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Items: 31

1.

Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small-Cell Lung Cancer.

Chang H, Sasson A, Srinivasan S, Golhar R, Greenawalt DM, Geese WJ, Green G, Zerba K, Kirov S, Szustakowski J.

Mol Diagn Ther. 2019 Aug;23(4):507-520. doi: 10.1007/s40291-019-00408-y.

2.

First-Line Nivolumab Plus Ipilimumab in Advanced Non-Small-Cell Lung Cancer (CheckMate 568): Outcomes by Programmed Death Ligand 1 and Tumor Mutational Burden as Biomarkers.

Ready N, Hellmann MD, Awad MM, Otterson GA, Gutierrez M, Gainor JF, Borghaei H, Jolivet J, Horn L, Mates M, Brahmer J, Rabinowitz I, Reddy PS, Chesney J, Orcutt J, Spigel DR, Reck M, O'Byrne KJ, Paz-Ares L, Hu W, Zerba K, Li X, Lestini B, Geese WJ, Szustakowski JD, Green G, Chang H, Ramalingam SS.

J Clin Oncol. 2019 Apr 20;37(12):992-1000. doi: 10.1200/JCO.18.01042. Epub 2019 Feb 20.

PMID:
30785829
3.

Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer.

Hellmann MD, Callahan MK, Awad MM, Calvo E, Ascierto PA, Atmaca A, Rizvi NA, Hirsch FR, Selvaggi G, Szustakowski JD, Sasson A, Golhar R, Vitazka P, Chang H, Geese WJ, Antonia SJ.

Cancer Cell. 2019 Feb 11;35(2):329. doi: 10.1016/j.ccell.2019.01.011. No abstract available.

PMID:
30753829
4.

STK11/LKB1 Mutations and PD-1 Inhibitor Resistance in KRAS-Mutant Lung Adenocarcinoma.

Skoulidis F, Goldberg ME, Greenawalt DM, Hellmann MD, Awad MM, Gainor JF, Schrock AB, Hartmaier RJ, Trabucco SE, Gay L, Ali SM, Elvin JA, Singal G, Ross JS, Fabrizio D, Szabo PM, Chang H, Sasson A, Srinivasan S, Kirov S, Szustakowski J, Vitazka P, Edwards R, Bufill JA, Sharma N, Ou SI, Peled N, Spigel DR, Rizvi H, Aguilar EJ, Carter BW, Erasmus J, Halpenny DF, Plodkowski AJ, Long NM, Nishino M, Denning WL, Galan-Cobo A, Hamdi H, Hirz T, Tong P, Wang J, Rodriguez-Canales J, Villalobos PA, Parra ER, Kalhor N, Sholl LM, Sauter JL, Jungbluth AA, Mino-Kenudson M, Azimi R, Elamin YY, Zhang J, Leonardi GC, Jiang F, Wong KK, Lee JJ, Papadimitrakopoulou VA, Wistuba II, Miller VA, Frampton GM, Wolchok JD, Shaw AT, Jänne PA, Stephens PJ, Rudin CM, Geese WJ, Albacker LA, Heymach JV.

Cancer Discov. 2018 Jul;8(7):822-835. doi: 10.1158/2159-8290.CD-18-0099. Epub 2018 May 17.

5.

Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer.

Hellmann MD, Callahan MK, Awad MM, Calvo E, Ascierto PA, Atmaca A, Rizvi NA, Hirsch FR, Selvaggi G, Szustakowski JD, Sasson A, Golhar R, Vitazka P, Chang H, Geese WJ, Antonia SJ.

Cancer Cell. 2018 May 14;33(5):853-861.e4. doi: 10.1016/j.ccell.2018.04.001. Epub 2018 May 3. Erratum in: Cancer Cell. 2019 Feb 11;35(2):329.

6.

Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden.

Hellmann MD, Ciuleanu TE, Pluzanski A, Lee JS, Otterson GA, Audigier-Valette C, Minenza E, Linardou H, Burgers S, Salman P, Borghaei H, Ramalingam SS, Brahmer J, Reck M, O'Byrne KJ, Geese WJ, Green G, Chang H, Szustakowski J, Bhagavatheeswaran P, Healey D, Fu Y, Nathan F, Paz-Ares L.

N Engl J Med. 2018 May 31;378(22):2093-2104. doi: 10.1056/NEJMoa1801946. Epub 2018 Apr 16.

7.

