Ramneek Gupta

Ramneek Gupta

Associate Professor

DTU BIOINFORMATICS
Department of Bio and Health Informatics

Disease Intelligence and Molecular Evolution
DTU Bioinformatics Employees

Technical University of Denmark

Kemitorvet

Building 208, room 021

2800 Kgs. Lyngby

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Fax +45 45 93 15 85
E-mail rg@bioinformatics.dtu.dk
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2018
 

Accurate genotyping across variant classes and lengths using variant graphs

Sibbesen, Jonas Andreas ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Dam-Als, Thomas ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: Nature Genetics, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41588-018-0145-5

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Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios

Matey-Hernandez, María Luisa ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Skov, Laurits ; Belling, Kirstine ; Theil Have, Christian ; Gonzalez-Izarzugaza, Jose Maria ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; Beusekom, Johan v. ; Espeseth, Thomas ; Flindt, Esben N. ; Friborg, Rune M. ; Halager, Anders Egerup ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Ali , Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide ; Izarzugaza, Jose M. G.
in: B M C Bioinformatics, vol: 19, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12859-018-2239-6

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Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study

Gudmundsdottir, Valborg ; Pedersen, Helle Krogh ; Allebrandt, Karla Viviani ; Brorsson, Caroline Anna ; van Leeuwen, Nienke ; Banasik, Karina ; Mahajan, Anubha ; Groves, Christopher J ; van de Bunt, Martijn ; Dawed, Adem Y ; Fritsche, Andreas ; Staiger, Harald ; Simonis-Bik, Annemarie M C ; Deelen, Joris ; Kramer, Mark H H ; Dietrich, Axel ; Hübschle, Thomas ; Willemsen, Gonneke ; Häring, Hans-Ulrich ; de Geus, Eco J C ; Boomsma, Dorret I ; Eekhoff, Elisabeth M W ; Ferrer, Jorge ; McCarthy, Mark I ; Pearson, Ewan R ; Gupta, Ramneek ; Brunak, Søren ; 't Hart, Leen M
in: P L o S One, vol: 13, issue: 1, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1371/journal.pone.0189886

 

Metabolite ratios as potential biomarkers for type 2 diabetes: a DIRECT study

Molnos, Sophie ; Wahl, Simone ; Haid, Mark ; Eekhoff, E. Marelise W. ; Pool, René ; Floegel, Anna ; Deelen, Joris ; Much, Daniela ; Prehn, Cornelia ; Breier, Michaela ; Draisma, Harmen H. ; van Leeuwen, Nienke ; Simonis-Bik, Annemarie M.C. ; Jonsson, Anna Elisabet ; Willemsen, Gonneke ; Bernigau, Wolfgang ; Wang-Sattler, Rui ; Suhre, Karsten ; Peters, Annette ; Thorand, Barbara ; Herder, Christian ; Rathmann, Wolfgang ; Roden, Michael ; Gieger, Christian ; Kramer, Mark H.H. ; van Heemst, Diana ; Pedersen, Helle Krogh ; Gudmundsdottir, Valborg ; Schulze, Matthias B. ; Pischon, Tobias ; de Geus, Eco J.C. ; Boeing, Heiner ; Boomsma, Dorret I. ; Ziegler, Anette G. ; Slagboom, P. Eline ; Hummel, Sandra ; Beekman, Marian ; Grallert, Harald ; Brunak, Søren ; McCarthy, Mark I. ; Gupta, Ramneek ; Pearson, Ewan R. ; Adamski, Jerzy ; 'T Hart, Leen M.
in: Diabetologia, vol: 61, pages: 117-129, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s00125-017-4436-7

 

NT5C2 germline variants alter thiopurine metabolism and are associated with acquired NT5C2 relapse mutations in childhood acute lymphoblastic leukaemia

Tulstrup, Morten ; Grosjean, Marie ; Nielsen, Stine Nygaard ; Grell, Kathrine ; Wolthers, Benjamin Ole ; Wegener, Peder Skov ; Jonsson, Olafur Gisli ; Lund, Bendik ; Harila-Saari, Arja ; Abrahamsson, Jonas ; Vaitkeviciene, Goda ; Pruunsild, Kaie ; Toft, Nina ; Holm, Mette ; Hulegårdh, Erik ; Liestøl, Sigurd ; Griskevicius, Laimonas ; Punab, Mari ; Wang, Jinhua ; Carroll, William L. ; Zhang, Zeyu ; Dalgaard, Marlene D. ; Gupta, Ramneek ; Nersting, Jacob ; Schmiegelow, Kjeld
in: Leukemia, vol: 2018, 2011

