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hms-dbmi / gehlenborglab-website

Code for Gehlenborg Lab website.
http://gehlenborglab.org
MIT License
6 stars 34 forks source link

Port gehlenborg publications #16

Closed mccalluc closed 7 years ago

mccalluc commented 7 years ago

filename convention: smith-2000-journal-of-synthetic-foo.md

mccalluc commented 7 years ago

Copy and pasted the html from the old site and ran it through perl -pne 's/<\/?p[^>]*>//g; s/\s+onclick="[^"]+"//g; s/&nbsp;/ /g; s/(.*"(https?:\/\/[^"]+)".*)/$2\t$1/; s/<\/?a[^>]*>//g; s/\*/\\*/g; s/<\/?em>/*/g; s/<\/?strong>/**/g;' to produce this markdown. (Something isn't right in the last bit, and I'll fix that, but do you want the whole list?)

@ngehlenborg: Should I go head and make files in _publications for all of these? Not hard, but I want to make sure there are no big changes you want to the structure before I jump into this.

article cell-thyroid 2014 http://www.cancerresearchuk.org/about-us/cancer-news/news-report/2014-10-23-large-study-sheds-light-on-the-genetic-causes-of-thyroid-cancer The Cancer Genome Atlas Network, incl. N Gehlenborg, “Integrated Genomic Characterization of Papillary Thyroid Carcinoma”. Cell 159:676–690 (2014). Featured in Clinical Sequencing News, Deutsches Ärtzeblatt, Cancer Research UK News. article pnas-hpv 2014 http://www.pnas.org/content/early/2014/10/10/1416074111.abstract M Parfenov*, CS Pedamallu*, N Gehlenborg, SS Freeman, L Danilova, CA Bristow, S Lee, A Hadjipanayis, E Ivanova, MD Wilkerson, A Protopopov, L Yang, S Seth, X Song, J Tang, X Ren, J Zhang, A Pantazi, N Santoso, AW Xu, H Mahadeshwar, DA Wheeler, RI Haddad, J Jung, AI Ojesina, N Isaeva, WG Yarbrough, DN Hayes, JR Grandis, AK El-Naggar, M Meyerson, PJ Park, L Chin, JG Seidman, PS Hammerman**, R Kucherlapati**, TCGA Network, “Characterization of HPV and Host-Genome Interactions in Primary Head and Neck Cancers”, Proceedings of the National Academy of Sciences USA 2014. article ieee-upset 2014 A Lex, N Gehlenborg, H Strobelt, R Vuillemot and H Pfister, “UpSet: Visualization of Intersecting Sets”. IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14). article ieee-domino 2014 S Gratzl, N Gehlenborg, A Lex, H Pfister and M Streit, “Domino: Extracting, Comparing, and Manipulating Subsets across Multiple Tabular Datasets”. IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis ’14). article nature-stratifications 2014 http://www.jku.at/content/e220992/e13428/e13415/e13414?apath=e32681/e225072/e254350/e254686 M Streit*, A Lex*, S Gratzl, C Partl, D Schmalstieg, H Pfister, PJ Park** and N Gehlenborg**, “Guided Visual Exploration of Genomic Stratifications in Cancer“. Nature Methods 11:884–885 (2014). Featured in GenomeWeb, Harvard Medical School News, The Crimson, Harvard SEAS News, JKU Campus News. article nature-chromatin 2014 http://www.nature.com/nature/journal/v512/n7515/full/nature13415.html JWK Ho, YL Jung, Tao Liu, BH Alver, S Lee, K Ikegami, K-A Sohn, A Minoda, MY Tolstorukov, A Appert, SCJ Parker, T Gu, A Kundaje, NC Riddle, E Bishop, TA Egelhofer, SS Hu, AA Alekseyenko, A Rechtsteiner, D Asker, JA Belsky, SK Bowman, QB Chen, RAJ Chen, DS Day, Y Dong, AC Dose, X Duan, CB Epstein, S Ercan, EA Feingold, F Ferrari, J M Garrigues, N Gehlenborg, PJ Good, P Haseley, D He, M Herrmann, MM Hoffman, TE Jeffers, PV Kharchenko, PK Zwierz, CV Kotwaliwale, N Kumar, SA Langley, EN Larschan, I Latorre, MW Libbrecht, X Lin, R Park, MJ Pazin, HN Pham, A Plachetka, B Qin, YB Schwartz, N Shoresh, P Stempor, A Vielle, C Wang, CM Whittle, H Xue, RE Kingston, JH Kim, BE Bernstein,AF Dernburg, V Pirrotta, MI Kuroda, WS Noble, TD Tullius, M Kellis, DM MacAlpine, S Strome, SCR Elgin, XS Liu, JD Lieb, J Ahringer, GH Karpen and PJ Park, “Comparative analysis of metazoan chromatin organization“. Nature 512:449–452 (2014). Featured in New York Times, The Scientist. article cell-signatures 2014 http://www.cell.com/cell/abstract/S0092-8674(14)00876-9# KA