412 results on '"Yilmaz, Pelin"'
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52. Utilization of low-cost bio-waste adsorbent for methylene blue dye removal from aqueous solutions and optimization of process variables by response surface methodology approach
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Yilmaz, Pelin, primary, Gunduz, Davut, additional, and Ozbek, Belma, additional
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- 2021
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53. SILVA Databases
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Quast, Christian, primary, Pruesse, Elmar, additional, Gerken, Jan, additional, Schweer, Timmy, additional, Yilmaz, Pelin, additional, Peplies, Jörg, additional, and Glockner, Frank Oliver, additional
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- 2012
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54. Metagenomes: 23S Sequences
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Yilmaz, Pelin, primary and Glöckner, Frank Oliver, additional
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- 2012
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55. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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Quast, Christian, Pruesse, Elmar, Yilmaz, Pelin, Gerken, Jan, Schweer, Timmy, Yarza, Pablo, Peplies, Jörg, and Glöckner, Frank Oliver
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- 2013
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56. SILVA: Comprehensive Databases for Quality Checked and Aligned Ribosomal RNA Sequence Data Compatible with ARB
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Prüsse, Elmar, primary, Quast, Christian, additional, Yilmaz, Pelin, additional, Ludwig, Wolfgang, additional, Peplies, Jörg, additional, and Glöckner, Frank Oliver, additional
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- 2011
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57. The Use of rRNA Gene Sequence Data in the Classification and Identification of Prokaryotes
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Ludwig, Wolfgang, primary, Oliver Glöckner, Frank, additional, and Yilmaz, Pelin, additional
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- 2011
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58. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities
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Waite, David W, primary, Chuvochina, Maria, additional, Pelikan, Claus, additional, Parks, Donovan H, additional, Yilmaz, Pelin, additional, Wagner, Michael, additional, Loy, Alexander, additional, Naganuma, Takeshi, additional, Nakai, Ryosuke, additional, Whitman, William B, additional, Hahn, Martin W, additional, Kuever, Jan, additional, and Hugenholtz, Philip, additional
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- 2020
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59. Versatile cyanobacteria control the timing and extent of sulfide production in a Proterozoic analog microbial mat
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Klatt, Judith M, primary, Gomez-Saez, Gonzalo V, additional, Meyer, Steffi, additional, Ristova, Petra Pop, additional, Yilmaz, Pelin, additional, Granitsiotis, Michael S, additional, Macalady, Jennifer L, additional, Lavik, Gaute, additional, Polerecky, Lubos, additional, and Bühring, Solveig I, additional
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- 2020
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60. Role of Temperature and Growth Period in the Synthesis of Hydrothermally Grown TiO2 Nanorods
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Soosaimanickam, Ananthakumar, primary, Yilmaz, Pelin, additional, Li, Xuan, additional, Briscoe, Joe, additional, Anderson, Ann-Louise, additional, Dunn, Steve, additional, and Sridharan, Moorthy Babu, additional
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- 2020
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61. Spectrally Selective PANI/ITO Nanocomposite Electrodes for Energy-Efficient Dual Band Electrochromic Windows
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Yilmaz, Pelin, primary, Magni, Mirko, additional, Martinez, Sandra, additional, Gonzalez Gil, Rosa Maria, additional, Della Pirriera, Monica, additional, and Manca, Michele, additional
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- 2020
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62. Megx.net: integrated database resource for marine ecological genomics
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Kottmann, Renzo, Kostadinov, Ivalyo, Duhaime, Melissa Beth, Buttigieg, Pier Luigi, Yilmaz, Pelin, Hankeln, Wolfgang, Waldmann, Jost, and Glöckner, Frank Oliver
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- 2010
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63. Characterization of the Chemical Profile of Euphorbia Species from Turkey by Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS), and Liquid Chromatography-Ion Trap-Time-of-Flight-Mass Spectrometry (LC-IT-TOF-MS) and Chemometric Analysis
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Yener, Ismail, Ertas, Abdulselam, Yılmaz, Mustafa Abdullah, Olmez, Ozge Tokul, Yilmaz, Pelin Koseoglu, Yesil, Yeter, Kaplaner, Erhan, Ozturk, Mehmet, Temel, Hamdi, Kolak, Ufuk, Topcu, GÜLAÇTI, and TOPÇU, GÜLAÇTI
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Yener I., Ertas A., Yılmaz M. A. , Olmez O. T. , Yilmaz P. K. , Yesil Y., Kaplaner E., Ozturk M., Temel H., Kolak U., et al., -Characterization of the Chemical Profile of Euphorbia Species from Turkey by Gas Chromatography-Mass Spectrometry (GC-MS), Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS), and Liquid Chromatography-Ion Trap-Time-of-Flight-Mass Spectrometry (LC-IT-TOF-MS) and Chemometric Analysis-, ANALYTICAL LETTERS, cilt.52, ss.1031-1049, 2019 - Abstract
The Euphorbiaceae family comprises of about 300 genera and 5000 species primarily distributed in America and tropical Africa. The Euphorbia genus is represented by 105 species and locally named as -Sutlegen- and -Xasil- in Turkey. The present study aimed to determine the chemical constituents of E. aleppica, E. eriophora, E. macroclada, E. grisophylla, E. seguieriana subsp. seguieriana, E. craspedia, E. denticulata, E. falcata, and E. fistulosa, and classify them by utilizing the chemometric techniques of principal component analysis (PCA) and hierarchical cluster analysis (HCA). Linoleic acid, 17-tetratriacontane, palmitic acid, and hexatriacontane were the major fatty acids from the gas chromatography-mass spectrometry (GC/MS) analyses. Characterization of 268 constituents of the studied species was achieved by liquid chromatography-ion trap-time-of-flight-mass spectrometry (LC-IT-TOF-MS). Furthermore, a new liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the simultaneous quantitative determination of 11 compounds (quinic acid, protocatechuic acid, rutin, hesperidin, eugenol, p-coumaric acid, piceatannol, scopoletin, dl-kavain, chrysophanic acid, and resiniferatoxin) in these species. The developed method was validated for the linearity, limit of detection, limit of quantification, repeatability, and recovery.
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- 2019
64. ISPARTA ÜZÜM ÇARŞISI ÜST ÖRTÜ SORUNLARI
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HALAÇ, Hicran Hanım and YILMAZ, Pelin
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Tarih ,History ,Isparta Üzüm bazaar,Historical trade center,Top cover,Contemporary annex to historical Textiles ,Isparta Üzüm Çarşısı,Tarihi Ticaret Merkezi,Üst Örtü,Tarihi Dokuya Çağdaş Ek - Abstract
The trade has contributed to the development of citiesthroughout the centuries, and made it possible for the citizens to meet withdifferent worlds. Trade action, which is also an important factor in theformation of cities, designs a new space in the city center. In the past, thetrade in the open space, needed closed environments in time.Isparta has been an important trade focus during theOttoman period. With the developing trade routes and caravanserais, Trade inIsparta has developed.The historic Uzum Bazaar in Isparta continues itsexistence for 455 years. There are 16 commercial shops registered in theexisting historical texture. The area has covered with the second floor leveltop cover. In the light of the registration slips received, the top cover wasanalyzed according to the distribution in the commercial tissue. Photographs ofbuildings are documented through google streetview and the structure of thetissue is analyzed.The aim of this study is to create awareness about theelements that should be considered in designing and applying top coveringswhich are frequently encountered in the historical trade tissues in recentyears.The content of this article is supported with photographs and the designproblems of the Uzum market in Isparta were examined and suggestions were madefor the questions., Ticaretyüzyıllar boyunca kentlerin gelişmesine katkı yapmış, kentlilerin farklıdünyalarla tanışmasını sağlamıştır. Kentlerin oluşmasında da önemli bir etkenolan ticaret eylemi kent merkezinde kendisine yeni bir mekân tasarlar. Eskidönemlerde açık alanda gerçekleşen ticaret zamanla kapalı ortamlara ihtiyaçduymuştur. Ispartakenti Osmanlı döneminde önemli bir ticaret odağı olmuştur. Gelişen ticaretyolları ve kervansaraylar sayesinde Isparta kent ticareti gelişmiştir. Ispartatarihi Üzüm Çarşısı da 455 yıldır varlığını sürdürür. Mevcut tarihi dokudatescilli 16 ticari dükkân bulunmaktadır. Bölge günümüzde 2. kat seviyesinde birüst örtüyle kapalıdır. Alınan tescil fişleri ışığında üst örtü ticari dokudakidağılımına göre analiz edilmiştir. Yapıların fotoğrafları Google-streetviewaracılığıyla belgelenerek dokunun ve yapıların niteliğinin analiziyapılmışıdır. Buçalışma aracılığıyla son yıllarda tarihi ticaret dokularında sıkça karşılaşılanüst örtülerin tasarlanmasında ve uygulamasında dikkat edilmesi gerekenunsurlara yönelik farkındalık yaratılmaya çalışılmıştır. Bu makale içeriğifotoğraf ve çizimlerle desteklenerek Isparta Üzüm Çarşısı’nın tasarımsalsorunları irdelenmiş ve belirlenen sorulara öneriler getirilmiştir.
