BIO
Research Group Computational Biology

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1. Berzow D, Descamps D, Obermeier M, Charpentier C, Kaiser R, Guertler L, Eberle J, Wensing A, Sierra S, Ruelle J, Gomes P, Mansinho K, Taylor N, Jensen B, Döring M, Stürmer M, Rockstroh J, Camacho R: Human Immunodeficiency Virus-2 (HIV-2): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with HIV-2 in Western Europe. Clinical Infectious Diseases 2021, 72.
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@article{Berzow2021, TITLE = {Human Immunodeficiency Virus-2 ({HIV-2}): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with {HIV}-2 in {Western Europe}}, AUTHOR = {Berzow, Dirk and Descamps, Diane and Obermeier, Martin and Charpentier, Charlotte and Kaiser, Rolf and Guertler, Lutz and Eberle, Josef and Wensing, Annemarie and Sierra, Saleta and Ruelle, Jean and Gomes, Perpetua and Mansinho, Kamal and Taylor, Ninon and Jensen, Bj{\"o}rn and D{\"o}ring, Matthias and St{\"u}rmer, Martin and Rockstroh, J{\"u}rgen and Camacho, Ricardo}, LANGUAGE = {eng}, ISSN = {1058-4838}, DOI = {10.1093/cid/ciaa275}, PUBLISHER = {The University of Chicago Press}, ADDRESS = {Chicago, IL}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, JOURNAL = {Clinical Infectious Diseases}, VOLUME = {72}, NUMBER = {3}, PAGES = {503--509}, }
Endnote
%0 Journal Article %A Berzow, Dirk %A Descamps, Diane %A Obermeier, Martin %A Charpentier, Charlotte %A Kaiser, Rolf %A Guertler, Lutz %A Eberle, Josef %A Wensing, Annemarie %A Sierra, Saleta %A Ruelle, Jean %A Gomes, Perpetua %A Mansinho, Kamal %A Taylor, Ninon %A Jensen, Björn %A Döring, Matthias %A Stürmer, Martin %A Rockstroh, Jürgen %A Camacho, Ricardo %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Human Immunodeficiency Virus-2 (HIV-2): A Summary of the Present Standard of Care and Treatment Options for Individuals Living with HIV-2 in Western Europe : %G eng %U http://hdl.handle.net/21.11116/0000-0008-8DEF-D %R 10.1093/cid/ciaa275 %7 2021 %D 2021 %J Clinical Infectious Diseases %V 72 %N 3 %& 503 %P 503 - 509 %I The University of Chicago Press %C Chicago, IL %@ false
2. Drews F, Karunanithi S, Gätz U, Marker S, deWijn R, Pirritano M, Rodrigues-Viana AM, Jung M, Gasparoni G, Schulz MH, Simon M: Two Piwis with Ago-like Functions Silence Somatic Genes at the Chromatin Level. RNA Biology 2021.
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@article{Drews2021, TITLE = {Two {P}iwis with {A}go-like Functions Silence Somatic Genes at the Chromatin Level}, AUTHOR = {Drews, Franziska and Karunanithi, Sivarajan and G{\"a}tz, Ulrike and Marker, Simone and deWijn, Raphael and Pirritano, Marcello and Rodrigues-Viana, Angela M. and Jung, Martin and Gasparoni, Gilles and Schulz, Marcel Holger and Simon, Martin}, LANGUAGE = {eng}, ISSN = {1547-6286}, DOI = {10.1080/15476286.2021.1991114}, PUBLISHER = {Taylor \& Francis}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {RNA Biology}, PAGES = {1--13}, }
Endnote
%0 Journal Article %A Drews, Franziska %A Karunanithi, Sivarajan %A Gätz, Ulrike %A Marker, Simone %A deWijn, Raphael %A Pirritano, Marcello %A Rodrigues-Viana, Angela M. %A Jung, Martin %A Gasparoni, Gilles %A Schulz, Marcel Holger %A Simon, Martin %+ External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Two Piwis with Ago-like Functions Silence Somatic Genes at the Chromatin Level : %G eng %U http://hdl.handle.net/21.11116/0000-0009-70B4-D %R 10.1080/15476286.2021.1991114 %7 2021 %D 2021 %J RNA Biology %& 1 %P 1 - 13 %I Taylor & Francis %@ false
3. Durai DA: Novel graph based algorithms fortranscriptome sequence analysis. Universität des Saarlandes; 2021.
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@phdthesis{Duraiphd2020, TITLE = {Novel graph based algorithms fortranscriptome sequence analysis}, AUTHOR = {Durai, Dilip Ariyur}, LANGUAGE = {eng}, DOI = {10.22028/D291-34158}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, }
Endnote
%0 Thesis %A Durai, Dilip Ariyur %Y Schulz, Marcel %A referee: Helms, Volker %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T Novel graph based algorithms fortranscriptome sequence analysis : %G eng %U http://hdl.handle.net/21.11116/0000-0008-E4D6-5 %R 10.22028/D291-34158 %I Universität des Saarlandes %C Saarbrücken %D 2021 %P 143 p. %V phd %9 phd %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/31478
4. Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, et al.: Haplotype-resolved Diverse Human Genomes and Integrated Analysis of Structural Variation. Science 2021, 372.
