm.com/docs/Application_Note_Dynamic_Array_for_Single-Cell_GE_Analysis.pdfName: Nanostring nCounter Analysis System for digital gene expression analysisComment: The nCounter Analysis System utilizes a novel digital technology that is based on direct multiplexed measurement of gene expression and offers high levels of precision and sensitivity (< 1 copy per cell). The technology uses molecular "barcodes" and single molecule imaging to detect and count hundreds of unique transcripts in a single reaction.Website: http://www.nanostring.com/applications/technology/ExamplesName: NodalityComment:Single-cells network profiling (SCNP): advanced multiparametric quantitative flow cytometry to measure compound effects on multiple signaling cascades in a cell-type-specific mannerWebsite:http://www.nodalityinc.com/Name: NanoPro ImmunoassayComment:Characterization of proteins in extremely small and precious samples. Unlike traditional protein analysis techniques which require thousands to millions of cells, these assays require as few as 25 cells per assayWebsite:http://www.cellbiosciences.com/nanopro.htmlName: Invitrogen ImmunoassaysComment:Wide range of immunoassays using antibody pairs for single-analyte (ELISA kits) as well as multi-analyte (Lumibex assays) analysis or accurate quantitation of intracellular or extracellular proteinsWebsite:http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cell-and-Tissue-Analysis/Immunoassays.htmlName: Procarta Cytokine Profiling Assays (Luminex Assay)Comment:Quantitatively measure 3-30 cytokine proteins simultaneously from a variety of matrices including cell culture supernatants, serum or plasmaWebsite:http://www.panomics.com/index.php?id=products_luminexAssaysName: SearchLight Multiplex Immunoassay KitsComment:As many as 16 proteins (4 × 4 array in each well) can be measured per well simultaneously with each 50 μl sampleWebsite:http://www.aushon.com/Products-and-Services.phpName: MSD Multiplex Cytokines and ChemokinesComment:96-well; multiplex cytokine/chemokine kits for up to ten (10) analytes per well.384-well: Order multiplex cytokine/chemokine kits for up to four (4) analytes per wellWebsite:http://www.mesoscale.comName: ZeptomarkComment:Protein profiling for analysis of cell signaling pathwaysWebsite:http://www.zeptosens.com/en/Name: Signaling Protein Luminex AssaysComment:Multiplex assays for measuring signal transduction, post-translational modification & cleaved proteins in multiple research areas, using Luminexbead-based technologyWebsite:http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/Cell-and-Tissue-Analysis/Immunoassays/Immunoassays-misc/Multiplex-Bead-Based-Luminex-Technology/Luminex-Assays.htmlName: VeraCode Carboxyl Bead Sets and BeadXpress ReaderComment:Multiplexed protein arrays (up to 48 immunoassays in a single reaction in a standard 96-well microplate: detection of protein as low as 10 pg/ml)Website:http://www.illumina.com/products/veracode_carboxyl_bead_sets.ilmnName: Procarta SH2 Domain Plex Profiling Kits (Luminex Assay)Comment:Profile phosphotyrosine protein interactions against 30 SH2 binding in a single well using treated and untreated cell lysates. Protein-Protein interactionWebsite:http://www.panomics.com/downloads/13_4_SH2UM_2_V1.pdfName: Proto-ArrayComment:Advanced, high-content, functional protein microarray enables to scan thousands of proteins (> 9000) in as little as one day. Highly sensitive results for protein-protein interaction, kinase substrate identification, and serum profiling studiesWebsite:http://www.invitrogen.com/protoarrayName: Metal Nanoparticle Probes and Dynamic Light ScatteringComment:This assay is based on the use of gold nanoparticle probes combined with dynamic light scattering (DLS) technique, named nanoDLSAY, a highly sensitive, fast and convenient one-step homogeneous immunoassay for monitoring and detecting biotargets, including cancer biomarkersWebsite:http://tt.research.ucf.edu/LinkClick.aspx?fileticket=6p5A2nGSYzA%3d&tabid=119ExamplesName: BD LSRFortessa™ Cell AnalyzerComment:Up to 4 lasers to detect up to 18 colors