Genome-wide association analysis identifies genetic correlates of immune infiltrates in solid tumors.

Siemers NO, Holloway JL, Chang H, Chasalow SD, Ross-MacDonald PB, Voliva CF, Szustakowski JD.

PLoS One. 2017 Jul 27;12(7):e0179726. doi: 10.1371/journal.pone.0179726. eCollection 2017.

8.

Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families.

Ngcungcu T, Oti M, Sitek JC, Haukanes BI, Linghu B, Bruccoleri R, Stokowy T, Oakeley EJ, Yang F, Zhu J, Sultan M, Schalkwijk J, van Vlijmen-Willems IMJJ, von der Lippe C, Brunner HG, Ersland KM, Grayson W, Buechmann-Moller S, Sundnes O, Nirmala N, Morgan TM, van Bokhoven H, Steen VM, Hull PR, Szustakowski J, Staedtler F, Zhou H, Fiskerstrand T, Ramsay M.

Am J Hum Genet. 2017 May 4;100(5):737-750. doi: 10.1016/j.ajhg.2017.03.012. Epub 2017 Apr 27.

9.

Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization.

Bizet AA, Becker-Heck A, Ryan R, Weber K, Filhol E, Krug P, Halbritter J, Delous M, Lasbennes MC, Linghu B, Oakeley EJ, Zarhrate M, Nitschké P, Garfa-Traore M, Serluca F, Yang F, Bouwmeester T, Pinson L, Cassuto E, Dubot P, Elshakhs NAS, Sahel JA, Salomon R, Drummond IA, Gubler MC, Antignac C, Chibout S, Szustakowski JD, Hildebrandt F, Lorentzen E, Sailer AW, Benmerah A, Saint-Mezard P, Saunier S.

Nat Commun. 2015 Oct 21;6:8666. doi: 10.1038/ncomms9666.

10.

The use of haplotype-specific transcripts improves sample annotation consistency.

Hartmann N, Luesink E, Khokhlovich E, Szustakowski JD, Baeriswyl L, Peterson J, Scherer A, Nanguneri NR, Staedtler F.

Biomark Res. 2014 Sep 30;2:17. doi: 10.1186/2050-7771-2-17. eCollection 2014.

11.

Whole-exome sequencing reveals overlap between macrophage activation syndrome in systemic juvenile idiopathic arthritis and familial hemophagocytic lymphohistiocytosis.

Kaufman KM, Linghu B, Szustakowski JD, Husami A, Yang F, Zhang K, Filipovich AH, Fall N, Harley JB, Nirmala NR, Grom AA.

Arthritis Rheumatol. 2014 Dec;66(12):3486-95. doi: 10.1002/art.38793.

12.

LMX1B mutations cause hereditary FSGS without extrarenal involvement.

Boyer O, Woerner S, Yang F, Oakeley EJ, Linghu B, Gribouval O, Tête MJ, Duca JS, Klickstein L, Damask AJ, Szustakowski JD, Heibel F, Matignon M, Baudouin V, Chantrel F, Champigneulle J, Martin L, Nitschké P, Gubler MC, Johnson KJ, Chibout SD, Antignac C.

J Am Soc Nephrol. 2013 Jul;24(8):1216-22. doi: 10.1681/ASN.2013020171. Epub 2013 May 16.

13.

DeconRNASeq: a statistical framework for deconvolution of heterogeneous tissue samples based on mRNA-Seq data.

Gong T, Szustakowski JD.

Bioinformatics. 2013 Apr 15;29(8):1083-5. doi: 10.1093/bioinformatics/btt090. Epub 2013 Feb 21.

PMID:
23428642
14.

RAMP: a bioinformatics framework for researching imaging agents through molecular pathways.

Khokhlovich E, Wahl D, Masiello A, Parisot P, El-Ghatta S, Szustakowski JD, Nirmala N, Tuch DS.

Mol Imaging. 2013 Jan-Feb;12(1):2-7.

PMID:
23348786
15.

Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples.

Gong T, Hartmann N, Kohane IS, Brinkmann V, Staedtler F, Letzkus M, Bongiovanni S, Szustakowski JD.

PLoS One. 2011;6(11):e27156. doi: 10.1371/journal.pone.0027156. Epub 2011 Nov 16.

16.

Human cytomegalovirus escapes a naturally occurring neutralizing antibody by incorporating it into assembling virions.

Manley K, Anderson J, Yang F, Szustakowski J, Oakeley EJ, Compton T, Feire AL.