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41375-018-0245-3

 

Prediction of liver fat in people with and without type 2 diabetes: an IMI DIRECT study

Pasdar, N. Atabaki ; Ohlsson, M. ; Vinuela, A. ; Frau, F. ; Koivula, R. ; Fernández, J ; Thomas, E. ; Mari, A. ; Gupta, R. ; Kurbasic, A. ; Pearson, E. ; Pavo, I. ; Bell, J. ; Franks, Paul W.
in: Diabetologia, vol: 61, issue: 1S, pages: S581, 2011

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s00125-018-4693-0

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The governance structure for data access in the DIRECT consortium: an innovative medicines initiative (IMI) project

Teare, Harriet J. A. ; De Masi, Federico ; Banasik, Karina ; Barnett, Anna ; Herrgard, Sanna ; Jablonka, Bernd ; Postma, Jacqueline W. M. ; McDonald, Timothy J. ; Forgie, Ian ; Chmura, Piotr Jaroslaw ; Rydzka, Emil K. ; Gupta, Ramneek ; Brunak, Søren ; Pearson, Ewan ; Kaye, Jane
in: Life Sciences, Society and Policy, vol: 14

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s40504-018-0083-0

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Transcriptome analysis of root-knot nematode (Meloidogyne incognita)-infected tomato (Solanum lycopersicum) roots reveals complex gene expression profiles and metabolic networks of both host and nematode during susceptible and resistance responses

Shukla, Neha ; Yadav, Rachita ; Kaur, Pritam ; Rasmussen, Simon ; Goel, Shailendra ; Agarwal, Manu ; Jagannath, Arun ; Gupta, Ramneek ; Kumar, Amar
in: Molecular Plant Pathology, vol: 19, issue: 3, pages: 615-633, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1111/mpp.12547

2017
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Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion

Gonzalez-Izarzugaza, Jose Maria ; Skov, Laurits ; Maretty, Lasse ; Jensen, Jacob Malte ; Petersen, Bent ; Andreas Sibbesen, Jonas ; Liu, Siyang ; Villesen, Palle ; Belling, Kirstine González-Izarzugaza ; Theil Have, Christian ; Grosjean, Marie ; Bork-Jensen, Jette ; Grove, Jakob ; Als, Thomas D. ; Huang, Shujia ; Chang, Yuqi ; Xu, Ruiqi ; Ye, Weijian ; Rao, Junhua ; Guo, Xiaosen ; Sun, Jihua ; Cao, Hongzhi ; Ye, Chen ; van Beusekom, Johan ; Espeseth, Thomas ; Flindt, Esben ; Friborg, Rune M. ; Halager, Anders E. ; Le Hellard, Stephanie ; Hultman, Christina M. ; Lescai, Francesco ; Li, Shengting ; Lund, Ole ; Løngren, Peter ; Mailund, Thomas ; Matey-Hernandez, María Luisa ; Mors, Ole ; Pedersen, Christian N. S. ; Sicheritz-Pontén, Thomas ; Sullivan, Patrick F. ; Qaswar Ali Shah, Syed ; Westergaard, David ; Yadav, Rachita ; Li, Ning ; Xu, Xun ; Hansen, Torben ; Krogh, Anders ; Bolund, Lars ; Sørensen, Thorkild I. A. ; Pedersen, Oluf ; Gupta, Ramneek ; Rasmussen, Simon ; Besenbacher, Søren ; Børglum, Anders D. ; Wang, Jun ; Eiberg, Hans ; Kristiansen, Karsten ; Brunak, Søren ; Schierup, Mikkel Heide
in: P L o S Genetics, vol: 13, issue: 8, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1371/journal.pgen.1006834

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Cerebellar mutism syndrome in children with brain tumours of the posterior fossa

Wibroe, Morten ; Cappelen, Johan ; Castor, Charlotte ; Clausen, Niels ; Grillner, Pernilla ; Gudrunardottir, Thora ; Gupta, Ramneek ; Gustavsson, Bengt ; Heyman, Mats ; Holm, Stefan ; Karppinen, Atte ; Klausen, Camilla ; Lonnqvist, Tuula ; Mathiasen, Rene ; Nilsson, Pelle ; Nysom, Karsten ; Persson-Waller, Karin ; Rask, Olof ; Schmiegelow, Kjeld ; Sehested, Astrid ; Thomassen, Harald ; Tonning-Olsson, Ingrid ; Zetterqvist, Barbara ; Juhler, Marianne
in: B M C Cancer, vol: 17, 2011

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1186/s12885-017-3416-0