# The below includes publications with AltAnalyze citations - updated May 17, 2021 -- includes AltAnalyze and AltAnalyze tools (ICGS2, cellHarmony, NetPerspective, MultiPath-PSI)

Alternative Splicing Regulation

Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. Salomonis N, Nelson B, Vranizan K, Pico AR, Hanspers K, Kuchinsky A, Ta L, Mercola M, Conklin BR. PLoS Comput Biol. 2009 Nov;5(11):e1000553. Epub 2009 Nov 6.

Gi-Coupled GPCR Signaling Controls the Formation and Organization of Human Pluripotent Colonies. K Nakamura, N Salomonis, K Tomoda, S Yamanaka, and BR Conklin. PLoS One. 2009; 4(11): e7780. Published online 2009 November 10. doi: 10.1371/journal.pone.0007780.

AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W755-62. Epub 2010 May 31.

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation. Salomonis N, Schlieve CR, Pereira L, Wahlquist C, Colas A, Zambon AC, Vranizan K, Spindler MJ, Pico AR, Cline MS, Clark TA, Williams A, Blume JE, Samal E, Mercola M, Merrill BJ, Conklin BR. Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10514-9. Epub 2010 May 24.

Analysis of whole genome biomarker expression in blood and brain. Rollins B, Martin MV, Morgan L, Vawter MP. Am J Med Genet B Neuropsychiatr Genet. 2010 Jun 5;153B(4):919-36.

Stem cell pluripotency: alternative modes of transcription regulation. Salomonis N, Conklin BR. Cell Cycle. 2010 Aug 15;9(16):3133-4. Epub 2010 Aug 2.

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging. Keith E Szulwach, Xuekun Li, Yujing Li, Chun-Xiao Song, Hao Wu, Qing Dai, Hasan Irier, Anup K Upadhyay, Marla Gearing, Allan I Levey, Aparna Vasanthakumar, Lucy A Godley, Qiang Chang, Xiaodong Cheng, Chuan He & Peng Jin. Nature Neuroscience(2011) doi:10.1038/nn.2959

Cholinergic-associated loss of hnRNP-A/B in Alzheimer's disease impairs cortical splicing and cognitive function in mice. Berson A, Barbash S, Shaltiel G, Goll Y, Hanin G, Greenberg DS, Ketzef M, Becker AJ, Friedman A, Soreq H. EMBO Mol Med. doi: 10.1002/emmm.201100995

Differentially regulated splice variants and systems biology analysis of Kaposi's sarcoma-associated herpesvirus-infected lymphatic endothelial cells.Ting-Yu Chang, Yu-Hsuan Wu, Cheng-Chung Cheng and Hsei-Wei Wang. Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr405.

Exon array analysis reveals neuroblastoma tumors have distinct alternative splicing patterns according to stage and MYCN amplification status. Xiang Guo, Qing-Rong Chen, Young K Song, Jun S Wei and Javed Khan. BMC Medical Genomics 2011, 4:35doi:10.1186/1755-8794-4-35.

Exon Arrays Reveal Alternative Splicing Aberrations in Parkinson’s Disease Leukocytes. Lilach Soreq, Hagai Bergman, Zvi Israel, Hermona Soreq. Neurodegener Dis. 2011 Dec 9.

Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events. Pascal Gellert, Mizue Teranishi, Katharina Jenniches, Piera De Gaspari, David John, Karsten grosse Kreymborg, Thomas Braun and Shizuka Uchida. Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr1110

Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability. Neelanjan Mukherjee, David L. Corcoran, Jeffrey D. Nusbaum, David W. Reid, Stoyan Georgiev, Markus Hafner, Manuel Ascano Jr., Thomas Tuschl, Uwe Ohler, and Jack D. Keene. Mol Cell. 2011 Jun 29.

