April 2009 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] [Fwd: Re: Computational Systems Biology]
by Tom Michoel 28 Apr '09

28 Apr '09

This book <http://www.springer.com/humana+press/book/978-1-58829-905-5> will be in the library soon, apparently some of you asked for it as well. Tom -------- Original Message -------- Subject: Re: Computational Systems Biology Date: Tue, 28 Apr 2009 09:42:51 +0200 From: Jacques De Laet <jalae(a)psb.vib-ugent.be> To: Tom Michoel <tom.michoel(a)psb.vib-ugent.be> CC: psblib >> "psblib(a)psb.ugent.be" <psblib(a)psb.vib-ugent.be> References: <49F03DED.7060806(a)psb.vib-ugent.be> Bete Tom, wegens de grote vraag naar dit boek , wordt het aangekocht. Jacques Tom Michoel wrote: > Dag Jaques, > > Hebben wij op een of andere manier toegang tot de online versie van > dit boek? > > <http://www.springer.com/humana+press/book/978-1-58829-905-5> > > Zoniet, kan het eventueel aangekocht worden? > > Alvast bedankt, > Tom -- ================================================================== Jacques De Laet Tel:+32 (0)9 331 36 91 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM jalae(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ================================================================== -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] FYI
by Yvan Saeys 27 Apr '09

27 Apr '09

http://users.cs.fiu.edu/~taoli/kdd09-workshop/ -- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

1 0

[Beg-sysbiol] Methods to reconstruct and compare transcriptional...[Methods Mol Biol. 2009] - PubMed Result
by Yves Van de Peer 26 Apr '09

26 Apr '09

http://www.ncbi.nlm.nih.gov/pubmed/19381525?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] Report on EU-USA workshop: how systems biology can...[Mol Oncol. 2009] - PubMed Result
by Yves Van de Peer 26 Apr '09

26 Apr '09

http://www.ncbi.nlm.nih.gov/pubmed/19383362?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks -- Bindea et al. 25 (8): 1091 -- Bioinformatics
by Klaas Vandepoele 17 Apr '09

17 Apr '09

http://bioinformatics.oxfordjournals.org/cgi/content/full/25/8/1091 -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- it's hard to keep the animo from driftin' away nowadays

1 0

[Beg-sysbiol] dream interview
by Eric Bonnet 17 Apr '09

17 Apr '09

http://www.bio-itworld.com/pb/2009/04/16/dream3-update.html

1 0

[Beg-sysbiol] brainstorm
by Vanessa Vermeirssen 16 Apr '09

16 Apr '09

Hi all, shall we have a group discussion friday afternoon on which possible topics we can bring up as discussion points for the brainstorm? If everyone could think already of one idea and/or abstract/paper from which we can start, that would be great. We can take it from there... Let's meet at 2 pm if that's OK with everybody. Vanessa -- ================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 10 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei(a)psb.vib-ugent.be http://www.psb.vib-ugent.be ==================================================================

1 0

[Beg-sysbiol] Cross species analysis of microarray expression data -- Lu et al., 10.1093/bioinformatics/btp247 -- Bioinformatics
by Tom Michoel 16 Apr '09

16 Apr '09

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp247v1?etoc

1 0

[Beg-sysbiol] [Fwd: Fw: Fully funded faculty positions in genomics and bioinformatics]
by Yves Van de Peer 09 Apr '09

