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2020-06-25

Developing scientific software can be challenging - this paper by Julia and the RosettaCommons details essential lessons we have learned while developing Rosetta

2020-06-13

Congrats Thomas and co-authors for publishing a paper in Frontiers in Cellular and Infection Microbiology on the role of microRNAs in parasitism

2020-06-08

Check out this paper if you are interested in macromolecular modeling using rosetta: http://lars.malmstroem.net/publications/p32483333/

2019-01-14

Congrats Simon and Hamed for publishing a technology we call TX-MS in Nature Communications. TX-MS integrates structure modeling with Crosslinking Mass Spectrometry, thereby allowing us to study quaternary protein structures directly in complex samples.

2017-11-03

Congrats Ömer and co-authors for publishing a paper in Nature Methods on how to track cells in movies

2017-07-02

Congrats George for publishing a paper in Nature Biotechnology, detecting so-called PTMs in large sample cohorts

2017-02-23

Congrats Kristoffer for publishing a paper in MCP, building a model of host-pathogen protein-protein interactions

2016-09-01

Congrats Hannes for publishing a paper in Nature Methods describing OpenMS 2.0, an open-source MS analysis software

2016-08-03

Congrats Hannes for publishing a paper in Nature Methods describing TRIC, a method to improve MS reproducibility

2016-06-10

Postdoc in Bioinformatics

2016-01-29

Congrats Emil for publishing a paper in Chemical Science describing the enzymatic action of the enzyme DS-EPI1

2016-01-25

Congrats Erik for publishing a paper in Nature Communications on plasma proteomes during bacterial infections

2015-11-09

Congrats Hannes for publishing a paper discussing the importance of almost complete protein expression matrices

2015-10-28

Congrats Thomas for publishing a paper describing the software tool xTract in Nature Methods

2015-09-25

I am pleased that our latest paper is now available online. I'd like to extend a big thanks to all collaborators!

2015-06-11

Congrats Hannes for being awarded the SIB Best Swiss Bioinformatics Graduate Paper 2015 for the openSWATH paper

2015-05-07

Congrats Martin for publishing a paper on cancer biomarkers and mass spectrometry in JPR

2015-05-02

Congrats Hannes for publishing a paper describing how to process large mass spectrometry data files

2015-04-21

We have an open PhD position in computational structural biology. Please help us spread the word!!

2015-03-21

Congrats Hannes for publishing a paper on visualizing proteomics data

2015-03-04

We are looking for new co-workers. Please forward this ad to anybody you think might be interested!

2015-03-04

Bioinformatics Analyst - Genomics

2014-11-21

We are looking for a system administrator to help us build a cloud for scientific computing. Jobangebote für Systemadministrator in Schweiz (2 neu) Top-Jobs des Tages im Bereich Systemadministrator: 259 Stellen in Schweiz. Nutzen Sie Ihr berufliches Netzwerk und finden Sie einen Job. Jeden Tag werden neue Jobs in Systemadministrator hinzugefügt. ch.linkedin.com

2014-11-19

Congrats Andreas for publishing a paper on optimizing mass spec search engines using synthetic peptides

2014-11-07

Congrats Johan for publishing DIANA in Bioinformatics

2014-09-04

We are looking for new co-workers. Please forward this ad to anybody you think might be interested!

2014-05-22

Congrats Peter for publishing a paper describing our efforts developing iportal, a workflow manager

2014-05-22

Congrats Magdalena for the new paper in JBC describing a novel virulence factor from a human pathogen

2014-05-22

We are looking for a scientific data application specialist. Please spread the word if you know somebody! Thanks!

2014-04-23

Congrats George for publishing a paper in Bioinformatics describing the software package aLFQ

2014-04-19

Congrats Hannes and George for publishing a paper in Nature Biotechnology describing OpenSWATH

2014-04-19

Congrats Johan for publishing a paper in MCP describing NumPress

2014-01-15

Congrats Hannes and Uwe for publishing a paper describing pyOpenMS

2013-09-27

Congrats Abdullah and Franz for publishing a paper on how to dock proteins using XL-MS data

2013-06-15

Published my first independent recommendation after F1000 promoted me to Faculty member

2013-02-11

Congrats Hendrik for publishing a paper on how to calculate protein abundance from shotgun data

2012-12-21

Congrats Christofer for publishing a paper on targeted mass spectrometry assays for all proteins from a pathogen

2012-10-24

Please consider signing http://no-cuts-on-research.eu if you think Europe should prioritize research funding. Thanks!