Hoadley*, C Yau*, DM Wolf*, AD Cherniack*, D Tamborero, S Ng, MDM Leiserson, B Niu, MD McLellan, V Uzunangelov, J Zhang, C Kandoth, R Akbani, H Shen, L Omberg, A Chu, AA Margolin, LJ van’t Veer, N Lopez-Bigas, PW Laird, BJ Raphael, L Ding, AG Robertson, LA Byers, GB Mills, JN Weinstein, C Van Waes, Z Chen, EA Collisson, The Cancer Genome Atlas Network incl. N Gehlenborg, CC Benz, CM Perou, JM Stuart, “Multi-platform integration of 12 cancer types reveals cell-of-origin classes with distinct molecular signatures”, Cell 158:929–944 (2014). article nature-gastric 2014 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13480.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive Molecular Characterization of Gastric Adenocarcinoma”, Nature. article nature-lung 2014 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13385.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular profiling of lung adenocarcinoma“, Nature. article ieee-ontologies 2014 http://www.computer.org/csdl/mags/co/2014/05/mco2014050004-abs.html S Carpendale, M Chen, D Evanko, N Gehlenborg, C Görg, L Hunter, F Rowland, M-A Storey, H Strobelt, “Ontologies in Biological Data Visualization“, IEEE Computer Graphics and Applications 34(2):8-15 (2014). Featured in IEEE Computer in May 2014. article nature-bladder 2014 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive Molecular Characterization of Urothelial Bladder Carcinoma“, Nature 507:315–322 (2014). article ieee-lineup 2013 http://derstandard.at/1389859388328/Heimische-Forscher-machen-die-Dynamik-hinter-Rankings-sichtbar S Gratzl, A Lex, N Gehlenborg, HP Pfister and M Streit, “LineUp: Visual Analysis of Multi-Attribute Rankings“, IEEE Transactions on Visualization and Computer Graphics 19:2277-2286 (2013). IEEE InfoVis 2013 Best Paper Award | Featured in IEEE Computing Now, Harvard SEAS News, Forbes, Scientific Computing, Der Standard article cell-glioblastoma 2013 http://www.cell.com/abstract/S0092-8674(13)01208-7 CW Brennan, RG Verhaak, A McKenna, B Campos, H Noushmehr, SR Salama, S Zheng, D Chakravarty, JZ Sanborn, SH Berman, R Beroukhim, B Bernard, CJ Wu, G Genovese, I Shmulevich, J Barnholtz-Sloan, L Zou, R Vegesna, SA Shukla, G Ciriello, WK Yung, W Zhang, C Sougnez, T Mikkelsen, K Aldape, DD Bigner, EG Van Meir, M Prados, A Sloan, KL Black, J Eschbacher, G Finocchiaro, W Friedman, DW Andrews, A Guha, M Iacocca, BP O’Neill, G Foltz, J Myers, DJ Weisenberger, R Penny, R Kucherlapati, CM Perou, DN Hayes, R Gibbs, M Marra, GB Mills, E Lander, P Spellman, R Wilson, C Sander, J Weinstein, M Meyerson, S Gabriel, PW Laird, D Haussler, G Getz, L Chin, The Cancer Genome Atlas Network, incl. N Gehlenborg, “The somatic genomic landscape of glioblastoma“, Cell 155:462-77 (2013). article nature-atlas 2013 http://www.nature.com/ng/journal/v45/n10/full/ng.2764.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “The Cancer Genome Atlas Pan-Cancer analysis project“, Nature Genetics 45:1113–1120 (2013). article nature-renal 2013 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12222.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular characterization of clear cell renal cell carcinoma“, Nature 499:43–49 (2013). article cell-mechanisms 2013 http://www.cell.com/abstract/S0092-8674(13)00451-0 L Yang, LJ Luquette, N Gehlenborg, R Xi, PS Haseley, C-H Hsieh, C Zhang, X Ren, A Protopopov, L Chin, R Kucherlapati, C Lee, PJ Park and The Cancer Genome Atlas Network, “Diverse mechanisms of somatic structural variations in human cancer genomes“, Cell 153:919-929 (2013). article bioinformatics-nozzle 2013 http://www.genomeweb.com/informatics/februarys-bioinformatics-papers-note N Gehlenborg, MS Noble, G Getz, L Chin and PJ Park, “Nozzle: a report generation toolkit for data analysis pipelines“, Bioinformatics 29:1089-1091 (2013). Featured in GenomeWeb Bioinformatics Papers of Note for February 2013. article nature-breast 2012 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11412.