09 Apr '09

-------- Original Message -------- Subject: [Beg-sysbiol] Fw: Fully funded faculty positions in genomics and bioinformatics Date: Wed, 8 Apr 2009 20:18:54 +0200 From: Yves Van De Peer <yves.vandepeer(a)psb.vib-ugent.be> Reply-To: beg-sysbiol(a)psb.vib-ugent.be To: <beg-sysbiol(a)psb.vib-ugent.be> ----- Original Message ----- From: Germain, Ronald (NIH/NIAID) [E] <RGERMAIN(a)niaid.nih.gov> To: yves.vandepeer(a)psb.ugent.be <yves.vandepeer(a)psb.vib-ugent.be> Sent: Wed Apr 08 19:11:10 2009 Subject: Fully funded faculty positions in genomics and bioinformatics Dear Dr. van de Peer I am writing to bring to your attention the next round of faculty recruitment for the NIAID Intramural research effort called the Program in Systems Immunology and Infectious Disease Modeling (PSIIM), which is focused on combining computational modeling with quantitative experimental exploration of the immune system, pathogens, and host-pathogen interactions at various biological scales, from intracellular signaling and gene regulatory pathways to the whole organism level. These positions are fully supported by the Division of Intramural Research, NIAID, making them especially attractive in the current funding environment. The PSIIM has already recruited individuals to lead groups in the areas of computer modeling and simulation (Dr. Martin Meier-Schellersheim), molecular and cell biology/high throughput screening (Dr. Iain D.C. Fraser), proteomics (Dr. Aleksandra Nita-Lazar), and immunology (Dr. Ronald N. Germain, who also serves as PSIIM Director). As the attached advertisement details, the PSIIM is now recruiting to fill tenure / tenure-track positions in two remaining critical areas bioinformatics and genomics. It is important to note that in contrast to most typical NIH intramural research activities involving small, focused, and quite independent laboratory groups, the PSIIM is organized around a Oteam science¹ concept in which the various research groups headed by these recruits will be expected to devote a substantial amount of their effort towards larger, shared goals. To support career development in this new environment, NIH has modified its rules for granting tenure / assessing performance to take specific account of accomplishments made in a team setting. Support from internal NIAID research funds will be provided on a continuing basis that covers the salaries of the group leader, technical staff and fellows, along with generous budgets for equipment, laboratory reagents, animals, travel, and publication costs (or in the case of computational groups, computers, shared computing costs, and software licenses). The successful candidates will also be able to take advantage of numerous cores within the NIAID and NIH that include state-of-the-art support in the areas of gene microarrays, optical imaging, and cluster computing as well as both trans-NIH and PSIIM-specific robotics platforms for high throughput / high content drug and RNAi screening. The PSIIM also has purchased a next-generation sequencer whose use will be primarily devoted to the genomics recruit. Although the PSIIM is currently supported solely by the NIAID, it is already providing leadership across the NIH in the area of computational systems biology and it is expected to continue in this role as NIH develops a trans-Institute effort in this area in the future. The tenure / tenure-track positions now open in the PSIIM thus represent extremely attractive positions for individuals interested in playing a key role in creating and applying new methods for quantitative analysis of biological systems. The PSIIM will invest heavily in the development of novel, broadly applicable tools for systems biology research, with an emphasis on software for modeling and simulation [for example, see PLoS Comput Biol. 2006 Jul 21;2(7):e82. Epub 2006 May 25, PMID: 16854213], the integration of this software with bioinformatics applications, and the establishment of methods for providing the numerical data necessary for computational efforts. The PSIIM will conduct biological studies in the areas of immunology and infectious diseases, taking maximal advantage of the latest technological advances, but extension of the systems approach of the PSIIM to other areas of biomedicine will be possible through collaboration. The integrated, multidisciplinary nature of the PSIIM research effort is expected to markedly facilitate its ability to make significant contributions in the arena of complex biosystems analysis. Studies of the host immune system will include such topics as signaling by microbial receptors (TLRs, NODs, and RIGI), regulation of differentiation of T cell subsets, and tissue level as well as whole body analysis of protective and pathologic innate and adaptive immune responses to infectious agents. Pathogen biology will also be a focus of PSIIM efforts, with studies ranging from signaling networks and gene regulatory pathways controlling pathogenicity to determination of points of vulnerability to drug therapy or immune effectors. I ask that you bring this exciting new program and the group leader positions being advertised to the attention of any outstanding fellows or colleagues you believe have an interest in systems biology, irrespective of their background in immunology. A new website is currently under construction that will provide additional information about the PSIIM and its research program, but for now the recruiting advertisement provides a good, if brief, introduction to the available opportunities. Additional information about the PSIIM is available in an article at http://www.nih.gov/catalyst/2006/06.09.01/page1.html and also at http://www3.niaid.nih.gov/labs/aboutlabs/psiim/. I have attached a formal version of this note and a copy of the ad for these positions, to be posted in your department and distributed to students, fellows, or colleagues you believe would be outstanding candidates for these openings. With thanks in advance for your help, Ronald N. Germain, M.D., Ph. D. Deputy Chief, Laboratory of Immunology Chief, Lymphocyte Biology Section, Laboratory of Immunology Director, Program in Systems Immunology and Infectious Disease Modeling (PSIIM) Associate Director, Trans-NIH Center for Human Immunology (CHI) National Institute of Allergy and Infectious Diseases National Institutes of Health, DHHS Bldg. 10 Rm. 11N311 10 Center Dr. MSC-1892 Bethesda, MD 20892-1892 Office Ph: 301-496-1904 Cell: 301-273-5537 FAX: 301-496-0222 e mail: rgermain(a)nih.gov The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ _______________________________________________ Beg-sysbiol mailing list Beg-sysbiol(a)psb.ugent.be https://maillist.psb.ugent.be/mailman/listinfo/beg-sysbiol

1 0

[Beg-sysbiol] Fw: Fully funded faculty positions in genomics and bioinformatics
by Yves Van De Peer 08 Apr '09