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@article{Ebert2021, TITLE = {Haplotype-resolved Diverse Human Genomes and Integrated Analysis of Structural Variation}, AUTHOR = {Ebert, Peter and Audano, Peter A. and Zhu, Qihui and Rodriguez-Martin, Bernardo and Porubsky, David and Bonder, Marc Jan and Sulovari, Arvis and Ebler, Jana and Zhou, Weichen and Serra Mari, Rebecca and Yilmaz, Feyza and Zhao, Xuefang and Hsieh, PingHsun and Lee, Joyce and Kumar, Sushant and Lin, Jiadong and Rausch, Tobias and Chen, Yu and Ren, Jingwen and Santamarina, Martin and H{\"o}ps, Wolfram and Ashraf, Hufsah and Chuang, Nelson T. and Yang, Xiaofei and Munson, Katherine M. and Lewis, Alexandra P. and Fairley, Susan and Tallon, Luke J. and Clarke, Wayne E. and Basile, Anna O. and Byrska-Bishop, Marta and Corvelo, Andr{\'e} and Evani, Uday S. and Lu, Tsung-Yu and Chaisson, Mark J. P. and Chen, Junjie and Li, Chong and Brand, Harrison and Wenger, Aaron M. and Ghareghani, Maryam and Harvey, William T. and Raeder, Benjamin and Hasenfeld, Patrick and Regier, Allison A. and Abel, Haley J. and Hall, Ira M. and Flicek, Paul and Stegle, Oliver and Gerstein, Mark B. and Tubio, Jose M. C. and Mu, Zepeng and Li, Yang I. and Shi, Xinghua and Hastie, Alex R. and Ye, Kai and Chong, Zechen and Sanders, Ashley D. and Zody, Michael C. and Talkowski, Michael E. and Mills, Ryan E. and Devine, Scott E. and Lee, Charles and Korbel, Jan O. and Marschall, Tobias and Eichler, Evan E.}, LANGUAGE = {eng}, ISSN = {0036-8075}, DOI = {10.1126/science.abf7117}, PUBLISHER = {AAAS}, ADDRESS = {Washington, D.C.}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, JOURNAL = {Science}, VOLUME = {372}, NUMBER = {6537}, EID = {eabf7117}, }
Endnote
%0 Journal Article %A Ebert, Peter %A Audano, Peter A. %A Zhu, Qihui %A Rodriguez-Martin, Bernardo %A Porubsky, David %A Bonder, Marc Jan %A Sulovari, Arvis %A Ebler, Jana %A Zhou, Weichen %A Serra Mari, Rebecca %A Yilmaz, Feyza %A Zhao, Xuefang %A Hsieh, PingHsun %A Lee, Joyce %A Kumar, Sushant %A Lin, Jiadong %A Rausch, Tobias %A Chen, Yu %A Ren, Jingwen %A Santamarina, Martin %A Höps, Wolfram %A Ashraf, Hufsah %A Chuang, Nelson T. %A Yang, Xiaofei %A Munson, Katherine M. %A Lewis, Alexandra P. %A Fairley, Susan %A Tallon, Luke J. %A Clarke, Wayne E. %A Basile, Anna O. %A Byrska-Bishop, Marta %A Corvelo, André %A Evani, Uday S. %A Lu, Tsung-Yu %A Chaisson, Mark J. P. %A Chen, Junjie %A Li, Chong %A Brand, Harrison %A Wenger, Aaron M. %A Ghareghani, Maryam %A Harvey, William T. %A Raeder, Benjamin %A Hasenfeld, Patrick %A Regier, Allison A. %A Abel, Haley J. %A Hall, Ira M. %A Flicek, Paul %A Stegle, Oliver %A Gerstein, Mark B. %A Tubio, Jose M. C. %A Mu, Zepeng %A Li, Yang I. %A Shi, Xinghua %A Hastie, Alex R. %A Ye, Kai %A Chong, Zechen %A Sanders, Ashley D. %A Zody, Michael C. %A Talkowski, Michael E. %A Mills, Ryan E. %A Devine, Scott E. %A Lee, Charles %A Korbel, Jan O. %A Marschall, Tobias %A Eichler, Evan E. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T Haplotype-resolved Diverse Human Genomes and Integrated Analysis of Structural Variation : %G eng %U http://hdl.handle.net/21.11116/0000-0008-BFCA-E %R 10.1126/science.abf7117 %7 2021 %D 2021 %J Science %O Science %V 372 %N 6537 %Z sequence number: eabf7117 %I AAAS %C Washington, D.C. %@ false
