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Documents authored by Parida, Laxmi

Document
Complete Volume
DOI: 10.4230/LIPIcs.WABI.2018
LIPIcs, Volume 113, WABI'18, Complete Volume

Authors: Laxmi Parida and Esko Ukkonen

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
LIPIcs, Volume 113, WABI'18, Complete Volume
Cite as

18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Proceedings{parida_et_al:LIPIcs.WABI.2018,
  title =	{{LIPIcs, Volume 113, WABI'18, Complete Volume}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018},
  URN =		{urn:nbn:de:0030-drops-97246},
  doi =		{10.4230/LIPIcs.WABI.2018},
  annote =	{Keywords: Applied computing, Bioinformatics, Theory of computation, Design and analysis of algorithms, Mathematics of computing, Probabilistic inference problem}
}
Document
Front Matter
DOI: 10.4230/LIPIcs.WABI.2018.0
Front Matter, Table of Contents, Preface, Conference Organization

Authors: Laxmi Parida and Esko Ukkonen

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
Front Matter, Table of Contents, Preface, Conference Organization
Cite as

18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{parida_et_al:LIPIcs.WABI.2018.0,
  author =	{Parida, Laxmi and Ukkonen, Esko},
  title =	{{Front Matter, Table of Contents, Preface, Conference Organization}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{0:i--0:xvi},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.0},
  URN =		{urn:nbn:de:0030-drops-93028},
  doi =		{10.4230/LIPIcs.WABI.2018.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.14
Essential Simplices in Persistent Homology and Subtle Admixture Detection

Authors: Saugata Basu, Filippo Utro, and Laxmi Parida

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
We introduce a robust mathematical definition of the notion of essential elements in a basis of the homology space and prove that these elements are unique. Next we give a novel visualization of the essential elements of the basis of the homology space through a rainfall-like plot (RFL). This plot is data-centric, i.e., is associated with the individual samples of the data, as opposed to the structure-centric barcodes of persistent homology. The proof-of-concept was tested on data generated by SimRA that simulates different admixture scenarios. We show that the barcode analysis can be used not just to detect the presence of admixture but also estimate the number of admixed populations. We also demonstrate that data-centric RFL plots have the potential to further disentangle the common history into admixture events and relative timing of the events, even in very complex scenarios.
Cite as

Saugata Basu, Filippo Utro, and Laxmi Parida. Essential Simplices in Persistent Homology and Subtle Admixture Detection. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 14:1-14:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{basu_et_al:LIPIcs.WABI.2018.14,
  author =	{Basu, Saugata and Utro, Filippo and Parida, Laxmi},
  title =	{{Essential Simplices in Persistent Homology and Subtle Admixture Detection}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{14:1--14:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.14},
  URN =		{urn:nbn:de:0030-drops-93166},
  doi =		{10.4230/LIPIcs.WABI.2018.14},
  annote =	{Keywords: population admixture, topological data analysis, persistent homology, population evolution}
}
Document
DOI: 10.4230/DagMan.3.1.31
ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342)

Authors: Jonas S. Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida

Published in: Dagstuhl Manifestos, Volume 3, Issue 1 (2013)

Abstract
The systems paradigm of modern medicine presents both, an opportunity and a challenge, for current Information and Communication Technology (ICT). The opportunity is to understand the spatio-temporal organisation and dynamics of the human body as an integrated whole, incorporating the biochemical, physiological, and environmental interactions that sustain life. Yet, to accomplish this, one has to meet the challenge of integrating, visualising, interpreting, and utilising an unprecedented amount of in-silico, in-vitro and in-vivo data related to health care in a systematic, transparent, comprehensible, and reproducible fashion. This challenge is substantially compounded by the critical need to align technical solutions with the increasingly social dimension of modern ICT and the wide range of stakeholders in modern health-care systems. Unquestionably, advancing health-care related ICT has the potential of fundamentally revolutionising care-delivery systems, affecting all our lives both, personally and -- in view of the enormous costs of health--care systems in modern societies -- also financially. Accordingly, to ponder the options of ICT for delivering the promise of systems approaches to medical care, medical researchers and physicians, biologists and mathematicians, computer scientists and information--systems experts from three continents and from both, industry and academia, met in Dagstuhl for a Dagstuhl Perspectives Workshop on ICT Strategies for Bridging Biology and Medicine from August 18 to 23, 2013, to thoroughly discuss this multidisciplinary topic and to derive and compile a comprehensive list of pertinent recommendations -- rather than just to deliver a set package of sanitised powerpoint presentations on medical ICT. The recommendations in this manifesto reflect points of convergence that emerged during the intense discussions and analyses taking place the workshop. They also reflect a particular attention given to the identification of challenges for improving the effectiveness of ICT approaches to Systems Biomedicine.
Cite as

Jonas S. Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida. ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342). In Dagstuhl Manifestos, Volume 3, Issue 1, pp. 31-50, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)

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@Article{almeida_et_al:DagMan.3.1.31,
  author =	{Almeida, Jonas S. and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  title =	{{ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342)}},
  pages =	{31--50},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2014},
  volume =	{3},
  number =	{1},
  editor =	{Almeida, Jonas S. and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.3.1.31},
  URN =		{urn:nbn:de:0030-drops-44292},
  doi =		{10.4230/DagMan.3.1.31},
  annote =	{Keywords: Systems medicine, health-care related information systems, biomedical workflow engines, medical cloud, patient participation, ICT literacy}
}
Document
DOI: 10.4230/DagRep.3.8.87
ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342)