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular portraits of human breast tumours“, Nature 490:61–70 (2012). article nature-squamous 2012 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11404.html The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive genomic characterization of squamous cell lung cancers“, Nature 489:519–525 (2012). article nature-colon 2012 http://dx.doi.org/10.1038/nature11252 The Cancer Genome Atlas Network, incl. N Gehlenborg, “Comprehensive molecular characterization of human colon and rectal cancer“, Nature 487:330–337 (2012) . article computer-graphics 2012 http://www.cg.tuwien.ac.at/eurovis2012/awards/best-paper-award/ A Lex, M Streit, H-J Schulz, C Partl, D Schmalstieg, PJ Park, N Gehlenborg, “StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization“, Computer Graphics Forum 31:1175-1184 (2012). Proceedings of EuroVis Conference 2012 3rd Best Paper Award. article bioinformatics-mesothelioma 2012 http://bioinformatics.oxfordjournals.org/content/early/2011/11/20/bioinformatics.btr634.abstract J Caldas*, N Gehlenborg, E Kettunen, A Faisal, M Rönty, AG Nicholson, S Knuutila, A Brazma and S Kaski, “ Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural Mesothelioma“, Bioinformatics 28(2):246-253 (2012). article nature-methods-omics 2010 http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.1436.html N Gehlenborg, SI O’Donoghue, NS Baliga, A Goesmann, MA Hibbs, H Kitano, O Kohlbacher, H Neuweger, R Schneider, D Tenenbaum and AC Gavin, “Visualization of Omics Data for Systems Biology“, Nature Methods 7(3):S56-S68 (2010). article ieee-icassp 2010 http://dx.doi.org/10.1109/ICASSP.2010.5495665 J Peltonen, H Aidos, N Gehlenborg, A Brazma and S Kaski, “An Information Retrieval Perspective on Visualization of Gene Expression Data with Ontological Annotation“. In Proceedings of the IEEE 2010 International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2010), 2178-2181 (2010). article database 2009 http://dx.doi.org/10.1093/database/bap011 N Gehlenborg, D Hwang*, IY Lee*, H Yoo, B Petritis, D Baxter, R Pitstick, B Marzolf, SJ DeArmond, GA Carlson and LE Hood, “The Prion Disease Database: A Comprehensive Transcriptome Resource for Systems Biology Research in Prion Diseases“, Database 2009:bap011 (2009). article bioinformatics-microarray 2009 http://dx.doi.org/10.1093/bioinformatics/btp215 J Caldas, N Gehlenborg, A Faisal, A Brazma and S Kaski, “Probabilistic retrieval and visualization of biologically relevant microarray experiments“, Bioinformatics 25(12):i145-i153 (2009). article molecular-systems 2009 http://dx.doi.org/10.1038/msb.2009.10 D Hwang*, IY Lee*, H Yoo*, N Gehlenborg, J Cho, B Petritis, D Baxter, R Pitstick, R Young, D Spicer, N Price, JG Hohmann, SJ DeArmond, GA Carlson and LE Hood, “A Systems Approach to Prion Disease“, Molecular Systems Biology 5:252 (2009). article bioinformatics-prequips 2009 http://dx.doi.org/10.1093/bioinformatics/btp005 N Gehlenborg, W Yan, I Lee, H Yoo, K Nieselt, D Hwang, R Aebersold, L Hood, “Prequips – An Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics Data“, Bioinformatics 25(5):682-683 (2009). article proteomics-peptide 2008 http://dx.doi.org/10.1074/mcp.M700498-MCP200 A Schmidt, N Gehlenborg, B Bodenmiller, LN Mueller, D Campbell, M Mueller, R Aebersold and B Domon, “An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures“, Molecular & Cellular Proteomics 7:2138-2150 (2008). article bioinformatics-mayday 2006 http://dx.doi.org/10.1093/bioinformatics/btl070 J Dietzsch*, N Gehlenborg* and K Nieselt, “Mayday – A Microarray Data Analysis Workbench“, Bioinformatics 22(8):1010-1012 (2006). article information-visualization 2005 http://dx.doi.org/10.1057/palgrave.ivs.9500094 N Gehlenborg, J Dietzsch and K Nieselt, “A Framework for Visualization of Microarray Data and Integrated Meta Information“, Information Visualization 4(3):164-175 (2005).