5. Ebert P, Schulz MH: Fast Detection of Differential Chromatin Domains with SCIDDO. Bioinformatics 2021, 37.
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@article{Ebert2021b, TITLE = {Fast detection of differential chromatin domains with {SCIDDO}}, AUTHOR = {Ebert, Peter and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btaa960}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, JOURNAL = {Bioinformatics}, VOLUME = {37}, NUMBER = {9}, PAGES = {1198--1205}, }
Endnote
%0 Journal Article %A Ebert, Peter %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Fast Detection of Differential Chromatin Domains with SCIDDO : %G eng %U http://hdl.handle.net/21.11116/0000-0008-D98D-5 %R 10.1093/bioinformatics/btaa960 %2 PMC818969 %7 2021 %D 2021 %J Bioinformatics %V 37 %N 9 %& 1198 %P 1198 - 1205 %I Oxford University Press %C Oxford %@ false
6. Fischer J, Ardakani FB, Kattler K, Walter J, Schulz MH: CpG Content-dependent Associations between Transcription Factors and Histone Modifications. PLoS One 2021, 16.
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@article{fischer:21:cpgtfhm, TITLE = {{CpG} content-dependent associations between transcription factors and histone modifications}, AUTHOR = {Fischer, Jonas and Ardakani, Fatemeh Behjati and Kattler, Kathrin and Walter, J{\"o}rn and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0249985}, PUBLISHER = {Public Library of Science}, ADDRESS = {San Francisco, CA}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {PLoS One}, VOLUME = {16}, NUMBER = {4}, EID = {0249985}, }
Endnote
%0 Journal Article %A Fischer, Jonas %A Ardakani, Fatemeh Behjati %A Kattler, Kathrin %A Walter, Jörn %A Schulz, Marcel Holger %+ Databases and Information Systems, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T CpG Content-dependent Associations between Transcription Factors and Histone Modifications : %G eng %U http://hdl.handle.net/21.11116/0000-0008-5602-5 %R 10.1371/journal.pone.0249985 %7 2021 %D 2021 %J PLoS One %V 16 %N 4 %Z sequence number: 0249985 %I Public Library of Science %C San Francisco, CA %@ false
7. Forster J: Real-time human performance capture and synthesis. Universität des Saarlandes; 2021.
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@phdthesis{Forsterphd2020, TITLE = {Real-time human performance capture and synthesis}, AUTHOR = {Forster, Jan}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, }
Endnote
%0 Thesis %A Forster, Jan %Y Theobalt, Christian %A referee: Seidel, Hans-Peter %A referee: Hilton, Adrian %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computer Graphics, MPI for Informatics, Max Planck Society Computer Graphics, MPI for Informatics, Max Planck Society External Organizations %T Real-time human performance capture and synthesis : %G eng %U http://hdl.handle.net/21.11116/0000-0009-7D87-3 %I Universität des Saarlandes %C Saarbrücken %D 2021 %P 153 p. %V phd %9 phd
8. Kitanovski S, Horemheb-Rubio G, Adams O, Gärtner B, Lengauer T, Hoffmann D, Kaiser R: Rhinovirus Prevalence as Indicator for Efficacy of Measures against SARS-CoV-2. BMC Public Health 2021, 21.
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@article{Kitaovski2021, TITLE = {Rhinovirus Prevalence as Indicator for Efficacy of Measures against {SARS}-{CoV}-2}, AUTHOR = {Kitanovski, Simo and Horemheb-Rubio, Gibran and Adams, Ortwin and G{\"a}rtner, Barbara and Lengauer, Thomas and Hoffmann, Daniel and Kaiser, Rolf and {Respiratory Virus Network}}, LANGUAGE = {eng}, ISSN = {1471-2458}, DOI = {10.1186/s12889-021-11178-w}, PUBLISHER = {BioMed Central}, ADDRESS = {London, United Kingdom}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {BMC Public Health}, VOLUME = {21}, EID = {1178}, }
Endnote
%0 Journal Article %A Kitanovski, Simo %A Horemheb-Rubio, Gibran %A Adams, Ortwin %A Gärtner, Barbara %A Lengauer, Thomas %A Hoffmann, Daniel %A Kaiser, Rolf %A Respiratory Virus Network, %+ External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Rhinovirus Prevalence as Indicator for Efficacy of Measures against SARS-CoV-2 : %G eng %U http://hdl.handle.net/21.11116/0000-0008-D984-E %R 10.1186/s12889-021-11178-w %2 PMC8215636 %7 2021 %D 2021 %J BMC Public Health %V 21 %Z sequence number: 1178 %I BioMed Central %C London, United Kingdom %@ false
9. Lazareva O, Baumbach J, List M, Blumenthal DB: On the Limits of Active Module Identification. Briefings in Bioinformatics 2021, 22.