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- 2019
65. İş tatmini ile örgütsel vatandaşlık davranışları arasındaki ilişkide birey-örgüt ve birey – iş uyumunun şartlı değişken rolü
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Yilmaz, Pelin, Türker, Mine, and Psikoloji Ana Bilim Dalı
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Organizational citizenship behavior ,Psikoloji ,Job satisfaction ,Psychology ,Person organization fit - Abstract
95
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- 2019
66. Kimya öğretmen adaylarının pedagojik alan bilgilerinin geliştirilmesi ve sürecin değerlendirilmesi
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Yilmaz, Pelin, Karataş, Faik Özgür, and Ortaöğretim Fen ve Matematik Alanları Eğitimi Anabilim Dalı
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Eğitim ve Öğretim ,Education and Training - Abstract
Öğretmenlik mesleğini diğer mesleklerden ayıran en önemli özelliği; toplumdaki bireylerin yetişmesinde rol oynamasıdır. Bu nedenle geleceğe ışık tutacak gençler yetiştirebilmeleri için öğretmen adaylarının etkili bir eğitim-öğretim süreci gerçekleştirmeye özen göstermesi gerekmektedir. Öğretmenlerin ve/veya öğretmen adaylarının mesleki gelişimlerinde Pedagojik Alan Bilgisi (PAB), pedagoji bilgi ve içerik bilgisinin bütünleştirilerek kullanılması anlamına gelmektedir ve alan eğitiminin en önemli parçalarından biridir. Bu nedenle öğretmenlerin ve/veya öğretmen adaylarının PAB düzeylerinin geliştirilmesi, kimya öğretiminin niteliğinin de geliştirilmesi anlamına gelmektedir. Bu kapsamda gerçekleştirilen çalışmanın amacı mikro-öğretim merkezinde ve içerik gösterimi planı çerçevesinde tasarlanan `Pedagojik Alan Bilgisinin Akran ve Uzman Etkileşimli Mikro-Öğretim ile Geliştirilmesi (PABEM)` modelinin kimya öğretimi II dersi kapsamında kimya öğretmen adaylarının PAB'larını geliştirme sürecini değerlendirmektir. Araştırmanın amacına uygun olarak özel durum çalışmasından faydalanılmıştır. Öğretmen adaylarının PAB'larını geliştirmek ve mevcut durumlarını ortaya koymak için öğretmenlerin ve/veya öğretmen adaylarının derslerini planlarken kullanabilecekleri kapsamlı bir öğretim planı sunan içerik gösteriminden (Content Representation [CoRe]) yararlanılmıştır. Kimya öğretmen adaylarına araştırmacı tarafından sürekli rehberlik sağlanmış ve her bir öğretmen adayı bir pilot mikro-öğretim bir de mikro-öğretim olmak üzere toplam iki uygulama gerçekleştirmiştir. Araştırmanın çalışma grubunu 2017-2018 eğitim–öğretim yılının bahar döneminde Kimya Öğretimi II dersini alan toplam 8 3. sınıf kimya öğretmen adayı oluşmuştur. Çalışma sürecinde öncelikle öğretmen adaylarına içerik gösterimi, pedagojik alan bilgisi ve değerlendirme yöntemleri ile ilgili bilgiler verilmiştir. Öğretmen adaylarından hazırladıkları içerik gösterimleri, mikro-öğretim ders gözlem formları, yansıtıcı form ve yarı yapılandırılmış mülakatlar aracılığı ile veriler toplanmıştır. Elde edilen verilerin analizlerinde ise betimsel analiz ve içerik analizi teknikleri kullanılmıştır. PABEM uygulaması sonucunda kimya öğretmen adaylarının zamanla hem biçimlendirici hem de özetleyici değerlendirme üzerine yoğunlaşmayı öğrendikleri, kavram yanılgıları, öğrenme zorlukları ve seçilen stratejiye uygun olarak derslerini detaylı bir biçimde yapılandırmanın önemi ile ilgili farkındalıklarının geliştiğini tespit edilmiştir. Ancak yeni denemeler yerine en çok bildikleri 5E ders modelini sürekli kullandıkları ve öğretim programını kullanma konusunda eksiklikleri olduğu sonucuna varılmıştır. İçerik gösteriminin işe koşulduğu ve adaylara hem hazırlık hem de uygulama sürecinde sürekli rehberlik sağlandığı mikro-öğretim uygulamalarını içeren PABEM modelinin öğretmen adaylarının eğitiminde uygulamalı olarak kullanılması önerilmektedir. The most important characteristic that distinguishes the teaching profession from other professions is shaping the society by educating individuals. For this reason, in order to educate young people who will shed light on the future, pre-service teachers should pay attention to carry out an effective pre-service education. In the professional development of teachers and/or pre-service teachers, Pedagogical Content Knowledge (PCK) means the integration of pedagogical knowledge and content knowledge that a teacher should have, and is one of the main types of knowledge required for effective teaching. Therefore, the development of PCK levels of teachers or pre-service teachers also means
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- 2019
67. Kömürün kısa analiz sonuçlarına farklı matematiksel yöntemler uygulayarak elementel bileşiminin tahmini
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Baylan Yilmaz, Pelin, Ceylan, Selim, and Kimya Mühendisliği Ana Bilim Dalı
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Chemical Engineering ,Kimya Mühendisliği - Abstract
Bu tez çalışmasında, kömürün elementel analizinin deneysel olarak belirlenmesi uzun zaman gerektiren ve pahalı bir iş olduğundan dolayı, kömürün elementel bileşiminin tahmini üzerine bir çalışma gerçekleştirilmiştir. Geçmiş çalışmalarda elementel bileşim ile kısa analiz sonuçları arasındaki ilişkiler incelenmiş olup, karbon, hidrojen ve oksijen bileşimlerinin sırasıyla sabit karbon, uçucu madde ve külün nispi içerikleriyle orantılı olduğu görülmüştür. Kısa analiz sonuçlarını kullanılarak kömür ya da biyokütlenin elementel bileşimini tahmin etmek için çeşitli korelasyonlar sunulmuştur. Fakat sunulan çalışmalarda numune sayısının az ya da korelasyon değerlerinin doğru tahmin için yeterli olmadığı görülmüşür. Bu çalışmada, literatürde daha önce sunulmuş farklı çalışmalardan yararlanılarak büyük bir veri seti oluşturulmuştur. Farklı kalitede kömürlerden oluşturulan bu veri setine matematiksel modeller ve kısa analiz sonuçları uygulanarak kömürün elementel bileşiminin tahmini üzerine bir çalışma gerçekleştirilmiştir. Tahmin için çoklu lineer regresyon modeli ve yapay sinir ağlarından yararlanılmıştır. Elde edilen sonuçlar yaygın istatistiksel araçlar ile test edilmiştir. Çoklu lineer regresyon modeli ile regresyon katsayıları karbon, hidrojen ve oksijen için sırasıyla 0.99025, 0.64431 ve 0.98526 olarak elde edilmiştir. Yapay sinir ağları ile regresyon katsayıları karbon, hidrojen ve oksijen için sırasıyla 0.99177, 0.80452 ve 0.99113 olarak elde edilmiştir. Çalışma sonucu elde edilen modellerin, kısa analiz sonuçlarını kullanarak kömürün karbon, hidrojen ve oksijen yüzdesini yüksek doğruluk ile tahmin etme kabiliyetine sahip olduğu görülmüştür. Bu modeller zahmetli ve masraflı olan elementel analiz işleminin yerini alma potansiyeline sahiptir. In this thesis study, because the experimental determination of the elementel analysis of coal is a long time and expensive process, a study on the estimation of the elementel composition of coal has been carried out. In the past studies, the relationships between the elementel composition and the proximate analysis results were examined and it was found that the carbon, hydrogen and oxygen compounds were proportional to the