other nature-sets-intersections 2014 http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html A Lex and N Gehlenborg, “Points of View: Sets and Intersections“, Nature Methods 11(8):779 (2014). other nature-bar-box 2014 http://www.nature.com/nmeth/journal/v11/n2/abs/nmeth.2807.html M Streit and N Gehlenborg, “Points of View: Bar Charts and Box Plots“, Nature Methods 11(2):117 (2014). other amia-isa 2013 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814497/ S Ho Sui, E Merrill, N Gehlenborg, P Haseley, I Sytchev, R Park, P Rocca-Serra, S Corlosquet, A Gonzalez-Beltran, E Maguire, O Hofmann, PJ Park, S Das, SA Sansone, W Hide, “The Stem Cell Commons: an exemplar for data integration in the biomedical domain driven by the ISA framework“, AMIA Summits Translational Science Proceedings 2013:70 (2013). other plos-shoes 2013 http://www.ploscompbiol.org/article/metrics/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002834 J de Ridder*, T Abeel*, M Michaut, VP Satagopam and N Gehlenborg, “Don’t Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator” (Workshop Report), PLoS Computational Biology 9(1):e1002834 (2013). Most viewed article in PLoS Computational Biology during February/March 2013 with more than 12,000 views in 30 days. other nature-plane 2012 http://www.nature.com/nmeth/journal/v9/n10/full/nmeth.2186.html N Gehlenborg and B Wong, “Points of View: Power of the Plane“, Nature Methods 9(10):935 (2012). other nature-third 2012 http://www.nature.com/nmeth/journal/v9/n9/full/nmeth.2151.html N Gehlenborg and B Wong, “Points of View: Into the Third Dimension“, Nature Methods 9(9):851 (2012). other nature-color 2012 http://www.nature.com/nmeth/journal/v9/n8/full/nmeth.2134.html N Gehlenborg and B Wong, “Points of View: Mapping Quantitative Data to Color“, Nature Methods 9(8):769 (2012). other nature-integrating 2012 http://www.nature.com/nmeth/journal/v9/n4/abs/nmeth.1944.html N Gehlenborg and B Wong, “Points of View: Integrating Data“, Nature Methods 9(4):315 (2012). other nature-heat 2012 http://www.nature.com/nmeth/journal/v9/n3/abs/nmeth.1902.html N Gehlenborg and B Wong, “Points of View: Heat maps“, Nature Methods 9(3):213 (2012). other nature-networks 2012 http://www.nature.com/nmeth/journal/v9/n2/abs/nmeth.1862.html N Gehlenborg and B Wong, “Points of View: Networks“, Nature Methods 9(2):115 (2012). other nature-future 2010 http://www.nature.com/nmeth/journal/v7/n3s/abs/nmeth.f.301.html SI O’Donoghue, AC Gavin, N Gehlenborg, DS Goodsell, JK Heriche, CB Nielsen, C North, AJ Olson, JB Procter, DW Shattuck, T Walter and B Wong, “Visualizing biological data – now and