2012-09-19

Congrats Franz, Abdullah and Daniel for publishing a paper on how to use MS and modeling to probe protein complexes

2012-08-08

Congrats Daniel for publishing Bioinformatic challenges in targeted proteomics

2012-05-21

Congrats Hannes for publishing this paper

2012-05-10

Chimp Shows Planning Abilities

2012-05-10

Your Inner Bugs Are What You Eat - ScienceNOW

2011-11-29

We welcome Lorenz Blum to the lab. Lorenz will work in the SCIBUS portal project building web portals for scientific computing

2011-11-29

This paper describes how a human pathogen re-organizes its proteome in response to increasing amount of human plasma

2011-10-20

Posted a F1000 evaluation on a paper measuring growth rate phenotypes in > 1M conditions

2011-08-17

We're hiring! We are currently looking for a bioinformatician / software developer

2011-08-11

Congrats Kevin for publishing results from the Human Proteome Folding project

2011-08-04

Going to the RosettaCon2011 conference in Leavenworth outside Seattle.

2011-07-16

Trial and error talk on TED

2011-07-08

Finally, a press release in English about the computational experiment carried out on the IBM cloud

2011-07-06

I'm going to the openMS User meeting in Berlin in September - hope to see many of you there!

2011-06-15

Congrats Abdullah for publishing the Xwalk algorithm

2011-06-10

Article (in German) about our efforts to carry out high-performance computing tasks in the IBM cloud

2011-06-10

youtube video about high-performance computing in the IBM cloud.

2011-05-13

Finished a big computational experiment using the IBM cloud

2011-04-20

Hannes was awarded the ETH Medaille and the Willi-Studer Prize for his Master Thesis

2011-02-26

Just back from a conference in Leukerbad that offered some great talks and some decent skiing.

2010-12-19

Congrats Johan for the 'future scientific leader' award from the Swedish Foundation for Strategic Research (Swedish)

2010-12-04

Bacteria use arsenic instead of phosphorus which might have profound implications for biology

2010-11-14

EU and USA research dominance coming to an end?

2010-11-10

We are looking for a talented bioinformatician / software developer

2010-11-02

Attending the systemsx conference in Geneva.

2010-10-26

Posted a new evaluation for F1000

2010-10-20

Wild ideas on the role of bacteria in human health and disease

2010-10-11

Contributed a chapter to the Springer Protocols Methods in Molecular Biology series: http://www.ncbi.nlm.nih.gov/pubmed/20835793

2010-09-22

Story on how GPS was born - http://on.ted.com/8aKZ!. Also some thoughts on how good ideas come about.

2010-09-17

ETH is ranked at the 15th best institution in the world: http://t.co/Q2M0fcj

2010-09-17

TED organizer Chris Anderson compares the importance of youtube to the importance of Gutenberg's book press: http://on.ted.com/8Zfw

2010-08-24

Successor to social networks? Games maybe: http://on.ted.com/8WDL. Building a 'game layer' on top of the world.

2010-07-12

TV killing creativity? http://www.newsweek.com/2010/07/10/the-creativity-crisis.html

2010-05-27

I love Ken's TED talks, he's an awesome speaker. His message is important but seems difficult to achieve: http://on.ted.com/8LtJ

2010-05-26

Congrats to George for successfully finishing his Undergrad research project!

2010-05-19

Congratulations to Hannes for successfully finishing his Masters!

2010-05-03

Daniel Pink on motivation - money is not everything: http://www.pbs.org/newshour/bb/business/jan-june10/makingsense_04-15.html

2010-04-27

Posted an F1000 evaluation of a study investigating the spread of antibiotic-resistant bugs

2010-04-23

Why business people shouldn't build bridges: http://on.ted.com/8HJ4

2010-04-18

I'm excited people are citing my papers: my h-index (http://en.wikipedia.org/wiki/H-index) just reached 11! Thanks!