relative contents of the fixed carbon, volatile matter and ash, respectively. Various correlations are presented to estimate the elementel composition of coal or biomass using proximate analysis results. However, it was observed that the number of samples or the correlation values were not sufficient for accurate estimation. In this study, a large data set was created by using different studies previously presented in the literature. A mathematical model and proximate analysis results were applied to this data set composed of different quality coals, and a study was performed to estimate the elementel composition of coal. Multiple linear regression models and artificial neural networks were used for estimation. The results obtained were tested with common statistical tools. The regression coefficients were obtained as 0.99025, 0.64431 and 0.98526 for carbon, hydrogen and oxygen respectively with multiple linear regression model. The regression coefficients with artificial neural networks were obtained as 0.99177, 0.80452 and 0.99113 for carbon, hydrogen and oxygen, respectively. It was found that the models obtained as a result of the study were able to estimate the carbon, hydrogen and oxygen percentage of coal with high accuracy by using short analysis results. These models have the potential to replace the laborious and costly elementel analysis. 67
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- 2019
68. Production and characterization of hydroxyapatite-graphene oxide-chitosan scaffold for bone tissue engineering application
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Yilmaz, Pelin, Ülgen, Şefika Kutlu, Özbek, Belma, and Kimya Mühendisliği Anabilim Dalı
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Chemical Engineering ,Kimya Mühendisliği - Abstract
Kemik dokusu mühendisliği, kemik doku hücreleri için doğal hücre dışı matriksi taklit edebilen uygun doku iskeleleri kullanımı ile biyolojik mikroçevreyi sağlayarak hastalıklı veya hasarlı kemik dokularını iyileştirme stratejisidir. Literatürde; bu konuya yönelik çok sayıda çalışma mevcuttur. Ancak literatürde, yumurtadan elde edilen hidrokoksiapit (HAp), grafen oksit (GO), kitosan (CS) içeren üç bileşenli doku iskelesinin süper kritik jel kurutma işlemiyle üretimi ve üretilen doku iskelesi üzerinde GO'nun toksik etkisinin incelenmesine yönelik bir çalışmaya rastlanılamamıştır. Bu çalışmada, HAp-GO-CS'dan oluşan üç bileşenli doku iskelelerin üretilmesinde kullanılan HAp, kalsiyum kaynağı olan yumurta kabuklarından çöktürme yöntemi ile sentezlenmiştir. Osteokondüktif ajanı olarak kullanılan GO'in sentezi için Geliştirilmiş Hummer yöntemi kullanılmıştır. HAp, GO ve CS çözeltilerinin karıştırılmasıyla hazırlanan doku iskelesi karışımları kalıplanarak dondurulmuştur. Dondurulmuş örneklere su-aseton ikame işlemi uygulandıktan sonra, süperkritik jel kurutma işlemi uygulanarak doku iskeleleri üretilmiştir. GO'in toksik etkisini inceleyebilmek için farklı GO oranlarında üretilen üç bileşenli doku iskeleleri; FTIR, XRD, SEM, TEM, EDS, BET ve TG/DTA analizleri ile karakterize edilmiştir. Üretien doku iskelelerinin mekanik özelliklerini değerlendirmek için Universal Instron Mekanik Test Sistemi kullanılmıştır. Sitotoksisite analizi için doku iskeleleri MTT testine tabi tutulmuştur. MTT analizi ile GO'nun % 1'lik (g/g) orandan fazla kullanılmasının MC3T3-E1 hücreleri üzerinde toksik etkisinin olduğu tespit edilmiştir. Yapılan karakterizasyon çalışmaları ile % 1'lik (g/g) GO oranına sahip HAp-GO(%1)-CS üç bileşenli doku iskelesinin; üç boyutlu gözenekli yapıya, yüksek hücre canlılığına, uygun mekanik özelliklere sahip olduğu belirlenmiştir. Elde edilen bulgulara göre, HAp-GO(%1)-CS bir kompozit olarak üretilen üç bileşenli doku iskelesinin kemik doku mühendisliğindeki uygulamalar için kullanılabilir olduğu sonucuna varılmıştır. Bone tissue engineering is a strategy to regenerate diseased or damaged bone tissues by providing the biological microenvironment with the use of appropriate scaffolds that can mimic the native extracellular matrix for bone tissue cells. In the literature, there are many studies performed on this subject, but, no studies have been conducted on the investigation of the production of three-component scaffold, which composed of hydroxyapatite (HAp) derived from eggshells, graphene oxide (GO) and chitosan (CS), by using the supercritical gel drying method, and on the examination of the possible toxicity effects of GO additions. In the present study, HAp derived from the eggshells, which is used for the production of three-component scaffolds composed of HAp-GO-CS, was synthesized by using the precipitation method. Improved Hummer method was used for the synthesis of GO, which was used as an osteoconductive agent. The mixtures of scaffolds were prepared by mixing the solutions of HAp, GO and CS, and these mixtures were frozen after molded. Then, the water-acetone substitution procedure was applied to the frozen samples, the supercritical gel drying was performed to produce scaffolds. Three-component scaffolds, produced at different GO ratios to examine the toxic effect of GO, were characterized by FTIR, XRD, SEM, TEM, EDS, BET and TG/DTA analyses. For the evaluation of the mechanical properties of the produced scaffolds, Universal Instron Mechanical Test System was used. The scaffolds were subjected to MTT testing for cytotoxicity analysis. MTT analysis showed that the use of GO ratio more than 1% (w/w) had a toxic effect on MC3T3-E1 cells. According to the characterization studies performed, it was determined that HAp-GO(1%)-CS three-component scaffold including 1% (w/w) of GO ratio had three-dimensional porous structure, highest cell viability and reasonable mechanical properties. According to the findings, it was concluded that HAp-GO(1%)-CS based composite is a promising scaffold, and could be used for the applications in bone tissue engineering. 119
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- 2019
69. The importance of designating type material for uncultured taxa
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Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B., Hugenholtz, Philip, Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B., and Hugenholtz, Philip
- Abstract
Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum. Designation of nomenclature types is crucial for providing priority to names and ensures their uniqueness and stability. However, only legitimate names proposed for axenic cultures can be used for this purpose. Candidatus names reserved for taxa lacking cultured representatives may be granted this right if recent proposals to use genome sequences as type material are endorsed, thereby allowing the Code to be fully applied to lineages represented by metagenome-assembled genomes (MAGs) or single amplified genomes (SAGs). Genome quality standards need to be considered to ensure unambiguous assignment of type material. Here, we illustrate the recommended practice by proposing nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code.