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@article{10.1093/bib/bbab066, TITLE = {On the Limits of Active Module Identification}, AUTHOR = {Lazareva, Olga and Baumbach, Jan and List, Markus and Blumenthal, David B.}, LANGUAGE = {eng}, ISSN = {1467-5463}, PUBLISHER = {H. Stewart Publications}, ADDRESS = {London}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {Briefings in Bioinformatics}, VOLUME = {22}, NUMBER = {5}, EID = {bbab066}, }
Endnote
%0 Journal Article %A Lazareva, Olga %A Baumbach, Jan %A List, Markus %A Blumenthal, David B. %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T On the Limits of Active Module Identification : %G eng %U http://hdl.handle.net/21.11116/0000-0009-7E65-9 %7 2021 %D 2021 %J Briefings in Bioinformatics %V 22 %N 5 %Z sequence number: bbab066 %I H. Stewart Publications %C London %@ false
10. Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, et al.: A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved]. F1000Research 2021, 8.
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@article{Llamas2021, TITLE = {A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved]}, AUTHOR = {Llamas, B. and Narzisi, G. and Schneider, V. and Audano, P. A. and Biederstedt, E. and Blauvelt, L. and Bradbury, P. and Chang, X. and Chin, C. S. and Fungtammasan, A. and Clarke, W. E. and Cleary, A. and Ebler, Jana and Eizenga, J. and Sibbesen, J. A. and Markello, C. J. and Garrison, E. and Garg, S. and Hickey, G. and Lazo, G. R. and Lin, M. F. and Mahmoud, M. and Marschall, T. and Minkin, I. and Monlong, J. and Musunuri, R. L. and Sagayaradj, S. and Novak, A. M. and Rautiainen, M. and Regier, A. and Sedlazeck, F. J. and Siren, J. and Souilmi, Y. and Wagner, J. and Wrightsman, T. and Yokoyama, T. T. and Zeng, Q. and Zook, J. M. and Paten, B. and Busby, B.}, LANGUAGE = {eng}, ISSN = {2046-1402}, DOI = {10.12688/f1000research.19630.2}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {F1000Research}, VOLUME = {8}, EID = {1751}, }
Endnote
%0 Journal Article %A Llamas, B. %A Narzisi, G. %A Schneider, V. %A Audano, P. A. %A Biederstedt, E. %A Blauvelt, L. %A Bradbury, P. %A Chang, X. %A Chin, C. S. %A Fungtammasan, A. %A Clarke, W. E. %A Cleary, A. %A Ebler, Jana %A Eizenga, J. %A Sibbesen, J. A. %A Markello, C. J. %A Garrison, E. %A Garg, S. %A Hickey, G. %A Lazo, G. R. %A Lin, M. F. %A Mahmoud, M. %A Marschall, T. %A Minkin, I. %A Monlong, J. %A Musunuri, R. L. %A Sagayaradj, S. %A Novak, A. M. %A Rautiainen, M. %A Regier, A. %A Sedlazeck, F. J. %A Siren, J. %A Souilmi, Y. %A Wagner, J. %A Wrightsman, T. %A Yokoyama, T. T. %A Zeng, Q. %A Zook, J. M. %A Paten, B. %A Busby, B. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T A Strategy for Building and Using a Human Reference Pangenome [Version 2; Peer Review: 2 approved] : %G eng %U http://hdl.handle.net/21.11116/0000-0009-2A58-6 %R 10.12688/f1000research.19630.2 %7 2021 %D 2021 %J F1000Research %O F1000Research %V 8 %Z sequence number: 1751 %I BioMed Central %C London %@ false
11. Marty N, Saeng-Aroon S, Heger E, Thielen A, Obermeier M, Pfeifer N, Kaiser R, Klimkait T: Adapting the Geno2pheno[coreceptor] Tool to HIV-1 Subtype CRF01_AE by Phenotypic Validation Using Clinical Isolates from South-East Asia. Journal of Clinical Virology 2021, 136.
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@article{Marty_2021, TITLE = {Adapting the geno2pheno[coreceptor] tool to {HIV}-1 subtype {CRF01_AE} by phenotypic validation using clinical isolates from {South-East Asia}}, AUTHOR = {Marty, Nina and Saeng-Aroon, Siriphan and Heger, Eva and Thielen, Alexander and Obermeier, Martin and Pfeifer, Nico and Kaiser, Rolf and Klimkait, Thomas}, LANGUAGE = {eng}, ISSN = {1386-6532}, DOI = {10.1016/j.jcv.2021.104755}, PUBLISHER = {Elsevier}, ADDRESS = {Amsterdam}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, JOURNAL = {Journal of Clinical Virology}, VOLUME = {136}, EID = {104755}, }
Endnote
%0 Journal Article %A Marty, Nina %A Saeng-Aroon, Siriphan %A Heger, Eva %A Thielen, Alexander %A Obermeier, Martin %A Pfeifer, Nico %A Kaiser, Rolf %A Klimkait, Thomas %+ External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations %T Adapting the Geno2pheno[coreceptor] Tool to HIV-1 Subtype CRF01_AE by Phenotypic Validation Using Clinical Isolates from South-East Asia : %G eng %U http://hdl.handle.net/21.11116/0000-0008-62DD-1 %R 10.1016/j.jcv.2021.104755 %7 2021 %D 2021 %J Journal of Clinical Virology %V 136 %Z sequence number: 104755 %I Elsevier %C Amsterdam %@ false
12. Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T, Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Roettger R, Schwaemmle V, Sturm G, Traverso A, Van Steen K, de Freitas MV, Villalba Silva GC, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB: The AIMe Registry for Artificial Intelligence in Biomedical Research. Nature Methods 2021, Early Access.