Measuring and analyzing tissue specificity of human genes and protein complexes. Dorothea Emig, Tim Kacprowski and Mario Albrecht. EURASIP J Bioinform Syst Biol. 2011(1): 5. 10.1186/1687-4153-2011-5

MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes. Grigoryev YA, Kurian SM, Hart T, Nakorchevsky AA, Chen C, Campbell D, Head SR, Yates JR 3rd, Salomon DR. J Immunol. 2011 Sep 1;187(5):2233-43. doi: 10.4049/jimmunol.1101233.

Quaking Regulates Hnrnpa1 Expression through Its 3′ UTR in Oligodendrocyte Precursor Cells. N Ruth Zearfoss, Carina C Clingman, Brian M Farley, Lisa M McCoig?, Sean P Ryder. PLoS Genetics: Research Article, published 06 Jan 2011 10.1371/journal.pgen.1001269.

Son maintains accurate splicing for a subset of human pre-mRNAs. Alok Sharma, Michael Markey, Keshia Torres-Muñoz, Sapna Varia, Madhavi Kadakia, Athanasios Bubulya and Paula A. Bubulya. J Cell Sci. 2011 Dec 22 doi: 10.1242/​jcs.092239

Antagonistic function of the RNA-binding protein HuR and miR-200b in post-transcriptional regulation of VEGF-A expression and angiogenesis. Chang S, Lu Y, Li1 X, Hsieh WY, Xiong Y, Ghosh M, Evans T, Elemento O, Hla T. December 6, 2012, doi: 10.1074/jbc.M112.423871 jbc.M112.423871.

AS-EAST: A functional annotation tool for putative proteins encoded by alternatively spliced transcripts. Shionyu M, Takahashi KI, Go M. Bioinformatics. 2012 May 29.

BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments. Consiglio A, Carella M, Caro GD, Foglie GD, Giovannelli C, Grillo G, Ianigro M, Licciulli F, Palumbo O, Piepoli A, Ranieri E and Liuni S. BMC Bioinformatics 2012, 13(Suppl 4):S21 doi:10.1186/1471-2105-13-S4-S21

Functional characterization of human genes from exon expression and RNA interference results.Emig D, Blankenburg H, Ramírez F, Albrecht M.Methods Mol Biol. 2012;910:33-53. doi: 10.1007/978-1-61779-965-5_3.

Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs. Kandpal RP, Rajasimha HK, Brooks MJ, Nellissery J, Wan J, Qian J, Kern TS, Swaroop A. Molecular Vision 2012; 18:1123-1146

AMDA 2.13: A major update for automated cross-platform microarray data analysis. Kapetis D, Clarelli F, Vitulli1 F, de Rosbo NK, Beretta O, Foti1 M, Ricciardi-Castagnoli P, and Zolezzi F. BioTechniques? 53:33-40 ( July 2012) doi 10.2144/0000113889.

Contextualization Procedure and Modeling of Monocyte Specific TLR Signaling. MK Aurich, I Thiele . PLoS ONE 7(12): e49978. doi:10.1371/journal.pone.0049978

Fishing for melanoma markers through comparative transcriptome analysis. Mione M, Armant O. Pigment Cell & Melanoma Research. 2012. doi: 10.1111/pcmr.12011

GO-Elite: A Flexible Solution for Pathway and Ontology Over-Representation. Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N. Bioinformatics. 2012 Jun 27.

Growth factor independence 1 (Gfi1) regulates cell-fate decision of a bipotential granulocytic-monocytic precursor defined by expression of Gfi1 and CD48. Lothar Vassen1, Ulrich Dührsen, Christian Kosan, Hui Zeng, Tarik Möröy1. Am J Blood Res 2012;2(4):228-242

KLF10 gene expression is associated with high fetal hemoglobin levels and with response to hydroxyurea treatment in β-hemoglobinopathy patients. Borg J, Phylactides M, Bartsakoulia M, Tafrali C, Lederer C, Felice AE, Papachatzopoulou A, Kourakli A, Stavrou EF, Christou S, Hou J, Karkabouna S, Lappa-Manakou C, Ozgur Z, van Ijcken W, von Lindern M, Grosveld FG, Georgitsi M, Kleanthous M, Philipsen S, Patrinos GP. Pharmacogenomics. 2012 Oct;13(13):1487-500.