simultaneouslyWebsite:http://www.bdbiosciences.com/instruments/lsr/index.jspName: The MACSQuant® AnalyzerComment: Three lasers, up to 8 colors, compact benchtop flow cytometer that is small in size; ® Analyzer MACSQuantallows researchers to perform sensitive rare cell analysis using magnetic separationWebsite:http://www.miltenyibiotec.com/downloads/6760/6764/18602/MQ_brochure.pdfName: CyAn ADP AnalyzerComment:Up to 11 standard parameters and 9 colorsWebsite:http://www.coulterflow.com/bciflow/instrumentsus.phpName: Partec CyFlow® MLComment:3-laser configuration to detect up to 16 colorsWebsite:http://www.partec.com/cms/front_content.php?idcat=13Name: Accuri C6Comment:Standard 2-laser configuration, 4- color systemWebsite:http://www.accuricytometers.com/products/Next generation sequencing, possible applications: Whole Genome and Transcriptome Sequencing-Based analysis, Gene Regulation Analysis, SNP Discovery and Structural Variation Analysis, Cytogenetic Analysis, DNA-Protein Interaction Analysis (ChIP-Seq), Sequencing-Based Methylation Analysis, Small RNA Discovery and AnalysisExamplesName: Illumina - several systems, examples: HiSeq 2000 (Sequencing); HiScanSQ (Sequencing + Arrays) and MiSeqComment:Next generation sequencingWebsite:http://www.illumina.com/systems.ilmnName: Roche - several systems, examples: Genome Sequencer FLX System and GS Junior System (454 Sequencing)Comment:Next generation sequencingWebsite:http://www.454.com/Name: Applied Biosystems - several systems, examples: Solid 4 System and Solid PI System (Solid System)Comment:Next generation sequencingWebsite:http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.htmlName: Ion Torrent PGMComment:Next generation sequencing: semiconductor technology allows runs in about 2 hours.Website:http://www.iontorrent.com/products-ion-pgm/Name:PacBio RSComment:Third generation sequencing: Long readlengths, single molecule sequencingWebsite:http://www.pacificbiosciences.com/productsExamples:Name: BRB - ArrayToolsComment:Microarray/array CGH analysis. BRB-Array Tools was developed by Dr. Richard Simon and BRB-ArrayTools Development Team, NCI, NIH. The program can be used for non-commercial purposes free-of-chargeWebsite:http://linus.nci.nih.gov/pilot/index.htmLicense needed:NoName: PartekComment:Next generation sequencing technologies, including gene expression and DGE, RNA-seq and alternative splicing, copy number and association, ChIP-chip, ChIP-seq, microRNA and SNP association studyWebsite:http://www.partek.com/License needed:YesName: Nexus Copy NumberComment:aCGH and SNP copy number analysisWebsite:http://www.biodiscovery.com/index/nexusLicense needed:YesName: Nexus ExpressionComment:Microarray gene expression analysisWebsite:http://www.biodiscovery.com/index/nexus-expressionLicense needed:YesName: mAdb (aka Mad Bee)Comment:Microarray gene expression analysisWebsite:http://madb.nci.nih.gov/License needed:NoName: BioconductorComment:Tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming languageWebsite:http://www.bioconductor.org/License needed:NoName: MATLAB 7.11Comment:MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computationWebsite:http://www.mathworks.com/products/matlab/description1.htmlLicense needed:YesName: GeneSifter® AnalysisComment:Software microarray and next generation sequencing analysisWebsite:http://www.geospiza.com/Contact/genesiftertrial_ng.shtmlLicense needed:YesName: ADaCGHComment:Web tool for the analysis of aCGH data setsWebsite:http://adacgh.bioinfo.cnio.es/License needed:NoName: ArrayStarComment:Gene expression analysis software package that includes visualization tools to help analyze microarray data, including Venn diagrams, a scatter plot, heat maps and line graphs for clustering, and a gene ontology treeWebsite:http://www.dnastar.com/t-products-arraystar.aspxLicense needed:YesName: GeneSpring GXComment:Statistical tools for fast visualization and analysis of expression and genomic structural variation dataWebsite:http://www.chem.agilent.com/en-US/products/software/lifesciencesinformatics/genespringgx/pages/gp34525.aspxLicense needed:YesName: ANAISComment:User-friendly