WormBase 2014: new views of curated biology

by Harris, Todd W, Baran, Joachim, Bieri, Tamberlyn, Cabunoc, Abigail, Chan, Juancarlos, Chen, Wen J, Davis, Paul, Done, James, Grove, Christian, Howe, Kevin, Kishore, Ranjana, Lee, Raymond, Li, Yuling, Muller, Hans-Michael, Nakamura, Cecilia, Ozersky, Philip, Paulini, Michael, Raciti, Daniela, Schindelman, Gary, Tuli, Mary Ann, Van Auken, Kimberly, Wang, Daniel, Wang, Xiaodong, Williams, Gary, Wong, J D, Yook, Karen, Schedl, Tim, Hodgkin, Jonathan, Berriman, Matthew, Kersey, Paul, Spieth, John, Stein, Lincoln, Sternberg, Paul W
Published in Nucleic acids research

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

by Dumontier, Michel, Baker, Christopher Jo, Baran, Joachim, Callahan, Alison, Chepelev, Leonid, Cruz-Toledo, José, Del Rio, Nicholas R, Duck, Geraint, Furlong, Laura I, Keath, Nichealla, Klassen, Dana, McCusker, James P, Queralt-Rosinach, Núria, Samwald, Matthias, Villanueva-Rosales, Natalia, Wilkinson, Mark D, Hoehndorf, Robert
Published in Journal of biomedical semantics

pubmed2ensembl: a resource for mining the biological literature on genes

by Baran, Joachim, Gerner, Martin, Haeussler, Maximilian, Nenadic, Goran, Bergman, Casey M
Published in PloS one

The health care and life sciences community profile for dataset descriptions

by Dumontier, Michel, Gray, Alasdair J G, Marshall, M Scott, Alexiev, Vladimir, Ansell, Peter, Bader, Gary, Baran, Joachim, Bolleman, Jerven T, Callahan, Alison, Cruz-Toledo, José, Gaudet, Pascale, Gombocz, Erich A, Gonzalez-Beltran, Alejandra N, Groth, Paul, Haendel, Melissa, Ito, Maori, Jupp, Simon, Juty, Nick, Katayama, Toshiaki, Kobayashi, Norio, Krishnaswami, Kalpana, Laibe, Camille, Le Novère, Nicolas, Lin, Simon, Malone, James, Miller, Michael, Mungall, Christopher J, Rietveld, Laurens, Wimalaratne, Sarala M, Yamaguchi, Atsuko
Published in PeerJ (San Francisco, CA)

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

by Bolleman, Jerven T, Mungall, Christopher J, Strozzi, Francesco, Baran, Joachim, Dumontier, Michel, Bonnal, Raoul J P, Buels, Robert, Hoehndorf, Robert, Fujisawa, Takatomo, Katayama, Toshiaki, Cock, Peter J A
Published in Journal of biomedical semantics

GFVO: the Genomic Feature and Variation Ontology

by Baran, Joachim, Durgahee, Bibi Sehnaaz Begum, Eilbeck, Karen, Antezana, Erick, Hoehndorf, Robert, Dumontier, Michel
Published in PeerJ (San Francisco, CA)

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

by Zhang, Junjun, Baran, Joachim, Cros, A, Guberman, Jonathan M, Haider, Syed, Hsu, Jack, Liang, Yong, Rivkin, Elena, Wang, Jianxin, Whitty, Brett, Wong-Erasmus, Marie, Yao, Long, Kasprzyk, Arek
Published in Database : the journal of biological databases and curation