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- 2019
70. Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research
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Rambold, Gerhard, Harjes, Janno, Klaster, Sabrina, Sanz, Veronica, Yilmaz, Pelin, Glöckner, Frank Oliver, Link, Anton, Triebel, Dagmar, Rambold, Gerhard, Harjes, Janno, Klaster, Sabrina, Sanz, Veronica, Yilmaz, Pelin, Glöckner, Frank Oliver, Link, Anton, and Triebel, Dagmar
- Abstract
With the advent of advanced molecular meta-omics techniques and methods, a new era commenced for analysing and characterizing historic collection specimens, as well as recently collected environmental samples. Nucleic acid and protein sequencing-based analyses are increasingly applied to determine the origin, identity and traits of environmental (biological) objects and organisms. In this context, the need for new data structures is evident and former approaches for data processing need to be expanded according to the new meta-omics techniques and operational standards. Existing schemas and community standards in the biodiversity and molecular domain concentrate on terms important for data exchange and publication. Detailed operational aspects of origin and laboratory as well as object and data management issues are frequently neglected. Meta-omics Data and Collection Objects (MOD-CO) has therefore been set up as a new schema for meta-omics research, with a hierarchical organization of the concepts describing collection samples, as well as products and data objects being generated during operational workflows. It is focussed on object trait descriptions as well as on operational aspects and thereby may serve as a backbone for R&D laboratory information management systems with functions of an electronic laboratory notebook. The schema in its current version 1.0 includes 653 concepts and 1810 predefined concept values, being equivalent to descriptors and descriptor states, respectively. It is published in several representations, like a Semantic Media Wiki publication with 2463 interlinked Wiki pages for concepts and concept values, being grouped in 37 concept collections and subcollections. The SQL database application DiversityDescriptions, a generic tool for maintaining descriptive data and schemas, has been applied for setting up and testing MOD-CO and for concept mapping on elements of corresponding schemas
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- 2019
71. Minimum Information about an Uncultivated Virus Genome (MIUViG)
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Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Roux, Simon, Adriaenssens, Evelien M., Dutilh, Bas E., Koonin, Eugene V., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Brister, J. Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K., Bordenstein, Seth R., Bork, Peer, Breitbart, Mya, Cochrane, Guy R., Daly, Rebecca A., Desnues, Christelle, Duhaime, Melissa B., Emerson, Joanne B., Enault, François, Fuhrman, Jed A., Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L., Ivanova, Natalia N., Labonté, Jessica M., Lee, Kyung-Bum, Malmstrom, Rex R., Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F., Sullivan, Matthew B., Sunagawa, Shinichi, Suttle, Curtis A., Temperton, Ben, Tringe, Susannah G., Thurber, Rebecca Vega, Webster, Nicole S., Whiteson, Katrine L., Wilhelm, Steven W., Wommack, K. Eric, Woyke, Tanja, Wrighton, Kelly C., Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J., Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C., Eloe-Fadrosh, Emiley A., Universidad de Alicante. Departamento de Fisiología, Genética y Microbiología, Roux, Simon, Adriaenssens, Evelien M., Dutilh, Bas E., Koonin, Eugene V., Kropinski, Andrew M., Krupovic, Mart, Kuhn, Jens H., Lavigne, Rob, Brister, J. Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K., Bordenstein, Seth R., Bork, Peer, Breitbart, Mya, Cochrane, Guy R., Daly, Rebecca A., Desnues, Christelle, Duhaime, Melissa B., Emerson, Joanne B., Enault, François, Fuhrman, Jed A., Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L., Ivanova, Natalia N., Labonté, Jessica M., Lee, Kyung-Bum, Malmstrom, Rex R., Martinez-Garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-Espino, David, Petit, Marie-Agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-Valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F., Sullivan, Matthew B., Sunagawa, Shinichi, Suttle, Curtis A., Temperton, Ben, Tringe, Susannah G., Thurber, Rebecca Vega, Webster, Nicole S., Whiteson, Katrine L., Wilhelm, Steven W., Wommack, K. Eric, Woyke, Tanja, Wrighton, Kelly C., Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J., Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C., and Eloe-Fadrosh, Emiley A.
- Abstract
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
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- 2019
72. UniEuk: time to speak a common language in protistology
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Berney, Cedric, Siano, Raffaele, Montresor, Marina, Berdalet, Elisa, Guillou, Laure, Campo, Javier del, Quast, C., Yilmaz, Pelin, and Vargas, Colomban de
- Abstract
The 18th International Conference on Harmful Algae (ICHA), From ecosystems to socio-ecosystems, 21-26 October 2018, Nantes, France.-- Networking activities around HABs: GlobalHAB, Global HAB Status report, ICES-WGs and other initiatives.-- 1 page, Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, and bacteriology, as well as their large research communities. Animals and plants have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for three decades under coherent molecular taxonomic frameworks. By contrast, no such common language exists yet for microbial eukaryotes / protists, even though environmental `omics´ surveys suggest that they make up most of the genetic complexity of our planet¿s ecosystems. With the current deluge of eukaryotic molecular data, we urgently need a universal eukaryotic taxonomy bridging the `protist-omics´ age to the fragile, centuries-old body of classical knowledge linking protist taxa to morphological, physiological, and ecological information. UniEuk (www.unieuk.org) is an open, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes, focused primarily on protists. The UniEuk system comprises 3 complementary modules allowing direct community input: - EukRef, a standardized, open-source bioinformatics pipeline that allows taxonomic curation of publicly available phylogenetic marker sequences (starting with 18S rDNA), generating homogeneous sets of curated, aligned sequences and phylogenetic trees. - EukBank, a public repository of high-throughput metabarcoding datasets (starting with the V4 region of 18S rDNA) that allows monitoring of total eukaryotic diversity (e.g. saturation, phylogeny) across biomes, and identification of ecologically relevant new lineages. - EukMap, a user-friendly representation of the taxonomic framework in the form of a publicly navigable tree, fully editable by registered users, where each node/taxon is associated with standardized features (name, contextual data, links to pictures and literature, etc.). As a whole, the UniEuk system represents a community hub to centralize, safeguard and promote our current global knowledge on eukaryotic diversity and evolution, integrating expert knowledge on morphology and ecology with key molecular information from phylogenetic markers and environmental metabarcoding surveys. The resulting taxonomy, which will include toxic microalgae, will be implemented into the European Nucleotide Archive at EMBL-EBI and propagated to NCBI, and useable as a stand-alone resource for scientific, educational, or public outreach purposes. In this communication, we will present the project in more detail, and explain how members of the HAB community can get involved, including a EukRef workshop focusing on dinoflagellates (5-9 Nov 2018, Roscoff, France). Overall, UniEuk will contribute to advances on key taxonomic challenges crucial to ascertain the biogeographic distribution, range of expansion, ecology and links with toxin production of relevant harmful species
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- 2018
73. Self-adhesive electrode applied to ZnO nanorod-based piezoelectric nanogenerators
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Yilmaz, Pelin, primary, Greenwood, Peter, additional, Meroni, Simone, additional, Troughton, Joel, additional, Novák, Petr, additional, Li, Xuan, additional, Watson, Trystan, additional, and Briscoe, Joe, additional
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- 2019
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74. Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework
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Henderson, Gemma, primary, Yilmaz, Pelin, additional, Kumar, Sandeep, additional, Forster, Robert J., additional, Kelly, William J., additional, Leahy, Sinead C., additional, Guan, Le Luo, additional, and Janssen, Peter H., additional
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- 2019
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75. The importance of designating type material for uncultured taxa
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Chuvochina, Maria, primary, Rinke, Christian, additional, Parks, Donovan H., additional, Rappé, Michael S., additional, Tyson, Gene W., additional, Yilmaz, Pelin, additional, Whitman, William B., additional, and Hugenholtz, Philip, additional
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- 2019
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76. Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research
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Rambold, Gerhard, primary, Yilmaz, Pelin, additional, Harjes, Janno, additional, Klaster, Sabrina, additional, Sanz, Veronica, additional, Link, Anton, additional, Glöckner, Frank Oliver, additional, and Triebel, Dagmar, additional
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- 2019
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77. MetaBar - a tool for consistent contextual data acquisition and standards compliant submission
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Kottmann Renzo, Fink Dennis, Buttigieg Pier, Hankeln Wolfgang, Yilmaz Pelin, and Glöckner Frank
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as metadata or contextual data. The consistent capture and structured submission of these data is crucial for integrated data analysis and ecosystems modeling. The application MetaBar has been developed, to support consistent contextual data acquisition. Results MetaBar is a spreadsheet and web-based software tool designed to assist users in the consistent acquisition, electronic storage, and submission of contextual data associated to their samples. A preconfigured Microsoft® Excel® spreadsheet is used to initiate structured contextual data storage in the field or laboratory. Each sample is given a unique identifier and at any stage the sheets can be uploaded to the MetaBar database server. To label samples, identifiers can be printed as barcodes. An intuitive web interface provides quick access to the contextual data in the MetaBar database as well as user and project management capabilities. Export functions facilitate contextual and sequence data submission to the International Nucleotide Sequence Database Collaboration (INSDC), comprising of the DNA DataBase of Japan (DDBJ), the European Molecular Biology Laboratory database (EMBL) and GenBank. MetaBar requests and stores contextual data in compliance to the Genomic Standards Consortium specifications. The MetaBar open source code base for local installation is available under the GNU General Public License version 3 (GNU GPL3). Conclusion The MetaBar software supports the typical workflow from data acquisition and field-sampling to contextual data enriched sequence submission to an INSDC database. The integration with the megx.net marine Ecological Genomics database and portal facilitates georeferenced data integration and metadata-based comparisons of sampling sites as well as interactive data visualization. The ample export functionalities and the INSDC submission support enable exchange of data across disciplines and safeguarding contextual data.