in the future“. Nature Methods 7(3):S2-S4 (2010). other bmc-space 2009 http://www.biomedcentral.com/1471-2105/10/S13/O7 N Gehlenborg and A Brazma, “Visualization of Large Microarray Experiments with Space Maps” (Abstract), BMC Bioinformatics 10(Suppl 13):O7 (2009). other bmc-probabilistic 2009 http://www.biomedcentral.com/1471-2105/10/S13/P1 J Caldas, N Gehlenborg, A Faisal, A Brazma and S Kaski, “Probabilistic Retrieval and Visualization of Biologically Relevant Microarray Experiments” (Abstract), BMC Bioinformatics 10(Suppl 13):P1 (2009). other bmc-highlights 2008 http://dx.doi.org/10.1186/1471-2105-9-S10-I1 L Peixoto, N Gehlenborg and S Chandra Janga (Eds.), “Highlights from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium at the Sixteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)“, BMC Bioinformatics 9(Suppl 10):I1 (2008). other plos-ten 2008 http://dx.doi.org/10.1371/journal.pcbi.1000080 M Corpas, N Gehlenborg, S Chandra Janga and PE Bourne, “Ten Simple Rules for Organizing a Scientific Meeting“, PLoS Computational Biology 4(6):e1000080 (2008). other bmc-highlights 2007 http://dx.doi.org/10.1186/1471-2105-8-S8-I1 N Gehlenborg, M Corpas and S Chandra Janga (Eds.), “Highlights from the Third International Society for Computational Biology (ISCB) Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)“, BMC Bioinformatics 8(Suppl 8):I1 (2007). other softwareforschung-dna 2005 http://www.amazon.de/Aktuelle-Trends-Softwareforschung-Tagungsband-Software-Forschungstag/dp/3898644138 N Gehlenborg, “Visualisierung für DNA-Chip-Analysen“, in D. Spath, K. Haasis and D. Klumpp (Eds.), Aktuelle Trends in der Softwareforschung (Vol. 3), 259-270, IRB Fraunhofer Verlag, Stuttgart, Germany (2005).

thesis phd 2010 http://gehlenborg.com/wp-content/uploads/2012/11/nils-gehlenborg_phd.pdf N Gehlenborg, “Visualization and Exploration of Transcriptomics Data“, PhD Thesis, University of Cambridge, United Kingdom (2010). thesis diplomarbeit 2006 http://gehlenborg.com/wp-content/uploads/2011/12/nils-gehlenborg_masters.pdf N Gehlenborg, “Visualization and Integration of Liquid Chromatography/Mass Spectrometry Proteomics Data“, Diplomarbeit (eq. Masters Thesis), University of Tübingen, Germany (2006). thesis studienarbeit 2003 http://gehlenborg.com/wp-content/uploads/2011/12/nils-gehlenborg_bachelors.pdf N Gehlenborg, “Mayday – Microarray Data Analysis“, Studienarbeit (eq. Bachelors Thesis), University of Tübingen, Germany (2003). thesis

ngehlenborg commented 7 years ago

Wow, impressive expression! Why don't you give it a try? We'll most likely have to do some manual curation in any case.