Poly(ADP-ribose) polymerase 1 regulates nuclear reprogramming and promotes iPSC generation without c-Myc. Chiou SH, Jiang BH, Yu YL, Chou SJ, Tsai PH, Chang WC, Chen LK, Chen LH, Chien Y, Chiou GY. J Exp Med. 2012 Dec 31.

Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis. Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A. PLoS Genet. 2012 Apr;8(4):e1002649

A robust method to derive functional neural crest cells from human pluripotent stem cells. Kreitzer FR, Salomonis N, Sheehan A, Huang M, Park JS, Spindler MJ, Lizarraga P, Weiss WA, So PL, Conklin BR. Am J Stem Cells. 2013 Jun 30;2(2):119-31

Altered gene expression in dry age-related macular degeneration suggests early loss of choroidal endothelial cells. Whitmore SS, Braun TA, Skeie JM, Haas CM, Sohn EH, Stone EM, Scheetz TE, Mullins RF. Mol Vis. 2013 Nov 16;19:2274-2297.

Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity. Bishakha; M. Haupt, Larisa; R. Griffiths, Lyn. Current Genomics, Volume 14, Number 3, May 2013 , pp. 182-194(13).

An integrative framework identifies alternative splicing events in colorectal cancer development. Andrea Bisognina, Silvia Pizzinib,Lisa Perillib, Giovanni Espositoc, Simone Mocellind, Donato Nittid, Paola Zanovellob, Stefania Bortoluzzia, Susanna Mandruzzato. Mol. Oncology. 2013. dx.doi.org/10.1016/j.molonc.2013.10.004

Deep brain stimulation modulates nonsense-mediated RNA decay in Parkinson's patients leukocytes. Soreq L, Bergman H, Israel Z, Soreq H. BMC Genomics. 2013 Jul 16;14(1):478

Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge. Rodrigues R, Grosso AR, Moita L. PLoS One. 2013 Apr 17;8(4):e61975.

Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). Solomon O, Oren S, Safran M, Deshet-Unger N, Akiva P, Jacob-Hirsch J, Cesarkas K, Kabesa R, Amariglio N, Unger R, Rechavi G, Eyal E. RNA March 8, 2013.

GPViz: dynamic visualization of genomic regions and variants affecting protein domains. Snajder R, Trajanoski Z, Hackl H. Bioinformatics. 2013 Jul 5.

Protective Role of the Inflammatory CCR2/CCL2 Chemokine Pathway through Recruitment of Type 1 Cytotoxic γδ T Lymphocytes to Tumor Beds. Lança T, Costa MF, Gonçalves-Sousa N, Rei M, Grosso AR, Penido C, Silva-Santos B. J Immunol. 2013 May 17

Sarcoptes scabiei Mites Modulate Gene Expression in Human Skin Equivalents. Morgan MS, Arlian LG, Markey MP.PLoS One. 2013 Aug 5;8(8):e71143.

Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes.Soreq L, Salomonis N, Bronstein M, Greenberg D, Israel Z, Bergman H and Soreq H. Front. Mol. Neurosci., 13 May 2013

The Pattern of Cortical Dysfunction in a Mouse Model of a Schizophrenia-Related Microdeletion. Fénelon K, Xu B, Lai CS, Mukai J, Markx S, Stark KL, Hsu PK, Gan WB, Fischbach GD, Macdermott AB, Karayiorgou M, Gogos JA. J Neurosci. 2013 Sep 11;33(37):14825-14839.