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- 2010
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78. A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences
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Yarza, Pablo, Yilmaz, Pelin, Panzer, Katrin, Glöckner, Frank Oliver, and Reich, Marlis
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- 2017
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79. Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream
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Boeckmann, Brigitte, Marcet Houben, Marina, Rees, Jonathan A., Forslund, Kristoffer, Huerta Cepas, Jaime, Muffato, Matthieu, Yilmaz, Pelin, Xenarios, Ioannis, Bork, Peer, Lewis, Suzanna E., Gabaldón Estevan, Juan Antonio, 1973, Quest for Orthologs Species Tree Working Group, and Quest for Orthologs Species Tree Working Group
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0106 biological sciences ,Gene tree support ,010603 evolutionary biology ,01 natural sciences ,Genome ,03 medical and health sciences ,Tree of Life ,species tree ,gene tree support ,Phylogenetics ,Genetics ,Clade ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Bacteria ,biology ,Phylogenetic tree ,Eukaryota ,Ribosomal RNA ,biology.organism_classification ,16S ribosomal RNA ,Archaea ,Laurasiatheria ,Genes ,Cardiovascular and Metabolic Diseases ,Evolutionary biology ,Taxonomy (biology) ,Species tree ,Genètica ,Research Article ,Evolució (Biologia) - Abstract
Quest for Orthologs (QfO) is a community effort with the goal to improve and benchmark orthology predictions. As quality assessment assumes prior knowledge on species phylogenies, we investigated the congruency between existing species trees by comparing the relationships of 147 QfO reference organisms from six Tree of Life (ToL)/species tree projects: The National Center for Biotechnology Information (NCBI) taxonomy, Opentree of Life, the sequenced species/species ToL, the 16S ribosomal RNA (rRNA) database, and trees published by Ciccarelli et al. (Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287) and by Huerta-Cepas et al. (Huerta-Cepas J, Marcet-Houben M, Gabaldon T. 2014. A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life. PeerJ PrePrints 2:223) Our study reveals that each species tree suggests a different phylogeny: 87 of the 146 (60%) possible splits of a dichotomous and rooted tree are congruent, while all other splits are incongruent in at least one of the species trees. Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids. The evolutionary relationships of 27 archaea and bacteria are highly inconsistent. By assessing 458,108 gene trees from 65 genomes, we show that consistent species topologies are more often supported by gene phylogenies than contradicting ones. The largest concordant species tree includes 77 of the QfO reference organisms at the most. Results are summarized in the form of a consensus ToL (http://swisstree.vital-it.ch/species_tree) that can serve different benchmarking purposes. This work was supported by the Swiss Federal Government through the Federal Office of Education and/nScience (B.B.). Funding for open access charge: Swiss Institute of Bioinformatics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. T.G. group research is funded in part by a grant from the Spanish ministry of Economy and Competitiveness (BIO2012-37161), a Grant from the Qatar National Research Fund (NPRP 5-298-3-086), and a grant from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC (grant agreement no. ERC-2012-StG-310325). M.M. acknowledges support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory.
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- 2015
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80. Minimum Information about an Uncultivated Virus Genome (MIUViG)
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Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, Eloe-fadrosh, Emiley A, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-fadrosh, Emiley A
- Abstract
We present an extension of the Minimum Information about any (x) Sequence (MIxS) standard for reporting sequences of uncultivated virus genomes. Minimum Information about an Uncultivated Virus Genome (MIUViG) standards were developed within the Genomic Standards Consortium framework and include virus origin, genome quality, genome annotation, taxonomic classification, biogeographic distribution and in silico host prediction. Community-wide adoption of MIUViG standards, which complement the Minimum Information about a Single Amplified Genome (MISAG) and Metagenome-Assembled Genome (MIMAG) standards for uncultivated bacteria and archaea, will improve the reporting of uncultivated virus genomes in public databases. In turn, this should enable more robust comparative studies and a systematic exploration of the global virosphere.
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- 2018
81. Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893)
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Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, other, and, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J.G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, and other, and
- Abstract
In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.
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- 2018
82. Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
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Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., Bowers, Robert M., Woyke, Tanja, Hugenholtz, Philip, Banfield, Jillian F., Schriml, Lynn, Eren, A. M., Parks, Donovan H., Yilmaz, Pelin, Meyer, Folker, Lapidus, Alla, Rinke, Christian, Tyson, Gene W., Karsch-Mizrachi, Ilene, Cochrane, Guy, Finn, Rob, Knight, Rob, Fierer, Noah, McMahon, Katherine D., Hedlund, Brian, Eisen, Jonathan A., Rattei, Thomas, Baker, Brett J., Liu, Wen-Tso, Konstantinidis, Konstantinos T., Tighe, Scott, Ettema, Thijs J. G., Jungbluth, Sean P., Hallam, Steven J., Nelson, William C., Gilbert, Jack A., Glockner, Frank O., Sutton, Granger, Yooseph, Shibu, Dodsworth, Jeremy A., Garrity, George M., Weinstock, George M., Bork, Peer, Podar, Mircea, Birren, Bruce, Malmstrom, Rex R., Becraft, Eric D., Clum, Alicia, Copeland, Alex, Ivanova, Natalia N., Tringe, Susannah G., Eloe-Fadrosh, Emiley A., Rivers, Adam R., Jarett, Jessica, Schulz, Frederik, Reddy, T. B. K., Doud, Devin, Harmon-Smith, Miranda, Stepanauskas, Ramunas, Kyrpides, Nikos C., and Bowers, Robert M.
- Abstract
Nat. Biotechnol. 35, 725–731 (2017); published online 8 August 2017; corrected after print 29 November 2017; corrected after print 7 December 2017 In the version of this article initially published, the author A. Murat Eren was listed as A.M. Eren. The corresponding affiliation was given as the Knapp Center for Biomedical Discovery, rather than Department of Medicine, University of Chicago, Chicago, Illinois, USA, and Marine Biological Laboratory, Woods Hole, Massachusetts, USA. The errors have been corrected in the HTML and PDF versions of the article as of 29 November 2017. In the version of this article initially published, the following acknowledgment was omitted: A.L. was supported by the Russian Science Foundation (grant number 14-50-00069). The error has been corrected in the HTML and PDF versions of the article as of 7 December 2017.