Authors: Jonas Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida

Published in: Dagstuhl Reports, Volume 3, Issue 8 (2013)

Abstract
The systems paradigm of modern medicine presents both, an opportunity and a challenge, for current Information and Communication Technology (ICT). The opportunity is to understand the spatio-temporal organisation and dynamics of the human body as an integrated whole, incorporating the biochemical, physiological, and environmental interactions that sustain life. Yet, to accomplish this, one has to meet the challenge of integrating, visualising, interpreting, and utilising an unprecedented amount of in-silico, in-vitro and in-vivo data related to healthcare in a systematic, transparent, comprehensible, and reproducible fashion. This challenge is substantially compounded by the critical need to align technical solutions with the increasingly social dimension of modern ICT and the wide range of stakeholders in modern healthcare systems. Unquestionably, advancing healthcare-related ICT has the potential of fundamentally revolutionising care-delivery systems, affecting all our lives both, personally and -- in view of the enormous costs of healthcare systems in modern societies -- also financially. Accordingly, to ponder the options of ICT for delivering the promise of systems approaches to medicine and medical care, medical researchers, physicians, biologists, mathematicians, computer scientists, and information--systems experts from three continents and from both, industry and academia, met in Dagstuhl Castle for a Dagstuhl Perspectives Workshop on ICT Strategies for Bridging Biology and Medicine from August 18 to 23, 2013, to thoroughly discuss this multidisciplinary topic and to derive and compile a comprehensive list of pertinent recommendations -- rather than just to deliver a set package of sanitised powerpoint presentations on medical ICT. The recommendations in this manifesto reflect points of convergence that emerged during the intense analyses and discussions taking place at the workshop. They also reflect a particular attention given to the identification of challenges for improving the effectiveness of ICT approaches to Precision and Systems Biomedicine.
Cite as

Jonas Almeida, Andreas Dress, Titus Kühne, and Laxmi Parida. ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342). In Dagstuhl Reports, Volume 3, Issue 8, pp. 87-135, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@Article{almeida_et_al:DagRep.3.8.87,
  author =	{Almeida, Jonas and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  title =	{{ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342)}},
  pages =	{87--135},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2013},
  volume =	{3},
  number =	{8},
  editor =	{Almeida, Jonas and Dress, Andreas and K\"{u}hne, Titus and Parida, Laxmi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.3.8.87},
  URN =		{urn:nbn:de:0030-drops-43447},
  doi =		{10.4230/DagRep.3.8.87},
  annote =	{Keywords: Systems biomedicine, precision medicine, healthcare-related information systems, biomedical workflow engines, medical cloud, patient participation, IC}
}
Document
DOI: 10.4230/DagRep.2.7.92
Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291)

Authors: Alberto Apostolico, Andreas Dress, and Laxmi Parida

Published in: Dagstuhl Reports, Volume 2, Issue 7 (2013)

Abstract
From 15.07.12 to 20.07.12, the Dagstuhl Seminar 12291 "Structure Discovery in Biology: Motifs, Networks & Phylogenies" was held in Schloss Dagstuhl -- Leibniz Center for Informatics. The seminar was in part a follow-up to Dagstuhl Seminar 10231, held in June 2010, this time with a strong emphasis on large data. Both veterans and new participants took part in this edition. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar, as well as abstracts of seminar results and ideas, are put together in this report. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Alberto Apostolico, Andreas Dress, and Laxmi Parida. Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291). In Dagstuhl Reports, Volume 2, Issue 7, pp. 92-117, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@Article{apostolico_et_al:DagRep.2.7.92,
  author =	{Apostolico, Alberto and Dress, Andreas and Parida, Laxmi},
  title =	{{Structure Discovery in Biology: Motifs, Networks \& Phylogenies (Dagstuhl Seminar 12291)}},
  pages =	{92--117},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2012},
  volume =	{2},
  number =	{7},
  editor =	{Apostolico, Alberto and Dress, Andreas and Parida, Laxmi},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.2.7.92},
  URN =		{urn:nbn:de:0030-drops-37509},
  doi =		{10.4230/DagRep.2.7.92},
  annote =	{Keywords: mathematical biology, computational biology, algorithmic bioinformatics, pattern discovery, networks, phylogenetics, stringology}
}
Document
DOI: 10.4230/DagSemProc.10231.1
10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks & Phylogenies

Authors: Alberto Apostolico, Andreas Dress, and Laxmi Parida

Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)

Abstract
From 06.06. to 11.06.2010, the Dagstuhl Seminar 10231 ``Structure Discovery in Biology: Motifs, Networks & Phylogenies '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Alberto Apostolico, Andreas Dress, and Laxmi Parida. 10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks & Phylogenies. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InProceedings{apostolico_et_al:DagSemProc.10231.1,
  author =	{Apostolico, Alberto and Dress, Andreas and Parida, Laxmi},
  title =	{{10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks \& Phylogenies}},
  booktitle =	{Structure Discovery in Biology: Motifs, Networks \& Phylogenies},
  pages =	{1--20},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{10231},
  editor =	{Alberto Apostolico and Andreas Dress and Laxmi Parida},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.1},
  URN =		{urn:nbn:de:0030-drops-26910},
  doi =		{10.4230/DagSemProc.10231.1},
  annote =	{Keywords: Mathematical biology, computational biology, algorithmic bioinformatics, pattern discovery, phylogenetics, networks}
}
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