Ca2+/Calmodulin-dependent protein kinase II δ mediates myocardial ischemia/reperfusion injury through nuclear factor-κB. Ling H, Gray CB, Zambon AC, Grimm M, Gu Y, Dalton N, Purcell NH, Peterson K, Brown JH. Circ Res. 2013 Mar 15;112(6):935-44. doi: 10.1161/CIRCRESAHA.112.276915. Epub 2013 Feb 6.

Deficiency of the lipid synthesis enzyme, DGAT1, extends longevity in mice.Streeper RS, Grueter CA, Salomonis N, Cases S, Levin MC, Koliwad SK, Zhou P, Hirschey MD, Verdin E, Farese RV Jr.

Jmjd3 Controls Mesodermal and Cardiovascular Differentiation of Embryonic Stem Cells. Ohtani K, Zhao C, Dobreva G, Manavski Y, Kluge B, Braun T, Rieger MA, Zeiher AM, Dimmeler S. Circ Res. 2013 Jul 15.

Model-based rational design of an oncolytic virus with improved therapeutic potential. Le Boeuf F, Batenchuk C, Vähä-Koskela M, Breton S, Roy D, Lemay C, Cox J, Abdelbary H, Falls T, Waghray G, Atkins H, Stojdl D, Diallo JS, Kærn M, Bell JC. Nat Commun. 2013 Jun 14;4:1974.

The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics. Sigdel TK, Salomonis N, Nicora CD, Ryu S, He J, Dinh V, Orton DJ, Moore RJ, Hsieh SC, Dai H, Thien-Vu M, Xiao W, Smith RD, Qian WJ, Camp DG 2nd, Sarwal MM. Mol Cell Proteomics. 2013 Dec 12.

The zinc finger transcription factor ZXDC activates CCL2 gene expression by opposing BCL6-mediated repression. Ramsey JE, Fontes JD. Mol Immunol. 2013 Dec 31;56(4):768-80.

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants. Peterson TA, Doughty E, Kann MG. J Mol Biol. 2013 Nov 1;425(21):4047-4063.

A survey of software for genome-wide discovery of differential splicing in RNA-Seq data. Hooper JE. Human Genomics 2014, 8:3.

Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells. Lu Y, Loh YH, Li H, Cesana M, Ficarro SB, Parikh JR, Salomonis N, Toh CX, Andreadis ST, Luckey CJ, Collins JJ, Daley GQ, Marto JA. Cell Stem Cell. 2014 May 7

Computational extraction of a neural molecular network through alternative splicing. Alam S, Phan HT, Okazaki M, Takagi M, Kawahara K, Tsukahara T, Suzuki H.BMC Res Notes. 2014 Dec 19;7:934. http://www.ncbi.nlm.nih.gov/pubmed/25590302

ELAVL1 regulates alternative splicing of eIF4E transporter to promote postnatal angiogenesis. Chang SH, Elemento O, Zhang J, Zhuang ZW, Simons M, Hla T. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18309-14.

Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress. McDade1? SS, Patel D, Moran M, Campbell J, Fenwick K, Kozarewa, Orr NJ, Lord CJ, Ashworth AA, McCance? DJ. Nucl. Acids Res. first published online May 13, 2014

Growth factor independence 1b (gfi1b) is important for the maturation of erythroid cells and the regulation of embryonic globin expression. Vassen L, Beauchemin H, Lemsaddek W, Krongold J, Trudel M, Möröy T. PLoS One. 2014 May 6;9(5):e96636.

Hypoxia Regulates Alternative Splicing of HIF and non-HIF Target Genes. Sena JA, Wang L, Heasley LE, Hu CJ. Mol Cancer Res. 2014 May 21. pii: molcanres.0149.2014.

Integrated exon level expression analysis of driver genes explain their role in colorectal cancer. Aziz MA, Periyasamy S, Al Yousef Z, AlAbdulkarim? I, Al Otaibi M, Alfahed A, Alasiri G.PLoS One. 2014 Oct 21;9(10):e110134.

Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. Soreq L, Guffanti A, Salomonis N, Simchovitz A, Israel Z, Bergman H, Soreq H. PLoS Comput Biol. 2014 Mar 20;10(3):e1003517.

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data. Gan Z, Wang J, Salomonis N, Stowe JC, Haddad GG, McCulloch? AD, Altintas I, Zambon AC. BMC Bioinformatics. 2014 Mar 12;15:69. doi: 10.1186/1471-2105-15-69.

Mucin Family Genes are Downregulated in Colorectal Cancer Patients. Aziz MA, AlOtaibi? M, AlAbdulrahman? A, AlDrees? M, AlAbdulkarim? I. J Carcinogene Mutagene 2014. S10:009. doi: 10.4172/2157-2518.S10-009

Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis. Moore-Morris T, Guimarães-Camboa N, Banerjee I, Zambon AC, Kisseleva T, Velayoudon A, Stallcup WB, Gu Y, Dalton ND, Cedenilla M, Gomez-Amaro R, Zhou B, Brenner DA, Peterson KL, Chen J, Evans SM. Journal Clin Invest. 2014 Jul 1;124(7):2921-34. doi: 10.1172/JCI74783. Epub 2014 Jun 17.

Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Li HD, Menon R, Omenn GS, Guan Y. Proteomics. 2014 Dec;14(23-24):2709-18.

Splicing factor SRSF6 promotes hyperplasia of sensitized skin. Jensen MA, Wilkinson JE, Krainer AR. Nat Struct Mol Biol. 2014 Jan 19.

Splicing regulator SLU7 is essential for maintaining liver homeostasis. Elizalde M, Urtasun R, Azkona M, Latasa MU, Goñi S, García-Irigoyen O, Uriarte I, Segura V, Collantes M, Di Scala M, Lujambio A, Prieto J, Ávila MA, Berasain C.J Clin Invest. 2014 Jul;124(7):2909-20.

The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells. Ammon, T., Mishra, S. K., Kowalska, K., Popowicz, G. M., Holak, T. A., & Jentsch, S. (2014). Journal of molecular cell biology, mju026. Chicago

Transcriptome analysis in cardiomyocyte-specific differentiation of murine embryonic stem cells reveals transcriptional regulation network. Gan L, Schwengberg S, Denecke B. Gene Expr Patterns. 2014 Jul 21. pii: S1567-133X(14)00059-3. doi: 10.1016/j.gep.2014.07.002

ABCG2pos Lung Mesenchymal Stem Cells are a Novel Pericyte Subpopulation that Contributes to Fibrotic Remodeling. Marriott S, Baskir RS, Gaskill C, Menon S, Carrier EJ, Williams J, Talati M, Helm K, Alford CE, Kropski JA, Loyd J, Wheeler L, Johnson J, Austin E, Nozik-Grayck E, Meyrick BO, West JD, Klemm DJ, Majka SM. Am J Physiol Cell Physiol. 2014 Aug 13. pii: ajpcell.00114.2014.

Integrated differential transcriptome maps of Acute Megakaryoblastic Leukemia (AMKL) in children with or without Down Syndrome (DS). Pelleri M, Piovesan A, Caracausi M, Berardi A, Vitale L, Strippoli P. BMC Med Genomics. 2014 Dec 5;7(1):63.

RNA-seq Data: Challenges in and Recommendations for Experimental Design and Analysis.Williams AG, Thomas S, Wyman SK, Holloway AK.Curr Protoc Hum Genet. 2014 Oct 1;83:11.13.1-11.13.20.

Systems-level perspective of sudden infant death syndrome. Salomonis N. Pediatr Res. 2014 Jun 25. doi: 10.1038/pr.2014.90.