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- 2018
83. Minimum Information about an Uncultivated Virus Genome (MIUViG)
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Sub Bioinformatics, Theoretical Biology and Bioinformatics, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, Eloe-fadrosh, Emiley A, Sub Bioinformatics, Theoretical Biology and Bioinformatics, Roux, Simon, Adriaenssens, Evelien M, Dutilh, Bas E, Koonin, Eugene V, Kropinski, Andrew M, Krupovic, Mart, Kuhn, Jens H, Lavigne, Rob, Brister, J Rodney, Varsani, Arvind, Amid, Clara, Aziz, Ramy K, Bordenstein, Seth R, Bork, Peer, Breitbart, Mya, Cochrane, Guy R, Daly, Rebecca A, Desnues, Christelle, Duhaime, Melissa B, Emerson, Joanne B, Enault, François, Fuhrman, Jed A, Hingamp, Pascal, Hugenholtz, Philip, Hurwitz, Bonnie L, Ivanova, Natalia N, Labonté, Jessica M, Lee, Kyung-bum, Malmstrom, Rex R, Martinez-garcia, Manuel, Mizrachi, Ilene Karsch, Ogata, Hiroyuki, Páez-espino, David, Petit, Marie-agnès, Putonti, Catherine, Rattei, Thomas, Reyes, Alejandro, Rodriguez-valera, Francisco, Rosario, Karyna, Schriml, Lynn, Schulz, Frederik, Steward, Grieg F, Sullivan, Matthew B, Sunagawa, Shinichi, Suttle, Curtis A, Temperton, Ben, Tringe, Susannah G, Thurber, Rebecca Vega, Webster, Nicole S, Whiteson, Katrine L, Wilhelm, Steven W, Wommack, K Eric, Woyke, Tanja, Wrighton, Kelly C, Yilmaz, Pelin, Yoshida, Takashi, Young, Mark J, Yutin, Natalya, Allen, Lisa Zeigler, Kyrpides, Nikos C, and Eloe-fadrosh, Emiley A
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- 2018
84. Erratum: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
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Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M, Kyrpides, Nikos C, Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, TBK, Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A, Tringe, Susannah G, Ivanova, Natalia N, Copeland, Alex, Clum, Alicia, Becraft, Eric D, Malmstrom, Rex R, Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M, Garrity, George M, Dodsworth, Jeremy A, Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O, Gilbert, Jack A, Nelson, William C, Hallam, Steven J, Jungbluth, Sean P, Ettema, Thijs JG, Tighe, Scott, Konstantinidis, Konstantinos T, Liu, Wen-Tso, Baker, Brett J, Rattei, Thomas, Eisen, Jonathan A, Hedlund, Brian, McMahon, Katherine D, Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W, Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H, Eren, AM, Schriml, Lynn, Banfield, Jillian F, Hugenholtz, Philip, and Woyke, Tanja
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- 2018
85. Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus
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Füssel, Jessika, Lücker, S., Yilmaz, Pelin, Nowka, Boris, Kessel, M.A.H.J. van, Bourceau, Patric, Hach, Philipp F., Littmann, Sten, Berg, Jasmine, Spieck, Eva, Daims, Holger, Kuypers, Marcel M. M., and Lam, Phyllis
- Subjects
Ecological Microbiology ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) - Abstract
Nitrite-oxidizing bacteria (NOB) have conventionally been regarded as a highly specialized functional group responsible for the production of nitrate in the environment. However, recent culture-based studies suggest that they have the capacity to lead alternative lifestyles, but direct environmental evidence for the contribution of marine nitrite oxidizers to other processes has been lacking to date. We report on the alternative biogeochemical functions, worldwide distribution, and sometimes high abundance of the marine NOB Nitrococcus. These largely overlooked bacteria are capable of not only oxidizing nitrite but also reducing nitrate and producing nitrous oxide, an ozone-depleting agent and greenhouse gas. Furthermore, Nitrococcus can aerobically oxidize sulfide, thereby also engaging in the sulfur cycle. In the currently fast-changing global oceans, these findings highlight the potential functional switches these ubiquitous bacteria can perform in various biogeochemical cycles, each with distinct or even contrasting consequences.
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- 2017
86. THE LEGAL PROTECTION OF PREGNANT WORKERS AND WORKING MOTHERS ACCORDING TO TURKISH LABOUR LAW
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TUAÇ YILMAZ, PELİN
- Abstract
The number of women that participated in the labour market is increasing with every passing day. Besides, the request to control one's own individual preferences and also the amount of time is emerging. Thus, to raise their children employees have recess to their occupation or they want to have short time working. In this context, the new regulations brought to working life that get out of traditional approach, has become to ensure harmony in work and family life.
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- 2017
87. Effects os Spinning System on Properties of Tencel Micro Fibre Yarns
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GULGUN, YONCA, BALCI KILIÇ, GONCA, YILMAZ, PELİN, KILIÇ, MUSA, and DEMİR, MURAT
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- 2017
88. UniEuk: Time to speak a common language in protistology!
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Berney, Cedric, Ciuprina, Andreea, Bender, Sara, Brodie, Juliet, Edgcomb, Virginia, Kim, Eunsoo, Rajan, Jeena, Parfrey, Laura Wegener, Adl, Sina, Audic, Stephane, Bass, David, Caron, David A., Cochrane, Guy, Czech, Lucas, Dunthorn, Micah, Geisen, Stefan, Gloeckner, Frank Oliver, Mahe, Frederic, Quast, Christian, Kaye, Jonathan Z., Simpson, Alastair G. B., Stamatakis, Alexandros, del Campo, Javier, Yilmaz, Pelin, de Vargas, Colomban, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Jacobs University [Bremen], Gordon and Betty Moore Foundation, The Natural History Museum [London] (NHM), Woods Hole Oceanographic Institution (WHOI), Division of Invertebrate Zoology [New York], American Museum of Natural History (AMNH), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of British Columbia (UBC), College of Agriculture and Bioresources, University of Saskatchewan [Saskatoon] (U of S), University of Southern California (USC), Heidelberg Institute for Theoretical Studies (HITS ), Technical University of Kaiserslautern (TU Kaiserslautern), Wageningen University and Research [Wageningen] (WUR), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Dalhousie University [Halifax], Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), and Terrestrial Ecology (TE)
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Bacteria ,EukBank ,DATA processing & computer science ,Fungi ,000 - Autres thèmes ,Eukaryota ,Biodiversity ,Review Article ,Community expertise ,Environment ,Classification ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,[SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology ,diversity ,taxonomy ,Eukaryotic Cells ,eukaryotes ,EukMap ,international ,Animals ,EukRef ,ddc:004 ,Databases, Nucleic Acid ,Ecosystem ,Phylogeny - Abstract
International audience; Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho-taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukary-otes, even though environmental '-omics' surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist-omics age to the fragile, centuries-old body of classical knowledge that has effectively linked pro-tist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community-based and expert-driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL-EBI, ensuring its broad use and long-term preservation as a reference taxonomy for eukaryotes.