08 Apr '09

----- Original Message ----- From: Germain, Ronald (NIH/NIAID) [E] <RGERMAIN(a)niaid.nih.gov> To: yves.vandepeer(a)psb.ugent.be <yves.vandepeer(a)psb.vib-ugent.be> Sent: Wed Apr 08 19:11:10 2009 Subject: Fully funded faculty positions in genomics and bioinformatics Dear Dr. van de Peer I am writing to bring to your attention the next round of faculty recruitment for the NIAID Intramural research effort called the Program in Systems Immunology and Infectious Disease Modeling (PSIIM), which is focused on combining computational modeling with quantitative experimental exploration of the immune system, pathogens, and host-pathogen interactions at various biological scales, from intracellular signaling and gene regulatory pathways to the whole organism level. These positions are fully supported by the Division of Intramural Research, NIAID, making them especially attractive in the current funding environment. The PSIIM has already recruited individuals to lead groups in the areas of computer modeling and simulation (Dr. Martin Meier-Schellersheim), molecular and cell biology/high throughput screening (Dr. Iain D.C. Fraser), proteomics (Dr. Aleksandra Nita-Lazar), and immunology (Dr. Ronald N. Germain, who also serves as PSIIM Director). As the attached advertisement details, the PSIIM is now recruiting to fill tenure / tenure-track positions in two remaining critical areas bioinformatics and genomics. It is important to note that in contrast to most typical NIH intramural research activities involving small, focused, and quite independent laboratory groups, the PSIIM is organized around a Oteam science¹ concept in which the various research groups headed by these recruits will be expected to devote a substantial amount of their effort towards larger, shared goals. To support career development in this new environment, NIH has modified its rules for granting tenure / assessing performance to take specific account of accomplishments made in a team setting. Support from internal NIAID research funds will be provided on a continuing basis that covers the salaries of the group leader, technical staff and fellows, along with generous budgets for equipment, laboratory reagents, animals, travel, and publication costs (or in the case of computational groups, computers, shared computing costs, and software licenses). The successful candidates will also be able to take advantage of numerous cores within the NIAID and NIH that include state-of-the-art support in the areas of gene microarrays, optical imaging, and cluster computing as well as both trans-NIH and PSIIM-specific robotics platforms for high throughput / high content drug and RNAi screening. The PSIIM also has purchased a next-generation sequencer whose use will be primarily devoted to the genomics recruit. Although the PSIIM is currently supported solely by the NIAID, it is already providing leadership across the NIH in the area of computational systems biology and it is expected to continue in this role as NIH develops a trans-Institute effort in this area in the future. The tenure / tenure-track positions now open in the PSIIM thus represent extremely attractive positions for individuals interested in playing a key role in creating and applying new methods for quantitative analysis of biological systems. The PSIIM will invest heavily in the development of novel, broadly applicable tools for systems biology research, with an emphasis on software for modeling and simulation [for example, see PLoS Comput Biol. 2006 Jul 21;2(7):e82. Epub 2006 May 25, PMID: 16854213], the integration of this software with bioinformatics applications, and the establishment of methods for providing the numerical data necessary for computational efforts. The PSIIM will conduct biological studies in the areas of immunology and infectious diseases, taking maximal advantage of the latest technological advances, but extension of the systems approach of the PSIIM to other areas of biomedicine will be possible through collaboration. The integrated, multidisciplinary nature of the PSIIM research effort is expected to markedly facilitate its ability to make significant contributions in the arena of complex biosystems analysis. Studies of the host immune system will include such topics as signaling by microbial receptors (TLRs, NODs, and RIGI), regulation of differentiation of T cell subsets, and tissue level as well as whole body analysis of protective and pathologic innate and adaptive immune responses to infectious agents. Pathogen biology will also be a focus of PSIIM efforts, with studies ranging from signaling networks and gene regulatory pathways controlling pathogenicity to determination of points of vulnerability to drug therapy or immune effectors. I ask that you bring this exciting new program and the group leader positions being advertised to the attention of any outstanding fellows or colleagues you believe have an interest in systems biology, irrespective of their background in immunology. A new website is currently under construction that will provide additional information about the PSIIM and its research program, but for now the recruiting advertisement provides a good, if brief, introduction to the available opportunities. Additional information about the PSIIM is available in an article at http://www.nih.gov/catalyst/2006/06.09.01/page1.html and also at http://www3.niaid.nih.gov/labs/aboutlabs/psiim/. I have attached a formal version of this note and a copy of the ad for these positions, to be posted in your department and distributed to students, fellows, or colleagues you believe would be outstanding candidates for these openings. With thanks in advance for your help, Ronald N. Germain, M.D., Ph. D. Deputy Chief, Laboratory of Immunology Chief, Lymphocyte Biology Section, Laboratory of Immunology Director, Program in Systems Immunology and Infectious Disease Modeling (PSIIM) Associate Director, Trans-NIH Center for Human Immunology (CHI) National Institute of Allergy and Infectious Diseases National Institutes of Health, DHHS Bldg. 10 Rm. 11N311 10 Center Dr. MSC-1892 Bethesda, MD 20892-1892 Office Ph: 301-496-1904 Cell: 301-273-5537 FAX: 301-496-0222 e mail: rgermain(a)nih.gov The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

1 0