Urinary exosomes: a novel means to non-invasively assess changes in renal gene and protein expression. Spanu S, van Roeyen CR, Denecke B, Floege J, Mühlfeld AS.PLoS One. 2014 Oct 13;9(10):e109631.

A survey of computational methods in transcriptome-wide alternative splicing analysis.Wang J, Ye Z, Huang TH, Shi H, Jin V. Biomol Concepts. 2015 Mar 1;6(1):59-66.

Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing. Jimeno-González S, Payán-Bravo L, Muñoz-Cabello AM, Guijo M, Gutierrez G, Prado F, Reyes JC. Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):14840-5. doi: 10.1073/pnas.1506760112

Distinct brain transcriptome profiles in C9orf72-associated and sporadic ALS. Prudencio M, Belzil VV, Batra R, Ross CA, Gendron TF, Pregent LJ, Murray ME, Overstreet KK, Piazza-Johnston AE, Desaro P, Bieniek KF, DeTure? M, Lee WC, Biendarra SM, Davis MD, Baker MC, Perkerson RB, van Blitterswijk M, Stetler CT, Rademakers R, Link CD, Dickson DW, Boylan KB, Li H, Petrucelli L. Nat Neurosci. 2015 Aug;18(8):1175-82. doi: 10.1038/nn.4065.

Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.Sheng Z, Sun Y, Zhu R, Jiao N, Tang K, Cao Z, Ma C.PLoS One. 2015 Nov 25;10(11):e0143742. doi: 10.1371/journal.pone.0143742.

FUS/TLS deficiency causes behavioral and pathological abnormalities distinct from amyotrophic lateral sclerosis. Kino Y, Washizu C, Kurosawa M, Yamada M, Miyazaki H, Akagi T, Hashikawa T, Doi H, Takumi T, Hicks GG, Hattori N, Shimogori T, Nukina N. Acta Neuropathol Commun. 2015 Apr 25;3:24. doi: 10.1186/s40478-015-0202-6.

Identification of novel radiation-induced p53-dependent transcripts extensively regulated during mouse brain development. Quintens R, Verreet T, Janssen A, Neefs M, Leysen L, Michaux A, Verslegers M, Samari N, Pani G, Verheyde J, Baatout S, Benotmane MA.Biol Open. 2015 Feb 13;4(3):331-44.

Long non-coding RNA LINC01296 is a potential prognostic biomarker in patients with colorectal cancer. Qiu JJ, Yan JB. Tumour Biol. 2015 Apr 17

MBNL1-mediated regulation of differentiation RNAs promotes myofibroblast transformation and the fibrotic response.Davis J, Salomonis N, Ghearing N, Lin SC, Kwong JQ, Mohan A, Swanson MS, Molkentin JD.Nat Commun. 2015 Dec 16;6:10084

Microtubule disruption synergizes with oncolytic virotherapy by inhibiting interferon translation and potentiating bystander killing. Arulanandam R, Batenchuk C, Varette O, Zakaria C, Garcia V, Forbes NE, Davis C, Krishnan R, Karmacharya R, Cox J, Sinha A, Babawy A, Waite K, Weinstein E, Falls T, Chen A, Hamill J, De Silva N, Conrad DP, Atkins H, Garson K, Ilkow C, Kærn M, Vanderhyden B, Sonenberg N, Alain T, Le Boeuf F, Bell JC, Diallo JS.Nat Commun. 2015 Mar 30;6:6410. doi: 10.1038/ncomms7410.

Novel transcription factor variants through RNA-sequencing: the importance of being "alternative". Scarpato M, Federico A, Ciccodicola A, Costa V.Int J Mol Sci. 2015 Jan 13;16(1):1755-71.

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression.Will T, Helms V.Bioinformatics. 2015 Oct 27. pii: btv620.

SplicingTypesAnno: Annotating and quantifying alternative splicing events for RNA-Seq data. Sun X, Zuo F, Ru Y, Guo J, Yan X, Sablok G.Comput Methods Programs Biomed. 2015 Apr;119(1):53-62.

Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity. Kamath-Rayne BD, Du Y, Hughes M, Wagner EA, Muglia LJ, DeFranco EA, Whitsett JA, Salomonis N, Xu Y.BMC Med Genomics. 2015 Oct 22;8(1):67. doi: 10.1186/s12920-015-0138-5.

The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells.Whisenant TC, Peralta ER, Aarreberg LD, Gao NJ, Head SR, Ordoukhanian P, Williamson JR, Salomon DR.PLoS One. 2015 Dec 7;10(12):e0144409

Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations. Vaz-Drago R, Pinheiro MT, Martins S, Enguita FJ, Carmo-Fonseca M, Custódio N.Hum Mol Genet. 2015 Feb 4. pii: ddv039.

A cytoplasmic C-terminal fragment of Syndecan-1 is generated by sequential proteolysis and antagonizes Syndecan-1 dependent lung tumor cell migration.Pasqualon T, Pruessmeyer J, Jankowski V, Babendreyer A, Groth E, Schumacher J, Koenen A, Weidenfeld S, Schwarz N, Denecke B, Jahr H, Dreymueller D, Jankowski J, Ludwig A.Oncotarget. 2015 Oct 13;6(31):31295-312.

ATF4 Gene Network Mediates Cellular Response to the Anticancer PAD Inhibitor YW3-56 in Triple Negative Breast Cancer Cells. Wang S, Chen XA, Hu J, Jiang JK, Li Y, Chen-Salis KY, Gu Y, Chen G, Thomas C, Pugh BF, Wang Y.Mol Cancer Ther. 2015 Jan 22.

Heme oxygenase-1 induction prevents autoimmune diabetes in association with pancreatic recruitment of M2-like macrophages, mesenchymal cells, and fibrocytes. Husseini M, Wang GS, Patrick C, Crookshank JA, MacFarlane? AJ, Noel JA, Strom A, Scott FW. Endocrinology. 2015 Aug 7:en20151304.

HIF1α Represses Cell Stress Pathways to Allow Proliferation of Hypoxic Fetal Cardiomyocytes. Guimarães-Camboa N, Stowe J, Aneas I, Sakabe N, Cattaneo P, Henderson L, Kilberg MS, Johnson RS, Chen J, McCulloch? AD, Nobrega MA, Evans SM, Zambon AC. Dev Cell. 2015 Jun 8;33(5):507-21. doi: 10.1016/j.devcel.2015.04.021.

Hyperosmotic stress activates the expression of members of the miR-15/107 family and induces downregulation of anti-apoptotic genes in rat liver. Santosa D, Castoldi M, Paluschinski M, Sommerfeld A, Häussinger D. Sci Rep. 2015 Jul 21;5:12292. doi: 10.1038/srep12292.

Identification of rod- and cone-specific expression signatures to identify candidate genes for retinal disease. Holt R, Brown L, Broadgate S, Butler R, Jagannath A, Downes S, Peirson S, Halford S.Exp Eye Res. 2015 Mar;132:161-73.

Identification of target genes for a prolactin family paralog in mouse decidua. Alam SM, Konno T, Soares MJ.Reproduction. 2015 Jun;149(6):625-32.

Multiple criteria optimization joint analyses of microarray experiments in lung cancer: from existing microarray data to new knowledge.Camacho-Cáceres KI, Acevedo-Díaz JC, Pérez-Marty LM, Ortiz M, Irizarry J, Cabrera-Ríos M, Isaza CE.Cancer Med. 2015 Oct 16. doi: 10.1002/cam4.540

Reactive oxygen species-mediated therapeutic response and resistance in glioblastoma. Singer E, Judkins J, Salomonis N, Matlaf L, Soteropoulos P, McAllister? S, Soroceanu L.Cell Death Dis. 2015 Jan 15;6:e1601.