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- 2017
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89. Minimum Information about an Uncultivated Virus Genome (MIUViG)
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Roux, Simon, primary, Adriaenssens, Evelien M, additional, Dutilh, Bas E, additional, Koonin, Eugene V, additional, Kropinski, Andrew M, additional, Krupovic, Mart, additional, Kuhn, Jens H, additional, Lavigne, Rob, additional, Brister, J Rodney, additional, Varsani, Arvind, additional, Amid, Clara, additional, Aziz, Ramy K, additional, Bordenstein, Seth R, additional, Bork, Peer, additional, Breitbart, Mya, additional, Cochrane, Guy R, additional, Daly, Rebecca A, additional, Desnues, Christelle, additional, Duhaime, Melissa B, additional, Emerson, Joanne B, additional, Enault, François, additional, Fuhrman, Jed A, additional, Hingamp, Pascal, additional, Hugenholtz, Philip, additional, Hurwitz, Bonnie L, additional, Ivanova, Natalia N, additional, Labonté, Jessica M, additional, Lee, Kyung-Bum, additional, Malmstrom, Rex R, additional, Martinez-Garcia, Manuel, additional, Mizrachi, Ilene Karsch, additional, Ogata, Hiroyuki, additional, Páez-Espino, David, additional, Petit, Marie-Agnès, additional, Putonti, Catherine, additional, Rattei, Thomas, additional, Reyes, Alejandro, additional, Rodriguez-Valera, Francisco, additional, Rosario, Karyna, additional, Schriml, Lynn, additional, Schulz, Frederik, additional, Steward, Grieg F, additional, Sullivan, Matthew B, additional, Sunagawa, Shinichi, additional, Suttle, Curtis A, additional, Temperton, Ben, additional, Tringe, Susannah G, additional, Thurber, Rebecca Vega, additional, Webster, Nicole S, additional, Whiteson, Katrine L, additional, Wilhelm, Steven W, additional, Wommack, K Eric, additional, Woyke, Tanja, additional, Wrighton, Kelly C, additional, Yilmaz, Pelin, additional, Yoshida, Takashi, additional, Young, Mark J, additional, Yutin, Natalya, additional, Allen, Lisa Zeigler, additional, Kyrpides, Nikos C, additional, and Eloe-Fadrosh, Emiley A, additional
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- 2018
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90. Refining the taxonomic structure of the phylum Acidobacteria
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Dedysh, Svetlana N., primary and Yilmaz, Pelin, additional
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- 2018
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91. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- Author
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Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, Woyke, Tanja, Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P., Ettema, Thijs J. G., Tighe, Scott, Konstantinidis, Konstantinos T., Liu, Wen-Tso, Baker, Brett J., Rattei, Thomas, Eisen, Jonathan A., Hedlund, Brian, McMahon, Katherine D., Fierer, Noah, Knight, Rob, Finn, Rob, Cochrane, Guy, Karsch-Mizrachi, Ilene, Tyson, Gene W., Rinke, Christian, Lapidus, Alla, Meyer, Folker, Yilmaz, Pelin, Parks, Donovan H., Eren, A. M., Schriml, Lynn, Banfield, Jillian F., Hugenholtz, Philip, and Woyke, Tanja
- Abstract
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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- 2017
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92. The “Minimum Information about an ENvironmental Sequence” (MIENS) specification
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Sterk, Peter, Gordon, Jeffrey, White, Owen, Johnston, Anjanette, Nakielny, Sara, Weinstock, George, Arumugam, Mani, Guralnick, Robert, Neufeld, Josh, Wilke, Andreas, Cochrane, Guy, Nelson, Karen, Wendel, Doug, Baumgartner, Laura, Hugenholtz, Philip, Hankeln, Wolfgang, Pace, Norman, Wortmann, Jennifer, Nemergut, Diana, Bonazzi, Vivien, Birren, Bruce, Jansson, Janet, Highlander, Sarah, Palanisamy, Giriprakash, Glöckner, Frank Oliver, Bork, Peer, Blaser, Martin, Kennedy, Jerry, Peplies, Jörg, Knights, Dan, Peterson, Jane, Petrosino, Joseph, Buttigieg, Pier Luigi, Chain, Patrick, Koren, Omry, Costello, Elizabeth, Kuczynski, Justin, Proctor, Lita, Huot-Creasy, Heather, Kyrpides, Nikos, Raes, Jeroen, Dawyndt, Peter, Relman, David, Larsen, Robert, Ratnasingham, Sujeevan, Yilmaz, Pelin, DeSantis, Todd, Ley, Ruth, Assunta-Sansone, Susanna, Lauber, Christian, Ravel, Jacques, Gallery, Rachel, Kottmann, Renzo, Fierer, Noah, Lozupone, Catherine, Schriml, Lynn, Legg, Teresa, Vaughan, Robert, Gibbs, Richard, Field, Dawn, Fuhrman, Jed, Ludwig, Wolfgang, Sodergren, Erica, Knight, Rob, Giglio, Michelle Gwinn, Lyons, Donna, Spor, Aymé, Hunter, Christopher, Maguire, Eamonn, Cole, James, Stombaugh, Jesse, San Gil, Inigo, Park, Joonhong, Amaral-Zettler, Linda, Tiedje, James, Methé, Barbara, Gilbert, Jack, Glass, Elizabeth, Morrison, Norman, Meyer, Folker, Karsch-Mizrachi, Ilene, Gonzalez, Antonio, Rocca-Serra, Phillipe, and Ward, Doyle
- Published
- 2010
- Full Text
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93. The “Minimum Information about an ENvironmental Sequence” (MIENS) specification
- Author
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Yilmaz, Pelin, Kottmann, Renzo, Field, Dawn, Knight, Rob, Cole, James, Amaral-Zettler, Linda, Gilbert, Jack, Karsch-Mizrachi, Ilene, Johnston, Anjanette, Cochrane, Guy, Vaughan, Robert, Hunter, Christopher, Park, Joonhong, Morrison, Norman, Rocca-Serra, Phillipe, Sterk, Peter, Arumugam, Mani, Baumgartner, Laura, Birren, Bruce, Blaser, Martin, Bonazzi, Vivien, Bork, Peer, Buttigieg, Pier Luigi, Chain, Patrick, Costello, Elizabeth, Huot-Creasy, Heather, Dawyndt, Peter, DeSantis, Todd, Fierer, Noah, Fuhrman, Jed, Gallery, Rachel, Gibbs, Richard, Giglio, Michelle Gwinn, San Gil, Inigo, Glass, Elizabeth, Gonzalez, Antonio, Gordon, Jeffrey, Guralnick, Robert, Hankeln, Wolfgang, Highlander, Sarah, Hugenholtz, Philip, Jansson, Janet, Kennedy, Jerry, Knights, Dan, Koren, Omry, Kuczynski, Justin, Kyrpides, Nikos, Larsen, Robert, Lauber, Christian, Legg, Teresa, Ley, Ruth, Lozupone, Catherine, Ludwig, Wolfgang, Lyons, Donna, Maguire, Eamonn, Methé, Barbara, Meyer, Folker, Nakielny, Sara, Nelson, Karen, Nemergut, Diana, Neufeld, Josh, Pace, Norman, Palanisamy, Giriprakash, Peplies, Jörg, Peterson, Jane, Petrosino, Joseph, Proctor, Lita, Raes, Jeroen, Ratnasingham, Sujeevan, Ravel, Jacques, Relman, David, Assunta-Sansone, Susanna, Schriml, Lynn, Sodergren, Erica, Spor, Aymé, Stombaugh, Jesse, Tiedje, James, Ward, Doyle, Weinstock, George, Wendel, Doug, White, Owen, Wilke, Andreas, Wortmann, Jennifer, and Glöckner, Frank Oliver
- Published
- 2010
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94. Probleme Dayalı Senaryoların 9. Sınıf Öğrencilerinin Kimya Dersine Olan Tutumlarına, Laboratuvar Kaygılarına ve Problem Çözme Algılarına Etkisi
- Author
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KARATAŞ, Faik Özgür and YILMAZ, Pelin
- Abstract
Günümüzde, öğrencilerin bilgiye araştırarak ulaşmaları, olaylara eleştirel yaklaşmaları ve olaylar karşısında fikir üretebilmeleri beklenmektedir. PISA sonuçları her alanda ama özellikle de fen alanında maalesef ülkemiz için iç açıcı bir durumda değildir. Özellikle üst düzey zihinsel beceriler ve problem çözmeye yönelik sorularda öğrencilerimizin oldukça başarısız olduğu görülmektedir. Öğrenme ortamının ve öğretim materyallerinin üst düzey becerileri geliştirecek şekilde düzenlenmesi gerekmektedir. Senaryo temelli öğrenme öğrencilerin problem çözme becerilerini geliştiren, hayatın örgün eğitim ortamına taşınmasını sağlayan ve öğrencilerin süreçte aktif rol almalarına imkân tanıyan yöntemlerden biridir. Yapılan çalışmada, çalışma yapraklarıyla desteklenen probleme dayalı senaryoların 9.sınıf öğrencilerinin kimya dersine olan tutumlarına, laboratuvarı kullanmadan kaynaklı kaygılarına ve problem çözme algılarına etkisi incelenmiştir. Yapılan t-testi ile yapılan uygulamanın hiçbir değişken üzerinden manidar bir farklılık meydana getirmediği bulunmuştur ancak gözlem ve mülakatlarda olumlu yönde ki gelişmeler de dikkat çekmiştir.