Cell Host Microbe. 2011 Sep 15;10(3):197-209. doi: 10.1016/j.chom.2011.07.010.

17.

Bioinformatics analysis of microarray data.

Zhang Y, Szustakowski J, Schinke M.

Methods Mol Biol. 2009;573:259-84. doi: 10.1007/978-1-60761-247-6_15. Review.

PMID:
19763933
18.

Transcriptome changes in renal allograft protocol biopsies at 3 months precede the onset of interstitial fibrosis/tubular atrophy (IF/TA) at 6 months.

Scherer A, Gwinner W, Mengel M, Kirsch T, Raulf F, Szustakowski JD, Hartmann N, Staedtler F, Engel G, Klupp J, Korn A, Kehren J, Haller H.

Nephrol Dial Transplant. 2009 Aug;24(8):2567-75. doi: 10.1093/ndt/gfp183. Epub 2009 Apr 27.

PMID:
19398767
19.

Identification of novel genes and pathways regulating SREBP transcriptional activity.

Chatterjee S, Szustakowski JD, Nanguneri NR, Mickanin C, Labow MA, Nohturfft A, Dev KK, Sivasankaran R.

PLoS One. 2009;4(4):e5197. doi: 10.1371/journal.pone.0005197. Epub 2009 Apr 21.

20.

Uncovering mechanisms of transcriptional regulations by systematic mining of cis regulatory elements with gene expression profiles.

Ma Q, Chirn GW, Szustakowski JD, Bakhtiarova A, Kosinski PA, Kemp D, Nirmala N.

BioData Min. 2008 Jul 17;1(1):4. doi: 10.1186/1756-0381-1-4.

21.

Dynamic resolution of functionally related gene sets in response to acute heat stress.

Szustakowski JD, Kosinski PA, Marrese CA, Lee JH, Elliman SJ, Nirmala N, Kemp DM.

BMC Mol Biol. 2007 Jun 5;8:46.

22.

Estrogen-related receptor alpha is essential for the expression of antioxidant protection genes and mitochondrial function.

Rangwala SM, Li X, Lindsley L, Wang X, Shaughnessy S, Daniels TG, Szustakowski J, Nirmala NR, Wu Z, Stevenson SC.

Biochem Biophys Res Commun. 2007 May 25;357(1):231-6. Epub 2007 Mar 28.

PMID:
17418099
23.

Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation.

Kemp DM, Nirmala NR, Szustakowski JD.

Bioinformatics. 2007 Jun 1;23(11):1356-62. Epub 2007 Mar 28.

PMID:
17392327
24.

From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications.

Plikat U, Voshol H, Dangendorf Y, Wiedmann B, Devay P, Müller D, Wirth U, Szustakowski J, Chirn GW, Inverardi B, Puyang X, Brown K, Kamp H, Hoving S, Ruchti A, Brendlen N, Peterson R, Buco J, Oostrum Jv, Peitsch MC.

Proteomics. 2007 Mar;7(6):992-1003.

PMID:
17370256
25.

Pyruvate induces mitochondrial biogenesis by a PGC-1 alpha-independent mechanism.

Wilson L, Yang Q, Szustakowski JD, Gullicksen PS, Halse R.

Am J Physiol Cell Physiol. 2007 May;292(5):C1599-605. Epub 2006 Dec 20.

26.

Identification of novel pathway regulation during myogenic differentiation.

Szustakowski JD, Lee JH, Marrese CA, Kosinski PA, Nirmala NR, Kemp DM.

Genomics. 2006 Jan;87(1):129-38. Epub 2005 Nov 21.

27.

Less is more: towards an optimal universal description of protein folds.

Szustakowski JD, Kasif S, Weng Z.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii66-71.

PMID:
16204127
28.
29.

Computational identification of operons in microbial genomes.

Zheng Y, Szustakowski JD, Fortnow L, Roberts RJ, Kasif S.

Genome Res. 2002 Aug;12(8):1221-30.

30.

Gene discovery in the auditory system: characterization of additional cochlear-expressed sequences.

Resendes BL, Robertson NG, Szustakowski JD, Resendes RJ, Weng Z, Morton CC.

J Assoc Res Otolaryngol. 2002 Mar;3(1):45-53.

31.

Protein structure alignment using a genetic algorithm.

Szustakowski JD, Weng Z.

Proteins. 2000 Mar 1;38(4):428-40.

PMID:
10707029

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