BioMart Central Portal: an open database network for the biological community

by Guberman, Jonathan M, Ai, J, Arnaiz, O, Baran, Joachim, Blake, Andrew, Baldock, Richard, Chelala, Claude, Croft, David, Cros, Anthony, Cutts, Rosalind J, Di Génova, A, Forbes, Simon, Fujisawa, T, Gadaleta, E, Goodstein, D M, Gundem, Gunes, Haggarty, Bernard, Haider, Syed, Hall, Matthew, Harris, Todd, Haw, Robin, Hu, S, Hubbard, Simon, Hsu, Jack, Iyer, Vivek, Jones, Philip, Katayama, Toshiaki, Kinsella, R, Kong, Lei, Lawson, Daniel, Liang, Yong, Lopez-Bigas, Nuria, Luo, J, Lush, Michael, Mason, Jeremy, Moreews, Francois, Ndegwa, Nelson, Oakley, Darren, Perez-Llamas, Christian, Primig, Michael, Rivkin, Elena, Rosanoff, S, Shepherd, Rebecca, Simon, Reinhard, Skarnes, B, Smedley, Damian, Sperling, Linda, Spooner, William, Stevenson, Peter, Stone, Kevin, Teague, J, Wang, Jun, Wang, Jianxin, Whitty, Brett, Wong, D T, Wong-Erasmus, Marie, Yao, L, Youens-Clark, Ken, Yung, Christina, Zhang, Junjun, Kasprzyk, Arek
Published in Database : the journal of biological databases and curation

BioMart: a data federation framework for large collaborative projects

by Zhang, Junjun, Haider, Syed, Baran, Joachim, Cros, Anthony, Guberman, Jonathan M, Hsu, Jack, Liang, Yong, Yao, Long, Kasprzyk, Arek
Published in Database : the journal of biological databases and curation

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

by Bolleman, Jerven T., Mungall, Christopher J., Strozzi, Francesco, Baran, Joachim, Dumontier, Michel, Bonnal, Raoul J. P., Buels, Robert, Hoehndorf, Robert, Fujisawa, Takatomo, Katayama, Toshiaki, Cock, Peter J. A.
Published in Journal of biomedical semantics

BioMart: a data federation framework for large collaborative projects

by Zhang, J., Haider, S., Baran, J., Cros, A., Guberman, J. M., Hsu, J., Liang, Y., Yao, L., Kasprzyk, A.
Published in Database : the journal of biological databases and curation

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services [version 1; peer review: 2 approved with reservations]

by Katayama, Toshiaki, Kawashima, Shuichi, Micklem, Gos, Kawano, Shin, Kim, Jin-Dong, Kocbek, Simon, Okamoto, Shinobu, Wang, Yue, Wu, Hongyan, Yamaguchi, Atsuko, Yamamoto, Yasunori, Antezana, Erick, Aoki-Kinoshita, Kiyoko F., Arakawa, Kazuharu, Banno, Masaki, Baran, Joachim, Bolleman, Jerven T., Bonnal, Raoul J. P., Bono, Hidemasa, Fernández-Breis, Jesualdo T., Buels, Robert, Campbell, Matthew P., Chiba, Hirokazu, Cock, Peter J. A., Cohen, Kevin B., Dumontier, Michel, Fujisawa, Takatomo, Fujiwara, Toyofumi, Garcia, Leyla, Gaudet, Pascale, Hattori, Emi, Hoehndorf, Robert, Itaya, Kotone, Ito, Maori, Jamieson, Daniel, Jupp, Simon, Juty, Nick, Kalderimis, Alex, Kato, Fumihiro, Kawaji, Hideya, Kawashima, Takeshi, Kinjo, Akira R., Komiyama, Yusuke, Kotera, Masaaki, Kushida, Tatsuya, Malone, James, Matsubara, Masaaki, Mizuno, Satoshi, Mizutani, Sayaka, Mori, Hiroshi, Moriya, Yuki, Murakami, Katsuhiko, Nakazato, Takeru, Nishide, Hiroyo, Nishimura, Yosuke, Ogishima, Soichi, Ohta, Tazro, Okuda, Shujiro, Ono, Hiromasa, Perez-Riverol, Yasset, Shinmachi, Daisuke, Splendiani, Andrea, Strozzi, Francesco, Suzuki, Shinya, Takehara, Junichi, Thompson, Mark, Tokimatsu, Toshiaki, Uchiyama, Ikuo, Verspoor, Karin, Wilkinson, Mark D., Wimalaratne, Sarala, Yamada, Issaku, Yamamoto, Nozomi, Yarimizu, Masayuki, Kawamoto, Shoko, Takagi, Toshihisa
Published in F1000 research