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- 2016
95. MOESM1 of BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology
- Author
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Hardisty, Alex, Bacall, Finn, Beard, Niall, Maria-Paula Balcázar-Vargas, Balech, Bachir, Barcza, Zoltán, Bourlat, Sarah, Giovanni, Renato, Jong, Yde, Leo, Francesca, Dobor, Laura, Donvito, Giacinto, Fellows, Donal, Guerra, Antonio, Ferreira, Nuno, Fetyukova, Yuliya, Fosso, Bruno, Giddy, Jonathan, Goble, Carole, Güntsch, Anton, Haines, Robert, Ernst, Vera, Hettling, Hannes, Hidy, Dóra, Horváth, Ferenc, Ittzés, Dóra, Ittzés, Péter, Jones, Andrew, Kottmann, Renzo, Kulawik, Robert, Leidenberger, Sonja, Lyytikäinen-Saarenmaa, Päivi, Cherian Mathew, Morrison, Norman, Nenadic, Aleksandra, Hidalga, Abraham, Obst, Matthias, Oostermeijer, Gerard, Paymal, Elisabeth, Pesole, Graziano, Pinto, Salvatore, Poigné, Axel, Fernandez, Francisco, Santamaria, Monica, Saarenmaa, Hannu, Sipos, Gergely, Karl-Heinz Sylla, Tähtinen, Marko, Vicario, Saverio, Vos, Rutger, Williams, Alan, and Yilmaz, Pelin
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Data_FILES ,GeneralLiterature_MISCELLANEOUS - Abstract
Additional file 1. ‘How-to’ guidelines for the biodiversity virtual e-laboratory.
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- 2016
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96. SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees
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Beccati, Alan, primary, Gerken, Jan, additional, Quast, Christian, additional, Yilmaz, Pelin, additional, and Glöckner, Frank Oliver, additional
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- 2017
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97. Metadata Standards for Genomic Sequence Data: Past and Future of MIxS Standards Family
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Yilmaz, Pelin, primary
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- 2017
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98. Photoelectrocatalysis of Rhodamine B and Solar Hydrogen Production by TiO 2 and Pd/TiO 2 Catalyst Systems
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Yilmaz, Pelin, primary, Lacerda, Armando Marsden, additional, Larrosa, Igor, additional, and Dunn, Steve, additional
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- 2017
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99. Minimum Information about a Biosynthetic Gene cluster: commentary
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Medema, Marnix H, Kottmann, Renzo, Yilmaz, Pelin, Cummings, Matthew, Biggins, John B, Blin, Kai, de Bruijn, Irene, Chooi, Yit Heng, Claesen, Jan, Coates, R Cameron, Cruz-Morales, Pablo, Duddela, Srikanth, Dusterhus, Stephanie, Edwards, Daniel J, Fewer, David P, Garg, Neha, Geiger, Christoph, Gomez-Escribano, Juan Pablo, Greule, Anja, Hadjithomas, Michalis, Haines, Anthony S, Helfrich, Eric J N, Hillwig, Matthew L, Ishida, Keishi, Jones, Adam C, Jones, Carla S, Jungmann, Katrin, Kegler, Carsten, Kim, Hyun Uk, Kotter, Peter, Krug, Daniel, Masschelein, Joleen, Melnik, Alexey V, Mantovani, Simone M, Monroe, Emily A, Moore, Marcus, Moss, Nathan, Nutzmann, Hans-Wilhelm, Pan, Guohui, Pati, Amrita, Petras, Daniel, Reen, F Jerry, Rosconi, Federico, Rui, Zhe, Tian, Zhenhua, Tobias, Nicholas J, Tsunematsu, Yuta, Wiemann, Philipp, Wyckoff, Elizabeth, Yan, Xiaohui, Yim, Grace, Yu, Fengan, Xie, Yunchang, Aigle, Bertrand, Apel, Alexander K, Balibar, Carl J, Balskus, Emily P, Barona-Gomez, Francisco, Bechthold, Andreas, Bode, Helge B, Borriss, Rainer, Brady, Sean F, Brakhage, Axel A, Caffrey, Patrick, Cheng, Yi-Qiang, Clardy, Jon, Cox, Russell J, De Mot, Rene, Donadio, Stefano, Donia, Mohamed S, van der Donk, Wilfred A, Dorrestein, Pieter C, Doyle, Sean, Driessen, Arnold J M, Ehling-Schulz, Monika, Entian, Karl-Dieter, Fischbach, Michael A, Gerwick, Lena, Gerwick, William H, Gross, Harald, Gust, Bertolt, Hertweck, Christian, Hofte, Monica, Jensen, Susan E, Ju, Jianhua, Katz, Leonard, Kaysser, Leonard, Klassen, Jonathan L, Keller, Nancy P, Kormanec, Jan, Kuipers, Oscar P, Kuzuyama, Tomohisa, Kyrpides, Nikos C, Kwon, Hyung-Jin, Lautru, Sylvie, Lavigne, Rob, Lee, Chia Y, Linquan, Bai, Liu, Xinyu, Liu, Wen, Luzhetskyy, Andriy, Mahmud, Taifo, Mast, Yvonne, Mendez, Carmen, Metsa-Ketela, Mikko, Micklefield, Jason, Mitchell, Douglas A, Moore, Bradley S, Moreira, Leonilde M, Muller, Rolf, Neilan, Brett A, Nett, Markus, Nielsen, Jens, O'Gara, Fergal, Oikawa, Hideaki, Osbourn, Anne, Osburne, Marcia S, Ostash, Bohdan, Payne, Shelley M, Pernodet, Jean-Luc, Petricek, Miroslav, Piel, Jorn, Ploux, Olivier, Raaijmakers, Jos M, Salas, Jose A, Schmitt, Esther K, Scott, Barry, Seipke, Ryan F, Shen, Ben, Sherman, David H, Sivonen, Kaarina, Smanski, Michael J, Sosio, Margherita, Stegmann, Evi, Sussmuth, Roderich D, Tahlan, Kapil, Thomas, Christopher M, Tang, Yi, Truman, Andrew W, Viaud, Muriel, Walton, Jonathan D, Walsh, Christopher T, Weber, Tilmann, van Wezel, Gilles P, Wilkinson, Barrie, Willey, Joanne M, Wohlleben, Wolfgang, Wright, Gerard D, Ziemert, Nadine, Zhang, Changsheng, Zotchev, Sergey B, Breitling, Rainer, Takano, Eriko, Glockner, Frank Oliver, and Microbial Ecology (ME)
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international - Abstract
A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.
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- 2015
100. In vitro biological activities and fatty acid profiles of Pistacia terebinthus fruits and Pistacia khinjuk seeds
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Hacibekiroglu, IŞIL, Yilmaz, Pelin Koseoglu, Hasimi, Nesrin, Kilinc, Ersin, Tolan, Veysel, Kolak, Ufuk, and GAZİOĞLU, IŞIL
- Subjects
food and beverages ,Hacibekiroglu I., Yilmaz P. K. , Hasimi N., Kilinc E., Tolan V., Kolak U., -In vitro biological activities and fatty acid profiles of Pistacia terebinthus fruits and Pistacia khinjuk seeds-, NATURAL PRODUCT RESEARCH, cilt.29, ss.444-446, 2015 - Abstract
This study reports in vitro anticholinesterase, antioxidant and antimicrobial effects of the n-hexane, dichloromethane, ethanol and ethanol-water extracts prepared from Pistacia terebinthus L. fruits and Pistacia khinjuk Stocks seeds as well as their total phenolic and flavonoid contents, and fatty acid compositions. Ethanol and ethanol-water extracts of both species exhibited higher anticholinesterase activity than galanthamine. Among ABTS, DPPH and CUPRAC assays, the highest antioxidant capacity of the extracts was found in the last one. P. terebinthus ethanol extract being rich in flavonoid content showed the best cupric reducing effect. All extracts possessed no antimicrobial activity. The main fatty acid in P. terebinthus fruits (52.52%) and P. khinjuk seeds (59.44%) was found to be oleic acid. Our results indicate that P. terebinthus fruits and P. khinjuk seeds could be a good source of anticholinesterase compounds, and could be phytochemically investigated. İstanbul Üniversitesi
- Published
- 2015
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