Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs von Musacchia, Francesco, Basu, Swaraj, Petrosino, Giuseppe, Salvemini, Marco, Sanges, Remo

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Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom von Basu, Swaraj, Patil, Shrikant, Mapleson, Daniel, Russo, Monia Teresa, Vitale, Laura, Fevola, Cristina, Maumus, Florian, Casotti, Raffaella, Mock, Thomas, Caccamo, Mario, Montresor, Marina, Sanges, Remo, Ferrante, Maria Immacolata

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Copy-choice recombination during mitochondrial L-strand synthesis causes DNA deletions von Persson, Örjan, Muthukumar, Yazh, Basu, Swaraj, Jenninger, Louise, Uhler, Jay P., Berglund, Anna-Karin, McFarland, Robert, Taylor, Robert W., Gustafsson, Claes M., Larsson, Erik, Falkenberg, Maria

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Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing von Basu, Swaraj, Xie, Xie, Uhler, Jay P., Hedberg-Oldfors, Carola, Milenkovic, Dusanka, Baris, Olivier R., Kimoloi, Sammy, Matic, Stanka, Stewart, James B., Larsson, Nils-Goran, Wiesner, Rudolf J., Oldfors, Anders, Gustafsson, Claes M., Falkenberg, Maria, Larsson, Erik

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Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution von Van den Eynden, Jimmy, Basu, Swaraj, Larsson, Erik

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A Catalogue of Putative cis -Regulatory Interactions Between Long Non-coding RNAs and Proximal Coding Genes Based on Correlative Analysis Across Diverse Human Tumors von Basu, Swaraj, Larsson, Erik

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Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain von Petrosino, Giuseppe, Ponte, Giovanna, Volpe, Massimiliano, Zarrella, Ilaria, Ansaloni, Federico, Langella, Concetta, Di Cristina, Giulia, Finaurini, Sara, Russo, Monia T, Basu, Swaraj, Musacchia, Francesco, Ristoratore, Filomena, Pavlinic, Dinko, Benes, Vladimir, Ferrante, Maria I, Albertin, Caroline, Simakov, Oleg, Gustincich, Stefano, Fiorito, Graziano, Sanges, Remo

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Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulato... von Ashraf, Nasheeman, Ghai, Deepali, Barman, Pranjan, Basu, Swaraj, Gangisetty, Nagaraju, Mandal, Mihir K, Chakraborty, Niranjan, Datta, Asis, Chakraborty, Subhra

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Tissue- and Cell Type-Specific Expression of the Long Noncoding RNA Klhl14-AS in Mouse von De Felice, Mario, de Vita, Gabriella, Sanges, Remo, Di Guida, Luigi, Amendola, Elena, D’Andrea, Barbara, Basu, Swaraj, de Oliveira, Miriane, Lewin, Nicole, Credendino, Sara Carmela, Nardone, Antonio

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Mitochondrial DNA variants in inclusion body myositis characterized by deep sequencing von Hedberg‐Oldfors, Carola, Lindgren, Ulrika, Basu, Swaraj, Visuttijai, Kittichate, Lindberg, Christopher, Falkenberg, Maria, Larsson Lekholm, Erik, Oldfors, Anders

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Deorphanization of novel biogenic amine-gated ion channels identifies a new serotonin receptor for learning von Morud, Julia, Hardege, Iris, Liu, He, Wu, Taihong, Choi, Myung-Kyu, Basu, Swaraj, Zhang, Yun, Schafer, William R.

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Deorphanization of novel biogenic amine-gated ion channels identifies a new serotonin receptor for learning von Morud, Julia, Hardege, Iris, Liu, He, Wu, Taihong, Choi, Myung-Kyu, Basu, Swaraj, Zhang, Yun, Schafer, William R

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Topoisomerase 3α Is Required for Decatenation and Segregation of Human mtDNA von Nicholls, Thomas J., Nadalutti, Cristina A., Motori, Elisa, Sommerville, Ewen W., Gorman, Gráinne S., Basu, Swaraj, Hoberg, Emily, Turnbull, Doug M., Chinnery, Patrick F., Larsson, Nils-Göran, Larsson, Erik, Falkenberg, Maria, Taylor, Robert W., Griffith, Jack D., Gustafsson, Claes M.

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Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis von Baba, Shoib Ahmad, Mohiuddin, Tabasum, Basu, Swaraj, Swarnkar, Mohit Kumar, Malik, Aubid Hussain, Wani, Zahoor Ahmed, Abbas, Nazia, Singh, Anil Kumar, Ashraf, Nasheeman

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DamID transcriptional profiling identifies the Snail/Scratch transcription factor Kahuli as an Alk target in the Drosophila visceral mesoderm von Mendoza-Garcia, Patricia, Basu, Swaraj, Sukumar, Sanjay Kumar, Arefin, Badrul, Wolfstetter, Georg, Anthonydhason, Vimala, Molander, Linnea, Uckun, Ezgi, Lindehell, Henrik, Lebrero-Fernandez, Cristina, Larsson, Jan, Larsson, Erik, Bemark, Mats, Palmer, Ruth H.

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Examples of sequence conservation analyses capture a subset of mouse long non-coding RNAs sharing homology with fish conserved genomic elements von Basu, Swaraj, Müller, Ferenc, Sanges, Remo

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A ceRNA Circuitry Involving the Long Noncoding RNA Klhl14-AS, Pax8, and Bcl2 Drives Thyroid Carcinogenesis von Credendino, Sara C, Bellone, Maria L, Lewin, Nicole, Amendola, Elena, Sanges, Remo, Basu, Swaraj, Sepe, Romina, Decaussin-Petrucci, Myriam, Tinto, Nadia, Fusco, Alfredo, De Felice, Mario, De Vita, Gabriella

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VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database von Musacchia, F, Ciolfi, A, Mutarelli, M, Bruselles, A, Castello, R, Pinelli, M, Basu, S, Banfi, S, Casari, G, Tartaglia, M, Nigro, V

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Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi von Amato, Alberto, Sabatino, Valeria, Nylund, Göran M., Bergkvist, Johanna, Basu, Swaraj, Andersson, Mats X., Sanges, Remo, Godhe, Anna, Kiørboe, Thomas, Selander, Erik, Ferrante, Maria I.

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Integrative network analyses of wilt transcriptome in chickpea reveal genotype dependent regulatory hubs in immunity and susceptibility von Ashraf, Nasheeman, Basu, Swaraj, Narula, Kanika, Ghosh, Sudip, Tayal, Rajul, Gangisetty, Nagaraju, Biswas, Sushmita, Aggarwal, Pooja R., Chakraborty, Niranjan, Chakraborty, Subhra

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