web-based tool for the processing of NimbleGen expression dataWebsite:http://anais.versailles.inra.fr/License needed:NoName: JMPComment:Software for Microarray, SNP and Proteomics Expression AnalysisWebsite:http://www.jmp.com/software/webinars/jmp_microarray.shtmlLicense needed:YesName: SAM: Significance Analysis of MicroarraysComment:Supervised learning software for genomic expression data miningWebsite:http://www-stat.stanford.edu/~tibs/SAM/License needed:NoName: GenePublisherComment:Gene expression analysisWebsite:http://www.cbs.dtu.dk/services/GenePublisher/License needed:NoBlogName: SEQanswersComment:SEQanswers is a blog founded to be an information resource and user-driven community focused on all aspects of next-generation genomics. A reasonably thorough table of next-gen-seq software available in the commercial and public domain is providedWebsite:http://seqanswers.com/forums/showthread.php?t=43Note:ExamplesName: CufflinksComment:Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts, free of chargeWebsite:http://cufflinks.cbcb.umd.edu/License needed:NoName: BowtieComment:Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).Website:http://bowtie-bio.sourceforge.net/index.shtmlLicense needed:NoName: TophatComment:TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. TopHat runs on Linux and OS X.Website:http://tophat.cbcb.umd.edu/License needed:NoName: OasesComment:Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assemblyWebsite:http://www.ebi.ac.uk/~zerbino/oases/License needed:NoName: Genomatix Genome Analyzer (GGA) and Genomatix Software Suite (GSS)Comment:GGA comprehensive second-level analysis of Next Generation Sequencing (NGS) data from ChIP-Seq, RNA-Seq or genotyping experiments. GSS conducts a scientific analysis of genomic data in gene regulation, networks, pathways and genome annotation visualization.Website:http://www.genomatix.de/en/index.htmlLicense needed:yesName: ALLPATHS-LGComment:genome assembly algorithms recommended by the Broad InstituteWebsite:http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-developmentLicense needed:noExamplesName: FlowJoComment:FlowJo is designed around the structure of flow data and the researcher's experiments. Through FlowJo's patent-pending Groups structure, for example, gates can be applied to many samples as easily as oneWebsite:http://www.treestar.comLicense needed:YesName: WinList/FCOMComment:Load FCS files from instruments and do FACS data analysis with a full set of region tools and gates. The algorithms allow for rapid generation of registers with frequencies/numbers of all possible suphenotype combinations. Can be used to input data for cluster analysis and heat maps, allowing rapid visualization of numerous complex data sets.Website:http://www.vsh.com/License needed:YesName: FCSPressComment:FCSPress is an easy-to-use Macintosh program that produces presentation quality graphics and generates statistics from flow-cytometric dataWebsite:http://www.fcspress.com/License needed:YesName: FCS EXpressComment:FCS Express is designed to bring the power sophisticated analysis protocols to users in an intuitive, easy to grasp mannerWebsite:http://www.denovosoftware.com/License needed:YesName: GemStoneComment:GemStone is software for analysis of high-dimensional, flow cytometry data. Based on patented Probability State Modeling technology, GemStone eliminates some problems that have faced flow cytometry. Subjective gating and associated errors are eliminated. Population overlaps in multidimensional data are accounted for. Multiple samples may be combined into one coherent analysisWebsite:http://www.vsh.com/License needed:YesName: SPICEComment:SPICE is a data mining software application that analyzes large FLOWJO data sets from polychromatic flow cytometry and organizes the normalized data graphically. SPICE enables users to discover potential correlations in their experimental data within complex data sets.Website:http://exon.niaid.nih.gov/spice/License needed:YesExamplesName: Ingenuity Pathway Analysis (IPA)Comment:User friendly software that allows analysis of biological and chemical