The health care and life sciences community profile for dataset descriptions

by Dumontier, Michel, Gray, Alasdair J G, Marshall, M Scott, Alexiev, Vladimir, Ansell, Peter, Bader, Gary D, Baran, Joachim, Bolleman, Jerven T, Callahan, Alison, Cruz-Toledo, José, Gaudet, Pascale, Gombocz, Erich A, Gonzalez Beltran, Alejandra N, Groth, Paul, Haendel, Melissa, Ito, Maori, Jupp, Simon, Juty, Nick, Katayama, Toshiaki, Kobayashi, Norio, Krishnaswami, Kalpana, Laibe, Camille, Nicolas Le Novère, Lin, Simon, Malone, James, Miller, Michael, Mungall, Chris, Rietveld, Laurens, Wimalaratne, Sarala M, Yamaguchi, Atsuko
Published in PeerJ preprints

GFVO: the Genomic Feature and Variation Ontology

by Baran, Joachim, Durgahee, Bibi Sehnaaz, Eilbeck, Karen, Antezana, Erick, Hoehndorf, Robert, Dumontier, Michel

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

by Katayama, Toshiaki, Wilkinson, Mark D, Aoki-Kinoshita, Kiyoko F, Kawashima, Shuichi, Yamamoto, Yasunori, Yamaguchi, Atsuko, Okamoto, Shinobu, Kawano, Shin, Kim, Jin-Dong, Wang, Yue, Wu, Hongyan, Kano, Yoshinobu, Ono, Hiromasa, Bono, Hidemasa, Kocbek, Simon, Aerts, Jan, Akune, Yukie, Antezana, Erick, Arakawa, Kazuharu, Aranda, Bruno, Baran, Joachim, Bolleman, Jerven, Bonnal, Raoul J. P, Buttigieg, Pier Luigi, Campbell, Matthew P, Chen, Yi-an, Chiba, Hirokazu, Cock, Peter J. A, Cohen, K. Bretonnel, Constantin, Alexandru, Duck, Geraint, Dumontier, Michel, Fujisawa, Takatomo, Fujiwara, Toyofumi, Goto, Naohisa, Hoehndorf, Robert, Igarashi, Yoshinobu, Itaya, Hidetoshi, Ito, Maori, Iwasaki, Wataru, Kalaš, Matúš, Katoda, Takeo, Kim, Taehong, Kokubu, Anna, Komiyama, Yusuke, Kotera, Masaaki, Laibe, Camille, Lapp, Hilmar, Lütteke, Thomas, Marshall, M. Scott, Mori, Takaaki, Mori, Hiroshi, Morita, Mizuki, Murakami, Katsuhiko, Nakao, Mitsuteru, Narimatsu, Hisashi, Nishide, Hiroyo, Nishimura, Yosuke, Nyström-Persson, Johan, Ogishima, Soichi, Okamura, Yasunobu, Okuda, Shujiro, Oshita, Kazuki, Packer, Nicki H, Prins, Pjotr, Ranzinger, Rene, Rocca-Serra, Philippe, Sansone, Susanna, Sawaki, Hiromichi, Shin, Sung-Ho, Splendiani, Andrea, Strozzi, Francesco, Tadaka, Shu, Toukach, Philip, Uchiyama, Ikuo, Umezaki, Masahito, Vos, Rutger, Whetzel, Patricia L, Yamada, Issaku, Yamasaki, Chisato, Yamashita, Riu, York, William S, Zmasek, Christian M, Kawamoto, Shoko, Takagi, Toshihisa

Genomic Analysis of Non-NF2 Meningiomas Reveals Mutations in TRAF7, KLF4, AKT1, and SMO

by Clark, Victoria E., Erson-Omay, E. Zeynep, Serin, Akdes, Yin, Jun, Cotney, Justin, Özduman, Koray, Avşar, Timuçin, Li, Jie, Murray, Phillip B., Henegariu, Octavian, Yilmaz, Saliha, Günel, Jennifer Moliterno, Carrión-Grant, Geneive, Yılmaz, Baran, Grady, Conor, Tanrıkulu, Bahattin, Bakırcıoǧlu, Mehmet, Kaymakçalan, Hande, Caglayan, Ahmet Okay, Sencar, Leman, Ceyhun, Emre, Atik, A. Fatih, Bayri, Yaşar, Bai, Hanwen, Kolb, Luis E., Hebert, Ryan M., Omay, S. Bulent, Mishra-Gorur, Ketu, Choi, Murim, Overton, John D., Holland, Eric C., Mane, Shrikant, State, Matthew W., Bilgüvar, Kaya, Baehring, Joachim M., Gutin, Philip H., Piepmeier, Joseph M., Vortmeyer, Alexander, Brennan, Cameron W., Pamir, M. Necmettin, Kılıç, Türker, Lifton, Richard P., Noonan, James P., Yasuno, Katsuhito, Günel, Murat
Published in Science (American Association for the Advancement of Science)