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@article{Matschinske2021, TITLE = {The {AIMe} Registry for Artificial Intelligence in Biomedical Research}, AUTHOR = {Matschinske, Julian and Alcaraz, Nicolas and Benis, Arriel and Golebiewski, Martin and Grimm, Dominik G. and Heumos, Lukas and Kacprowski, Tim and Lazareva, Olga and List, Markus and Louadi, Zakaria and Pauling, Josch K. and Pfeifer, Nico and Roettger, Richard and Schwaemmle, Veit and Sturm, Gregor and Traverso, Alberto and Van Steen, Kristel and de Freitas, Martiela Vaz and Villalba Silva, Gerda Cristal and Wee, Leonard and Wenke, Nina K. and Zanin, Massimiliano and Zolotareva, Olga and Baumbach, Jan and Blumenthal, David B.}, LANGUAGE = {eng}, ISSN = {1548-7091}, DOI = {10.1038/s41592-021-01241-0}, PUBLISHER = {Nature Pub. Group}, ADDRESS = {New York, NY}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Methods}, VOLUME = {Early Access}, }
Endnote
%0 Journal Article %A Matschinske, Julian %A Alcaraz, Nicolas %A Benis, Arriel %A Golebiewski, Martin %A Grimm, Dominik G. %A Heumos, Lukas %A Kacprowski, Tim %A Lazareva, Olga %A List, Markus %A Louadi, Zakaria %A Pauling, Josch K. %A Pfeifer, Nico %A Roettger, Richard %A Schwaemmle, Veit %A Sturm, Gregor %A Traverso, Alberto %A Van Steen, Kristel %A de Freitas, Martiela Vaz %A Villalba Silva, Gerda Cristal %A Wee, Leonard %A Wenke, Nina K. %A Zanin, Massimiliano %A Zolotareva, Olga %A Baumbach, Jan %A Blumenthal, David B. %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations %T The AIMe Registry for Artificial Intelligence in Biomedical Research : %G eng %U http://hdl.handle.net/21.11116/0000-0009-259D-D %R 10.1038/s41592-021-01241-0 %7 2021 %D 2021 %J Nature Methods %O Nature Methods %V Early Access %I Nature Pub. Group %C New York, NY %@ false
13. Mattonet K, Nowack-Weyers N, Vogel V, Moser D, Tierling S, Kasper-Sonnenberg M, Wilhelm M, Scherer M, Walter J, Hengstler JG, Schölmerich A, Kumsta R: Prenatal Exposure to Endocrine Disrupting Chemicals is Associated with Altered DNA Methylation in Cord Blood. Epigenetics 2021.
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@article{Mattonet2021, TITLE = {Prenatal exposure to endocrine disrupting chemicals is associated with altered {DNA} methylation in cord blood}, AUTHOR = {Mattonet, Katharina and Nowack-Weyers, Nikola and Vogel, Vanessa and Moser, Dirk and Tierling, Sascha and Kasper-Sonnenberg, Monika and Wilhelm, Michael and Scherer, Michael and Walter, J{\"o}rn and Hengstler, Jan G. and Sch{\"o}lmerich, Axel and Kumsta, Robert}, LANGUAGE = {eng}, ISSN = {1559-2294}, DOI = {10.1080/15592294.2021.1975917}, PUBLISHER = {Taylor \& Francis}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {Epigenetics}, }
Endnote
%0 Journal Article %A Mattonet, Katharina %A Nowack-Weyers, Nikola %A Vogel, Vanessa %A Moser, Dirk %A Tierling, Sascha %A Kasper-Sonnenberg, Monika %A Wilhelm, Michael %A Scherer, Michael %A Walter, Jörn %A Hengstler, Jan G. %A Schölmerich, Axel %A Kumsta, Robert %+ External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations %T Prenatal Exposure to Endocrine Disrupting Chemicals is Associated with Altered DNA Methylation in Cord Blood : %G eng %U http://hdl.handle.net/21.11116/0000-0009-49E8-0 %R 10.1080/15592294.2021.1975917 %7 2021 %D 2021 %J Epigenetics %I Taylor & Francis %@ false