systemsWebsite:http://www.ingenuity.com/License needed:YesName: GeneGo MetaCoreComment:User friendly software that allows analysis of biological and chemical systemsWebsite:http://www.genego.com/about.phpLicense needed:YesName: Ariadne Pathway StudioComment:Analysis of biological system with an interactive software interface and the computational approach to generating database content from the literatureWebsite:http://www.ariadnegenomics.com/License needed:YesName: DAVIDComment:Analysis of biological systemWebsite:http://david.abcc.ncifcrf.gov/content.jsp?file=functional_annotation.html#introLicense needed:NoName: KEGG PathwayComment:Collection of manually drawn pathway maps representing knowledge on the molecular interaction and reaction networks, free of chargeWebsite:http://www.genome.jp/kegg/pathway.htmlLicense needed:NoName: BioCarta pathwayComment:BioCarta pathway provides displays of gene interactions within pathways for human cellular processes, such as apoptosis and signal transductionWebsite:http://cgap.nci.nih.gov/Pathways/BioCarta_PathwaysLicense needed:NoName: Interactive Genomics ViewerComment:The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotationsWebsite:http://www.broadinstitute.org/igv/homeLicense needed:NoName: GSEAComment:Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states Website:http://www.broadinstitute.org/gsea/License needed:NoName: GOMinerComment:A tool for biological interpretation of 'omic' data - including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samplesWebsite:http://discover.nci.nih.gov/gominer/index.jspLicense needed:NoName: MatchMinerComment:Set of tools that enables the user to translate between disparate ids for the same gene. It uses data from the UCSC, LocusLink, Unigene, OMIM, Affymetrix and Jackson data sources to determine how different ids relate. Supported id types include, gene symbols and names, IMAGE and FISH clones, GenBank accession numbers and UniGene cluster idsWebsite:http://discover.nci.nih.gov/matchminer/index.jspLicense needed:NoName: PANTHER Classification SystemComment:Panther is a resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are also classifiedWebsite:http://www.pantherdb.org/License needed:YesExamplesName: Ambion siRNA LibrariesComment:siRNA LibrariesWebsite:http://www.ambion.com/techlib/tn/116/11.htmlName: Thermo Scientific siRNA LibrariesComment:siRNA LibrariesWebsite:http://www.dharmacon.com/catalog/catalogitemtemplate.aspx?id=1435&imageid=1882Name: siRNA LibrariesComment:siRNA LibrariesWebsite:http://genome.duke.edu/cores/rnai/libraries/qiagen/Name: NCBI DatabasesComment:Gene/Protein/SNP/Nucleotide and several other databasesWebsite:http://www.ncbi.nlm.nih.gov/gquery/Name: Gene Expression Omnibus (GEO)Comment:Public functional genomics data repository supporting MIAME-compliant (Minimum information about a microarray experiment) data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profilesWebsite:http://www.ncbi.nlm.nih.gov/geo/Name: Catalogue Of Somatic Mutations In Cancer (COSMIC)Comment:COSMIC is designed to store and display somatic mutation information and related details and contains information related to human cancersWebsite:http://www.sanger.ac.uk/genetics/CGP/cosmic/Name: The Cancer Genome Atlas (TCGA)Comment:The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. Launched in 2006 as a partnership between the National Cancer Institute and the National Human Genome Research Institute, both NIH components, The Cancer Genome Atlas (TCGA) has developed a comprehensive strategy for comparing the genome of cancer cells to the genome of normal cells from the same patientWebsite:http://cancergenome.nih.gov/Name: The Human Protein AtlasComment:The Human Protein Atlas portal is a publicly available database with millions of high-resolution images showing the spatial distribution of proteins in 46 different normal human tissues and 20 different cancer types, as well as 47 different human cell lines. The data is released together with application-specific validation performed for each antibody. The database was developed in a gene-centric