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Items: 1 to 20 of 77

1.

Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism.

Lerin C, Goldfine AB, Boes T, Liu M, Kasif S, Dreyfuss JM, De Sousa-Coelho AL, Daher G, Manoli I, Sysol JR, Isganaitis E, Jessen N, Goodyear LJ, Beebe K, Gall W, Venditti CP, Patti ME.

Mol Metab. 2016 Aug 6;5(10):926-36. doi: 10.1016/j.molmet.2016.08.001. eCollection 2016 Oct.

2.

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

Chang YC, Hu Z, Rachlin J, Anton BP, Kasif S, Roberts RJ, Steffen M.

Nucleic Acids Res. 2016 Jan 4;44(D1):D330-5. doi: 10.1093/nar/gkv1324. Epub 2015 Dec 3.

3.

Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes.

Nogiec C, Burkart A, Dreyfuss JM, Lerin C, Kasif S, Patti ME.

Mol Metab. 2015 Jan 2;4(3):151-63. doi: 10.1016/j.molmet.2014.12.012. eCollection 2015 Mar.

4.

Identification of rare germline copy number variations over-represented in five human cancer types.

Park RW, Kim TM, Kasif S, Park PJ.

Mol Cancer. 2015 Feb 3;14:25. doi: 10.1186/s12943-015-0292-6.

5.

Objective: biochemical function.

Anton BP, Kasif S, Roberts RJ, Steffen M.

Front Genet. 2014 Jul 8;5:210. doi: 10.3389/fgene.2014.00210. eCollection 2014. No abstract available.

6.

Hypermutable DNA chronicles the evolution of human colon cancer.

Naxerova K, Brachtel E, Salk JJ, Seese AM, Power K, Abbasi B, Snuderl M, Chiang S, Kasif S, Jain RK.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):E1889-98. doi: 10.1073/pnas.1400179111. Epub 2014 Apr 21.

7.

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.

Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, Beik S, Kadri S, Tirosh I, Wortman I, Shalek AK, Rozenblatt-Rosen O, Regev A, Louis DN, Bernstein BE.

Cell. 2014 Apr 24;157(3):580-94. doi: 10.1016/j.cell.2014.02.030. Epub 2014 Apr 10.

8.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

9.

To supplement or not to supplement: a metabolic network framework for human nutritional supplements.

Nogiec CD, Kasif S.

PLoS One. 2013 Aug 5;8(8):e68751. doi: 10.1371/journal.pone.0068751. eCollection 2013.

10.

Systems biology characterization of engineered tissues.

Rajagopalan P, Kasif S, Murali TM.

Annu Rev Biomed Eng. 2013;15:55-70. doi: 10.1146/annurev-bioeng-071811-150120. Review.

PMID:
23862675
11.

Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori.

Choi HP, Juarez S, Ciordia S, Fernandez M, Bargiela R, Albar JP, Mazumdar V, Anton BP, Kasif S, Ferrer M, Steffen M.

PLoS One. 2013 Jun 18;8(6):e66605. doi: 10.1371/journal.pone.0066605. Print 2013.

12.

An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma.

Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE.

Cell Rep. 2013 May 30;3(5):1567-79. doi: 10.1016/j.celrep.2013.04.021. Epub 2013 May 23.

13.

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.

Wood DE, Lin H, Levy-Moonshine A, Swaminathan R, Chang YC, Anton BP, Osmani L, Steffen M, Kasif S, Salzberg SL.

Biol Direct. 2012 Oct 30;7:37. doi: 10.1186/1745-6150-7-37.

14.

Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S.

PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919. Epub 2012 Jun 4.

15.

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S.

Nucleic Acids Res. 2011 Jan;39(Database issue):D11-4. doi: 10.1093/nar/gkq1168. Epub 2010 Nov 21.

16.

A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease.

Mori MA, Liu M, Bezy O, Almind K, Shapiro H, Kasif S, Kahn CR.

Diabetes. 2010 Nov;59(11):2960-71. doi: 10.2337/db10-0367. Epub 2010 Aug 16.

17.

Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle.

Mitrofanova A, Kleinberg S, Carlton J, Kasif S, Mishra B.

Artif Intell Med. 2010 Jul;49(3):167-76. doi: 10.1016/j.artmed.2010.04.013. Epub 2010 Jun 26.

PMID:
20580212
18.

Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis.

Anton BP, Russell SP, Vertrees J, Kasif S, Raleigh EA, Limbach PA, Roberts RJ.

Nucleic Acids Res. 2010 Oct;38(18):6195-205. doi: 10.1093/nar/gkq364. Epub 2010 May 14.

19.

Biochemical networks: the evolution of gene annotation.

Kasif S, Steffen M.

Nat Chem Biol. 2010 Jan;6(1):4-5. doi: 10.1038/nchembio.288. No abstract available.

20.

A predictive phosphorylation signature of lung cancer.

Wu CJ, Cai T, Rikova K, Merberg D, Kasif S, Steffen M.

PLoS One. 2009 Nov 25;4(11):e7994. doi: 10.1371/journal.pone.0007994.

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