Free volume in physical absorption of carbon dioxide in ionic liquids: Molecular dynamics supported modeling

by Eichenlaub, Joachim, Baran, Karol, Śmiechowski, Maciej, Kloskowski, Adam
Published in Separation and purification technology

Minimal Interleukin 6 (IL-6) Receptor Stalk Composition for IL-6 Receptor Shedding and IL-6 Classic Signaling

by Baran, Paul, Nitz, Rebecca, Grötzinger, Joachim, Scheller, Jürgen, Garbers, Christoph
Published in The Journal of biological chemistry

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

by Bernardes, Joana P., Tran, Florian, Best, Lena, Bordoni, Dora, Josephs-Spaulding, Jonathan, Köhler, Philipp, Künstner, Axel, Rosati, Elisa, Bacher, Petra, Bruse, Niklas, Franzenburg, Sören, Frey, Norbert, Fuß, Janina, Glück, Andreas, Hamm, Jacob, Imm, Simon, Kaiser, Sina, Lange, Christoph, Laue, Georg, Marinos, Georgios, Pickkers, Peter, Rabe, Klaus F., Renz, Alina, Röcken, Christoph, Rupp, Jan, Schaffarzyk, Annika, Scheffold, Alexander, Schulte-Schrepping, Jonas, Skowasch, Dirk, Ulas, Thomas, Wandinger, Klaus-Peter, Wittig, Michael, Zimmermann, Johannes, Busch, Hauke, Hoyer, Bimba F., Kaleta, Christoph, Heyckendorf, Jan, Rybniker, Jan, Schultze, Joachim L., Rosenstiel, Philip, Banovich, Nicholas E., Desai, Tushar, Eickelberg, Oliver, Haniffa, Muzlifa, Horvath, Peter, Kropski, Jonathan A., Lafyatis, Robert, Meyer, Kerstin, Nawijn, Martijn C., Nikolic, Marko, Ordovas Montanes, Jose, Pe’er, Dana, Tata, Purushothama Rao, Rawlins, Emma, Regev, Aviv, Reyfman, Paul, Samakovlis, Christos, Schultze, Joachim, Shalek, Alex, Shepherd, Douglas, Spence, Jason, Theis, Fabian, van den Berge, Maarten, von Papen, Michael, Whitsett, Jeffrey, Angelov, Angel, Bals, Robert, Bonifacio, Ezio, Colme-Tatche, Maria, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Gagneur, Julien, Goesmann, Alexander, Kallies, René, Kehr, Birte, Keller, Andreas, Kim-Hellmuth, Sarah, Korbel, Jan O., Kurth, Ingo, Landthaler, Markus, Li, Yang, Ludwig, Kerstin, Makarewicz, Oliwia, Nöthen, Markus, Nürnberg, Peter, Ohler, Uwe, Overmann, Jörg, Peter, Silke, Pfeffer, Klaus, Poetsch, Anna R., Rajewsky, Niklaus, Ralser, Markus, Saliba, Antoine-Emmanuel, Schulte, Eva-Christina, Sczyrba, Alexander, Stegle, Oliver, Stoye, Jens, von Kleist, Max, Walker, Andreas
Published in Immunity

The Multifaceted Roles of Mast Cells in Immune Homeostasis, Infections and Cancers

by Sobiepanek, Anna, Kuryk, Łukasz, Garofalo, Mariangela, Kumar, Sandeep, Baran, Joanna, Musolf, Paulina, Siebenhaar, Frank, Fluhr, Joachim Wilhelm, Kobiela, Tomasz, Plasenzotti, Roberto, Kuchler, Karl, Staniszewska, Monika
Published in International journal of molecular sciences