manner with the inclusion of all human genes predicted from genome effortsWebsite:http://www.proteinatlas.orgName:DIP (Database of Interacting Proteins)Comment:The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactionsWebsite:http://dip.doe-mbi.ucla.edu/dip/Main.cgiName:MINT (Molecular INTeraction Database)Comment:MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the 'MINT Viewer'Website:http://mint.bio.uniroma2.it/mint/Welcome.doName: Human Protein Reference DatabaseComment:The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteomeWebsite:http://www.hprd.orgName: Cancer Genome Anatomy Project (CGAP)Comment:The NCI's Cancer Genome Anatomy Project sought to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient. Resources generated by the CGAP initiative are available to the broad cancer communityWebsite:http://cgap.nci.nih.gov/cgap.htmlName: caBIGComment:caBIG stands for the cancer Biomedical Informatics Grid. caBIG is an information network enabling members of the cancer community - researchers, physicians, and patients - to share data and knowledgeWebsite:https://cabig.nci.nih.gov/Name: mirbaseComment:Searchable database of published miRNA sequences and annotationWebsite:http://www.mirbase.orgName: deepBaseComment:deepBase is a database for annotating and discovering small and long ncRNAs  from high-throughput deep sequencing dataWebsite:http://deepbase.sysu.edu.cn/miRDeep.phpName: Gene Ontology Annotation (UniProtKB-GOA) DatabaseComment:The UniProtKB-GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI) and is a central dataset for other major multi-species databases; such as Ensembl and NCBIWebsite:http://www.ebi.ac.uk/GOA/Name: ProtfunComment:The ProtFun 2.2 server produces ab initio predictions of protein function from sequenceWebsite:http://www.cbs.dtu.dk/services/ProtFun/Name: TRANSFAC 7.0 Public 2005Comment:Data on transcription factors, their experimentally-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matricesWebsite:http://www.gene-regulation.com/pub/databases.htmlName: OptiTopeComment:OptiTope aims at assisting immunologists in designing epitope-based vaccines. It is an easy-to-use tool to determine a provably optimal set of epitopes with respect to overall immunogenicity in a specific individual or a target population, free of chargeWebsite:http://www.epitoolkit.org/optitopeName: Cancer Central Clinical Database (C3D)Comment:Cancer Central Clinical Database (C3D) is a clinical trials data management system. C3D collects clinical trial data using standard case report forms (CRFs) based on common data elements (CDEs)Website:https://cabig.nci.nih.gov/tools/c3dName: UCSC Genome BrowserComment:Provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation dataWebsite:http://genome.ucsc.edu/Name: Next BioComment:Exhaustive collection of public microarray data. NextBio's platform combines powerful tools with unique correlated content. With NextBio you can search tens of thousands of studies containing billions of data points spanning different experimental platforms, organisms and data typesWebsite:http://www.nextbio.com/b/corp/faq.nbName: SYFPEITHIComment:SYFPEITHI is a database comprising more than 7,000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports onlyWebsite:http://www.syfpeithi.de/Name: Melanoma Molecular Map ProjectComment:MMMP Databases, putting together the pieces of the melanoma puzzle. Seven interconnected databanks for the interactive collection, update and consultation of the translational and clinical information on melanoma biology and treatment.Website:http://www.mmmp.orgName: The Targeted Therapy Database (TTD)Comment:Systematic collection of the scientific knowledge regarding the development of targeted therapy for melanomaWebsite:http://www.mmmp.orgExamplesName: Primer3Comment:Primer3 is a free online tool to design and analyze primers for PCR and real time PCR experiments. Primer3 can also select single primers for sequencing reactions and can design oligonucelotide hybridization probesWebsite:http://frodo.wi.mit.edu/primer3Name: Oligo Analyzer 3.0Comment:Software developed by IDT (Integrated DNA Technologies) that analyzes physical properties of a specific oligo sequence. The results show a complementary sequence, oligo length, GC content, melting temperature, extinction coefficient, molecular weight, μg/OD, and nmoles/OD.Website:http://www.idtdna.com/analyzer/applications/oligoanalyzerName: MethPrimerComment:MethPrimer is a program for designing bisulfite-conversion-based methylation PCR Primers. It can design primers for Methylation-Specific PCR (MSP), Bisulfite-Sequencing PCR (BSP) and Bisulfite-Restriction PCRWebsite:http://www.urogene.org/methprimer/index1.htmlExamplesName: TFSEARCHComment:TFSEARCH predicts transcription factors binding sites from a given sequence. It does simple correlation calculation with binding site profile matricesWebsite:http://www.cbrc.jp/research/db/TFSEARCH.htmlName: SfoldComment:Sfold predicts RNA duplex thermodynamics for rational siRNA design. It supports target accessibility prediction and rational design of antisense oligonucleotides (ASO) and nucleic acid probes. It can design an ASO for a gene of interest based on the mRNA sequenceWebsite:http://sfold.wadsworth.org/cgi-bin/soligo.plExamplesName: TargetScanComment:Prediction of biological targets of miRNAsWebsite:http://www.targetscan.org/License needed:NoName:http://microRNA.orgComment:A resource for predicted microRNA targets and expression, free of chargeWebsite:http://www.microrna.org/microrna/home.doLicense needed:NoName: DIANA LAbComment:miRNA computational predictive models. Experimental supported databasesWebsite:http://diana.cslab.ece.ntua.gr/?sec=homeLicense needed:NoName: RNA22Comment:This software first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNAWebsite:http://cbcsrv.watson.ibm.com/rna22.htmlName: PicTarComment:PicTar provides combinatorial microRNA target predictionsWebsite:http://pictar.mdc-berlin.deName: miRANDAComment:miRanda is an algorithm for finding genomic targets for microRNAsWebsite:http://www.microrna.org/microrna/home.doExampleName: SpliceCenterComment:The SpliceCenter applications are user-friendly tools that provide information on the target location of probesets, primers, or siRNAs within the known splice variants of a geneWebsite:http://www.tigerteamconsulting.com/SpliceCenter/License needed:NoExamplesName: PhATComment:It analyzes SNP data, showing pairwise Linkage Disequilibrium of various types ) and producing graphical matrices of obtained resultsWebsite:http://pharmgat.org/Tools/pbtoldplotformExamplesName: ImmuneeringComment: Computer Model. Development of computer models that aim to predict the response to biological therapies in cancer patientsWebsite:http://www.immuneering.com/Name: Cellumen CellCiphr Patient Sample ProfilingComment:To use the cellular systems biology approach to improve patient stratification for clinical trial enrollments. Cellumen is collaborating with the Mayo Clinic and Foundation to create panels of cellular biomarkers using multiplexed fluorescence to apply to patient cells and tissues, starting with breast cancerWebsite:http://www.cellumen.com/solutions/patient.phpName: BiotrackerComment: Lab Management. Biotracker is a specialty Lab Information Management Solution (LIMS) for enhancing productivity and effectiveness in life sciences research laboratoriesWebsite:http://www.ocimumbio.com/lims2/products/Name: Gene's Logic Expression Array AnalysisComment:Array analysis support; team dedicated to statistical and bioinformatic analyses of microarray data, ranging from basic quality control and differential gene expression analysisWebsite:http://www.genelogic.com/services/bioinformatic-analysisName: Microsoft Word Add-In for the GenePattern Reproducible Research Document (GRRD)Comment:To facilitate publishing reproducible results, GenePattern automatically captures the history of any computational work being done, allowing scientists to easily generate pipelines to reproduce computational methodsWebsite:http://www.broadinstitute.org/cancer/software/genepattern/grrd/AddIn.htmlLicense needed:NoName: IUBio ArchiveComment:Archive of biology data and software, established