14. Metzler S: Structural Building Blocks in Graph Data. Universität des Saarlandes; 2021.
Abstract
Graph data nowadays easily become so large that it is infeasible to study the underlying structures manually. Thus, computational methods are needed to uncover large-scale structural information. In this thesis, we present methods to understand and summarise large networks. We propose the hyperbolic community model to describe groups of more densely connected nodes within networks using very intuitive parameters. The model accounts for a frequent connectivity pattern in real data: a few community members are highly interconnected; most members mainly have ties to this core. Our model fits real data much better than previously-proposed models. Our corresponding random graph generator, HyGen, creates graphs with realistic intra-community structure. Using the hyperbolic model, we conduct a large-scale study of the temporal evolution of communities on online question–answer sites. We observe that the user activity within a community is constant with respect to its size throughout its lifetime, and a small group of users is responsible for the majority of the social interactions. We propose an approach for Boolean tensor clustering. This special tensor factorisation is restricted to binary data and assumes that one of the tensor directions has only non-overlapping factors. These assumptions – valid for many real-world data, in particular time-evolving networks – enable the use of bitwise operators and lift much of the computational complexity from the task.
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@phdthesis{SaskiaDiss21, TITLE = {Structural Building Blocks in Graph Data}, AUTHOR = {Metzler, Saskia}, LANGUAGE = {eng}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, ABSTRACT = {Graph data nowadays easily become so large that it is infeasible to study the underlying structures manually. Thus, computational methods are needed to uncover large-scale structural information. In this thesis, we present methods to understand and summarise large networks. We propose the hyperbolic community model to describe groups of more densely connected nodes within networks using very intuitive parameters. The model accounts for a frequent connectivity pattern in real data: a few community members are highly interconnected; most members mainly have ties to this core. Our model fits real data much better than previously-proposed models. Our corresponding random graph generator, HyGen, creates graphs with realistic intra-community structure. Using the hyperbolic model, we conduct a large-scale study of the temporal evolution of communities on online question--answer sites. We observe that the user activity within a community is constant with respect to its size throughout its lifetime, and a small group of users is responsible for the majority of the social interactions. We propose an approach for Boolean tensor clustering. This special tensor factorisation is restricted to binary data and assumes that one of the tensor directions has only non-overlapping factors. These assumptions -- valid for many real-world data, in particular time-evolving networks -- enable the use of bitwise operators and lift much of the computational complexity from the task.}, }
Endnote
%0 Thesis %A Metzler, Saskia %Y Miettinen, Pauli %Y Weikum, Gerhard %Y Günnemann, Stephan %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society External Organizations %T Structural Building Blocks in Graph Data : Characterised by Hyperbolic Communities and Uncovered by Boolean Tensor Clustering %G eng %U http://hdl.handle.net/21.11116/0000-0008-0BC1-2 %I Universität des Saarlandes %C Saarbrücken %D 2021 %P 196 p. %V phd %9 phd %X Graph data nowadays easily become so large that it is infeasible to study the underlying structures manually. Thus, computational methods are needed to uncover large-scale structural information. In this thesis, we present methods to understand and summarise large networks. We propose the hyperbolic community model to describe groups of more densely connected nodes within networks using very intuitive parameters. The model accounts for a frequent connectivity pattern in real data: a few community members are highly interconnected; most members mainly have ties to this core. Our model fits real data much better than previously-proposed models. Our corresponding random graph generator, HyGen, creates graphs with realistic intra-community structure. Using the hyperbolic model, we conduct a large-scale study of the temporal evolution of communities on online question–answer sites. We observe that the user activity within a community is constant with respect to its size throughout its lifetime, and a small group of users is responsible for the majority of the social interactions. We propose an approach for Boolean tensor clustering. This special tensor factorisation is restricted to binary data and assumes that one of the tensor directions has only non-overlapping factors. These assumptions – valid for many real-world data, in particular time-evolving networks – enable the use of bitwise operators and lift much of the computational complexity from the task. %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/30904
15. Rautiainen M, Marschall T: MBG: Minimizer-based Sparse de Bruijn Graph Construction. Bioinformatics 2021, 37.
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@article{Rautiainen2021, TITLE = {{MBG}: {M}inimizer-based sparse de {B}ruijn {G}raph construction}, AUTHOR = {Rautiainen, Mikko and Marschall, Tobias}, LANGUAGE = {eng}, ISSN = {1367-4803}, DOI = {10.1093/bioinformatics/btab004}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, JOURNAL = {Bioinformatics}, VOLUME = {37}, NUMBER = {16}, PAGES = {2476--2478}, }
Endnote
%0 Journal Article %A Rautiainen, Mikko %A Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations %T MBG: Minimizer-based Sparse de Bruijn Graph Construction : %G eng %U http://hdl.handle.net/21.11116/0000-0009-617C-F %R 10.1093/bioinformatics/btab004 %7 2021 %D 2021 %J Bioinformatics %V 37 %N 16 %& 2476 %P 2476 - 2478 %I Oxford University Press %C Oxford %@ false
16. Scherer M, Schmidt F, Lazareva O, Walter J, Baumbach J, Schulz MH, List M: Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation. Nature Computational Science 2021, 1.