2010-04-12

Thomas Denecke joined the lab to work on a distributed computing project: http://lars.malmstroem.net/science/the-lab.html

2010-04-12

Pedro Navarro started today. He is a post-doc and will be working on quantitative proteomics related problems.

2010-04-07

Hannes Roest will join my lab as a Ph.D. student this summer.

2010-02-22

Very true indeed! http://on.ted.com/89mF

2010-02-12

Leila Pirhaji will join my lab as a Ph.D. student as soon as all visa issues are cleared!

2010-02-03

Going to the Paul Scherrer Institute (www.psi.ch) to see if I can get access to their synchrotron.

2010-01-20

In Sweden to see my family

2010-01-18

Going to Geneva to present some research at the Swiss Institute of Bioinformatics

2010-01-13

posted an f1000 evaluation

2010-01-08

ETH is ranked 4th in Europe: http://www.arwu.org/ARWU2009.jsp

2010-01-03

Signing up on twitter

2010-01-03

Finished improving http://lars.malmstroem.net. Let me know what you think!

2009-12-02

Twitter: I now have a twitter account, see above.

2009-11-06

Associated faculty member of f1000 I'm now an associated faculty member of the F1000

2009-07-20

Organizing JoiningForces The joining forces symposium is scheduled for November 20th, 2009

2009-07-01

Software engineer hired Lucia Espona was hired to work on the Swiss grid portal

2009-06-03

Diatom biochemical pathways paper published. Deciphering diatom biochemical pathways via whole-cell proteomics was published in Aquat Microb Ecol.

2009-04-20

NEW POSITION! We're looking for a skilled computer programmer with experience from parallel computing and web portals for a 12 month project employment.

2009-02-01

Informatics specialist hired. Andreas Quandt was hired as informatics specialist and is responsible for the computational pipelines

2008-12-15

DXMS/de novo structure prediction paper accepted** On the use of hydrogen/deuterium exchange mass spectrometry data to improve de novo protein structure prediction was accepted for publication in RCM

2008-11-08

DS-epimerase characterization paper accepted Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function was accepted for publication in JBC

2008-09-15

Secreted glycoproteins paper accepted Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. was accepted for publication in Prostate

2008-09-01

New Job! New Country! I have a new job as a senior researcher (Oberassistent) in Ruedi Aebersolds group at the ETH in Zurich, Switzerland, where I hope to build a research group in protein structure and mass spectrometry related bioinformatics.

2008-06-04

Poster presentation at ASMS Lars presented a poster, Spectral Clustering and LC-MS Alignment Increase Annotation Rate of Tandem Mass Spectra from Shotgun Proteomics Data at the 56th ASMS in Denver

2007-12-05

Phytoplankton proteome analysis manuscript submitted A manuscript describing the proteome analysis of phytoplankton authored by Brook Nunn, Jocelyn Aker, Robert Strzepek, Theodore Freeman, Lars Malmstrom, Scott Shaffer and David Goodlett was submitted.

2007-09-25

The Baker groups CASP7 results published in Proteins Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. was published in Proteins

2007-08-03

Oral presentation at RosettaCon. Lars will present his work on integrating MS derived data to improve de novo protein structure prediction.

2007-06-06

Oral presentation at ASMS. Lars presented DXMS combined with de novo protein structure prediction facilitates model selection at the ASMS conference in Indianapolis.

2007-06-04

Co-author on an oral presentation at ASMS. David Goodlett, Ph.D. presented Cross-linked Peptide Data Obtained by Ion Mobility used to Sort Correct/Incorrect in silico Protein Conformation Predictions at the ASMS conference in Indianapolis.

2007-03-20

Structure prediction for yeast published in PLoS Biology. Protein tertiary structures for the yeast S.cerevisiae genome was generated using the de novo protein structure method Rosetta. The article was published in PLoS Biology.