in 1989 to promote public access to freely available information, primarily in the field of molecular biology and bioinformaticsWebsite:http://iubio.bio.indiana.edu/Name: LabomeComment:Tools for searching antibodies, siRNA/shRNA, ELISA, cDNA clones, proteins/peptides, microRNA, and biochemicals from all suppliersWebsite:http://www.labome.com/License needed:NoExamplesName: Inno.CNTComment:The Inno.CNT website gives an updated and wide overview of the research status of carbon nanotubes as one of the most promising nanomaterial to open up completely new dimensions in biomedical applicationsWebsite:http://www.inno-cnt.de/en/uebercnt.phpName: ObservatoryNanoComment:The ObservatoryNano provides wide-ranging analysis focusing on nanoscience and nanotechnology developmentsWebsite:http://www.observatory-nano.eu/project/Name: NanofuturesComment:Nanofutures is an integration platform aimed at becoming a long-lasting nanotechnology hub, connecting the most relevant nanotechnology stakeholdersWebsite:http://www.nanofutures.eu/Name: Nanotechnology MedicineComment:Nanotechnology Medicine brings you informative nanomedicine articles, educational nanomedicine videos, and lively nanomedicine dialogue and chatter.Website: http://nanotechnologymedicine.org/ExampleName: Clinical Trial RegistriesComment:The five clinical trials registries approved by the International Committee of Medical Journal Editors (ICMHE)Website:http://ClinicalTrials.gov, http://www.actr.org.au, http://www.ISRCTN.org, http://www.umin.ac.jp/ctr/index/htm, http://www.trialregister.nlImmune biomarkers are playing an increasingly important role in the successful development, clinical evaluation, and immune monitoring of cancer immunotherapies. The references, products and online resources in this Cancer Immunotherapy Biomarkers Resource Document were identified by the authors and the SITC/iSBTc Taskforce on Immunotherapy Biomarkers to support the discovery, evaluation and application of biomarkers for cancer immunotherapy. These selected references and links serve as a compass to point investigators to useful resources in this ever growing, and important field of cancer immunotherapy biomarkers. Emerging issues surrounding cancer immunotherapy biomarker discovery and clinical application will continue to be addressed in upcoming SITC Annual Meetings and Associated Programs .DB, JB, EW, MLD, CMB, LGD, ST, TFG, LHB and FFM declare that they have no competing interests. BAF is co-founder of UbiVac, LLC and serves on the scientific advisory boards of Micromet, Inc. and MannKind Corporation.DB and JB prepared the manuscript. EW, MLD, CMB, LGD, ST, BAF, TFG, FMM and LHB provided substantive editing and critical review. All authors read and approved the final manuscript.


The name of the third author is: Maartje G. NoordhuisVGF and PGP9.5 with Ovarian Cancer Progression. PLoS ONE 8(9): e70878. doi:10.1371/journal.pone.0070878 The correct version of the citation is: Brait M, Maldonado L, Noordhuis M, Begum S, Loyo M, et al. (2013) Association of Promoter Methylation of


The name of the fifth author is incorrectly represented in the Citation. The correct Citation is: Jamilloux Y, Liozon E, Pugnet G, Nadalon S, Ly KH, et al. (2013) Recovery of Adrenal Function after Long-Term Glucocorticoid Therapy for Giant Cell Arteritis: A Cohort Study. PLoS ONE 8(7): e68713. doi:10.1371/journal.pone.0068713.


The name of the first author is incorrectly represented in the Citation. The Citation should read: Barsotti MC, Losi P, Briganti E, Sanguinetti E, Magera A, et al. (2013) Effect of Platelet Lysate on Human Cells Involved in Different Phases of Wound Healing. PLoS ONE 8(12):e84753. doi:10.1371/journal.pone.0084753.


The name of the first author was spelled incorrectly. The correct name is: Alessandra Baragli. The correct citation is: Baragli A, Grande C, Gesmundo I, Settanni F, Taliano M, et al. (2013) Obestatin Enhances In Vitro Generation of Pancreatic Islets through Regulation of Developmental Pathways. PLoS ONE 8(5): e64374. doi:10.1371/journal.pone.0064374. The abbreviation in Contributions is correct.