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@article{Scherer2021, TITLE = {Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation}, AUTHOR = {Scherer, Michael and Schmidt, Florian and Lazareva, Olga and Walter, J{\"o}rn and Baumbach, Jan and Schulz, Marcel Holger and List, Markus}, LANGUAGE = {eng}, ISSN = {2662-8457}, DOI = {10.1038/s43588-021-00038-7}, PUBLISHER = {Nature Research}, ADDRESS = {London}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {Nature Computational Science}, VOLUME = {1}, }
Endnote
%0 Journal Article %A Scherer, Michael %A Schmidt, Florian %A Lazareva, Olga %A Walter, Jörn %A Baumbach, Jan %A Schulz, Marcel Holger %A List, Markus %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Machine Learning for Deciphering Cell Heterogeneity and Gene Regulation : %G eng %U http://hdl.handle.net/21.11116/0000-0008-2A4A-7 %R 10.1038/s43588-021-00038-7 %7 2021 %D 2021 %J Nature Computational Science %V 1 %I Nature Research %C London %@ false
17. Scherer M: Computational solutions for addressing heterogeneity in DNA methylation data. Universität des Saarlandes; 2021.
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@phdthesis{Schererphd2020, TITLE = {Computational solutions for addressing heterogeneity in {DNA} methylation data}, AUTHOR = {Scherer, Michael}, LANGUAGE = {eng}, DOI = {10.22028/D291-33808}, SCHOOL = {Universit{\"a}t des Saarlandes}, ADDRESS = {Saarbr{\"u}cken}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, }
Endnote
%0 Thesis %A Scherer, Michael %Y Lengauer, Thomas %A referee: Walther, Jörn %A referee: Marschall, Tobias %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society International Max Planck Research School, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Computational solutions for addressing heterogeneity in DNA methylation data : %G eng %U http://hdl.handle.net/21.11116/0000-0008-BA18-C %R 10.22028/D291-33808 %I Universität des Saarlandes %C Saarbrücken %D 2021 %P 147 p. %V phd %9 phd %U https://publikationen.sulb.uni-saarland.de/handle/20.500.11880/31186
18. Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J: Identification of Tissue-specific and Common Methylation Quantitative Trait Loci in Healthy Individuals Using MAGAR. Epigenetics & Chromatin 2021, 14.
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@article{Scherer2021b, TITLE = {Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using {MAGAR}}, AUTHOR = {Scherer, Michael and Gasparoni, Gilles and Rahmouni, Souad and Shashkova, Tatiana and Arnoux, Marion and Louis, Edouard and Nostaeva, Arina and Avalos, Diana and Dermitzakis, Emmanouil T. and Aulchenko, Yurii S. and Lengauer, Thomas and Lyons, Paul A. and Georges, Michel and Walter, J{\"o}rn}, LANGUAGE = {eng}, DOI = {10.1186/s13072-021-00415-6}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {Epigenetics \& Chromatin}, VOLUME = {14}, EID = {44}, }
Endnote
%0 Journal Article %A Scherer, Michael %A Gasparoni, Gilles %A Rahmouni, Souad %A Shashkova, Tatiana %A Arnoux, Marion %A Louis, Edouard %A Nostaeva, Arina %A Avalos, Diana %A Dermitzakis, Emmanouil T. %A Aulchenko, Yurii S. %A Lengauer, Thomas %A Lyons, Paul A. %A Georges, Michel %A Walter, Jörn %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Identification of Tissue-specific and Common Methylation Quantitative Trait Loci in Healthy Individuals Using MAGAR : %G eng %U http://hdl.handle.net/21.11116/0000-0009-42C0-3 %R 10.1186/s13072-021-00415-6 %7 2021 %D 2021 %J Epigenetics & Chromatin %V 14 %Z sequence number: 44 %I BioMed Central %C London
19. Scherer M, Gasparoni G, Rahmouni S, Shashkova T, Arnoux M, Louis E, Nostaeva A, Avalos D, Dermitzakis ET, Aulchenko YS, Lengauer T, Lyons PA, Georges M, Walter J: Identification of Tissue-specific and Common Methylation Quantitative Trait Loci in Healthy Individuals using MAGAR. Epigenetics & Chromatin 2021, 14.
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@article{Scherer2021, TITLE = {Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using {MAGAR}}, AUTHOR = {Scherer, Michael and Gasparoni, Gilles and Rahmouni, Souad and Shashkova, Tatiana and Arnoux, Marion and Louis, Edouard and Nostaeva, Arina and Avalos, Diana and Dermitzakis, Emmanouil T. and Aulchenko, Yurii S. and Lengauer, Thomas and Lyons, Paul A. and Georges, Michel and Walter, J{\"o}rn}, LANGUAGE = {eng}, DOI = {10.1186/s13072-021-00415-6}, PUBLISHER = {BioMed Central}, ADDRESS = {London}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, JOURNAL = {Epigenetics \& Chromatin}, VOLUME = {14}, NUMBER = {1}, EID = {44}, }
Endnote
%0 Journal Article %A Scherer, Michael %A Gasparoni, Gilles %A Rahmouni, Souad %A Shashkova, Tatiana %A Arnoux, Marion %A Louis, Edouard %A Nostaeva, Arina %A Avalos, Diana %A Dermitzakis, Emmanouil T. %A Aulchenko, Yurii S. %A Lengauer, Thomas %A Lyons, Paul A. %A Georges, Michel %A Walter, Jörn %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations %T Identification of Tissue-specific and Common Methylation Quantitative Trait Loci in Healthy Individuals using MAGAR : %G eng %U http://hdl.handle.net/21.11116/0000-0009-49EA-E %R 10.1186/s13072-021-00415-6 %7 2021 %D 2021 %J Epigenetics & Chromatin %V 14 %N 1 %Z sequence number: 44 %I BioMed Central %C London
20. Schmidt F, Marx A, Baumgarten N, Hebel M, Wegner M, Kaulich M, Leisegang MS, Brandes RP, Göke J, Vreeken J, Schulz MH: Integrative Analysis of Epigenetics Data Identifies Gene-specific Regulatory Elements. Nucleic Acids Research (London) 2021, 49.
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@article{Schmidt_NAR21, TITLE = {Integrative Analysis of Epigenetics Data Identifies Gene-specific Regulatory Elements}, AUTHOR = {Schmidt, Florian and Marx, Alexander and Baumgarten, Nina and Hebel, Marie and Wegner, Martin and Kaulich, Manuel and Leisegang, Matthias S. and Brandes, Ralf P and G{\"o}ke, Jonathan and Vreeken, Jilles and Schulz, Marcel Holger}, LANGUAGE = {eng}, ISSN = {0305-1048}, DOI = {10.1093/nar/gkab798}, PUBLISHER = {Oxford University Press}, ADDRESS = {Oxford}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, DATE = {2021}, JOURNAL = {Nucleic Acids Research (London)}, VOLUME = {49}, NUMBER = {18}, PAGES = {10397--10418}, }
Endnote
%0 Journal Article %A Schmidt, Florian %A Marx, Alexander %A Baumgarten, Nina %A Hebel, Marie %A Wegner, Martin %A Kaulich, Manuel %A Leisegang, Matthias S. %A Brandes, Ralf P %A Göke, Jonathan %A Vreeken, Jilles %A Schulz, Marcel Holger %+ Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society Databases and Information Systems, MPI for Informatics, Max Planck Society External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations External Organizations Databases and Information Systems, MPI for Informatics, Max Planck Society Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T Integrative Analysis of Epigenetics Data Identifies Gene-specific Regulatory Elements : %G eng %U http://hdl.handle.net/21.11116/0000-0009-6D54-F %R 10.1093/nar/gkab798 %2 PMC8501997 %7 2021 %D 2021 %J Nucleic Acids Research (London) %O Nucleic Acids Res %V 49 %N 18 %& 10397 %P 10397 - 10418 %I Oxford University Press %C Oxford %@ false
21. Ünal AB, Akgün M, Pfeifer N: ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare. In AAAI Technical Track on Machine Learning IV. AAAI; 2021.
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@inproceedings{Uenal_AAAI21, TITLE = {ESCAPED: {E}fficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare}, AUTHOR = {{\"U}nal, Ali Burak and Akg{\"u}n, Mete and Pfeifer, Nico}, LANGUAGE = {eng}, ISBN = {978-1-57735-866-4}, URL = {https://ojs.aaai.org/index.php/AAAI/article/view/17199}, PUBLISHER = {AAAI}, YEAR = {2021}, MARGINALMARK = {$\bullet$}, BOOKTITLE = {AAAI Technical Track on Machine Learning IV}, PAGES = {9988--9996}, ADDRESS = {Virtual Conference}, }
Endnote
%0 Conference Proceedings %A Ünal, Ali Burak %A Akgün, Mete %A Pfeifer, Nico %+ External Organizations External Organizations Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society %T ESCAPED: Efficient Secure and Private Dot Product Framework for Kernel-based Machine Learning Algorithms with Applications in Healthcare : %G eng %U http://hdl.handle.net/21.11116/0000-0009-3FAC-0 %U https://ojs.aaai.org/index.php/AAAI/article/view/17199 %D 2021 %B Thirty-Fifth AAAI Conference on Artificial Intelligence %Z date of event: 2021-02-02 - 2021-02-09 %C Virtual Conference %B AAAI Technical Track on Machine Learning IV %P 9988 - 9996 %I AAAI %@ 978-1-57735-866-4 %U https://ojs.aaai.org/index.php/AAAI/article/view/17199/17006