PUBLICATION

1. Zitnik M, Li MM, Wells A, Glass K, Gysi DM, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline S, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, ong H, Yang XH, Yoon BJ, Yu H, Milenković T. Current and future directions in network biology. Bioinformatics Advances. arXiv:2309.08478v2

1. Broman M, Nadadur R, Perez-Cervantes C, Burnicka-Turek O, Lazarevic S, Gams A, Laforest B, Steimle J, Iddir S, Smith L, Wang Z, Mazurek S, Olivey H, Zhou P, Gadek M, Shen K, Khan Z, Theisen J, Yang X, Ikegami K, Efimov I, Pu W, Weber C, McNally E, Svensson E, and Moskowitz I. A genomic link from heart failure to atrial fibrillation risk: FOG2 modulates a TBX5/GATA4-dependent atrial gene regulatory network. Circulation. PMID: 38189150.

1. Yang XH*, Goldstein A, Sun Y, Wang Z, Wei M, Moskowitz IP, Cunningham JM. Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors. Nucleic Acids Research. PMID: 35640613

• Analyzing single-cell transcriptomes promises to decipher the plasticity, heterogeneity, and rapid switches in developmental cellular state transitions. Such analyses require the identification of gene markers for semi-stable transition states.

• BioTIP is unique in inferring lineage-determining transcription factors governing critical transition.

2. Rowton M, Perez-Cervantes C, Hur S, Jacobs-Li J, Lu E, Deng N, Guzzetta A, Hoffmann AD, Stocker M, Steimle JD, Lazarevic S, Oubaha S, Yang XH, Kim C, Yu S, Eckart H, Koska M, Hanson E, Chan SSK, Garry DJ, Kyba M, Basu A, Ikegami K, \Pott S, and Moskowitz IP. Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. Dev Cell. PMID: 36108627.

1. Rankin SA, Steimle JD, Yang XH, Rydeen AB, Agarwal K, Chaturvedi P, Ikegami K, Herriges MJ, Moskowitz IP, Zorn AM.. Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development. Elife. PubMed PMID: 34643182

1. Burnicka-Turek O, Broman MT, Steimle JD, Boukens BJ, Petrenko NB, Ikegami K, Nadadur RD, Qiao Y, Arnolds DE, Yang XH, Patel VV, Nobrega MA, Efimov IR, Moskowitz IP. Transcriptional Patterning of the Ventricular Cardiac Conduction System. Circulation Research, PubMed PMID: 32290757

2. Sun X, Wang Z, Hall JM, Perez-Cervantes1 C, Ruthenburg AJ, Moskowitz IP, Gribskov M, Yang XH*. Chromatin-enriched RNAs mark active and repressive cis-regulation: an analysis of nuclear RNA-seq. PLoS Comput Biol. 2020 DOI: 10.1101/646950. PMC7034927

1. Wang Z, Moskowitz1 AP, Cunningham JM, Yang XH*. Abstract 411: Risk-dependent enhancer transcription defines oncogenic gene regulatory networks for high-risk neuroblastoma. Cancer Research. DOI: 10.1158/1538-7445.AM2018-411.

1. Steimle J, Rankin S, Slagle CE, Bekeny J, Rydeen AB, Chan SS, Kweon J, Yang XH, Ikegami K, Nadadur RD, Rowton M, Hoffmann AD, Lazarevic S, Thomas W, Anderson EAT, Horb ME, Luna-Zurita L, Ho RK, Kyba M, Jensen B, Zorn AM, Conlon FL, Moskowitz IP. An evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development. Proc Natl Acad Sci U S A. 2018 Nov 6;115(45):E10615-E10624. PMID: 30352852.

2. Wang ZZ, Cunningham JM and Yang XH*. CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs. Bioinformatics, 2018 Sep 1; 34(17): i664-i670. PMC6129262

• Selected by the OMICtools (http://omictools.com/), an informative directory for multi-omic data analysis

1. Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W, Ruthenburg AJ, Moskowitz IP. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. eLife. 2017 Dec; 6: e31683.

2. Yang XH*, Tang F, Shin J, Cunningham J*. A cMyc regulated stem cell-like signature in high-risk neuroblastoma: a systematic discovery. Sci Rep. 2017 Dec;7(1):41

• Selected by American Association for Cancer Research as one “Breaking Advance” (Cancer Res 2017;77(9):2177-2178).

• Highlighted as one of the “Cancer Stem Cell News” on March 8, 2017 (https://www.cancerstemcellnews.com/issue/volume-6-09-mar-8/).

3. Yang XH*, Tang F, Shin J, Cunningham J. Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma. BMC Systems Biology. BMC Syst Biol. 2017 Oct 3;11(Suppl 5):92

1. Nadadur RD, Broman MT, Boukens B, Mazurek S, Yang XH, Boogaard M, Bekeny J, Gadek M, Ward T, Zhang M, Qiao Y, Martin JF, Seidman CE, Seidman J, Christoffels V, Efimov I, McNally EM, Weber CR, Moskowitz IP. Pitx2 modulates a Tbx5-dependent gene regulatory network to maintain atrial rhythm. Sci Transl Med. 2016 Aug 31;8(354):354ra115

2. Burnicka-Turek O, Steimle JD, Huang W, Felker L, Kamp A, Kweon J, Peterson M, Maslen CL, Gruber PJ, Yang XH, Shendure J, Moskowitz IP. Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms. Hum Mol Genet. 2016 Jun 23. pii: ddw155

3. Li H, Achour I, Bastarache L, Berghout J, Gardeux V, Li J, Lee Y, Pesce L, Yang X, Ramos KS, Foster I, Denny JC, Moore JH, Lussier YA. Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. npj Genomic Medicine 1: 16006

4. Waldron L, Steimle J, Greco TM, Gomez NC, Dorr KM, Kweon J, Temple B, Yang XH, Wilczewski CM, Davis I, Cristea IM, Moskowitz IP, Conlon FL. The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. Developmental Cell. 36 (3): 262–275.

5. Priest JR, Osoegawa K, Mohammed N, Nanda V, Ramendra K, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D, Haddad F, Reddy S, Bernstein D, Burns T, Steimle JD, Yang XH, Moskowitz I, Hurles M, Lifton RP, Nickerson D, Bamshad M, Eichler EE, Mital S, Sheffield V, Quertermous T, Gelb BD, Portman M, Ashley. EA. De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS Genet. 2016 Apr 8;12(4):e1005963

1.Yang XH*, Wang B and Cunningham JM. Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles. BMC Medical Genomics. 2015; 8 Suppl 2:S6

2. Wang B, Cunningham JM and Yang XH*. Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics. 2015; 31(18):3043-5

3. Yang XH*, Li M, Wang B, Zhu W, Desgardin A, Onel K, de Jong J, Chen J, Chen L, Cunningham JM. Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinformatics. 2015 Mar 24;16(1):97. doi: 10.1186/s12859-015-0510-7.

1. Hoffmann A, Yang X*, Burnicka-Turek O, Bosman J, Ren X, Hanson E, Steimle J, Vokes S, McMahon A, Kalinichenko V, Moskowitz I*. Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation. PLoS Genet. 2014 Oct 30;10(10):e1004604

2. Yang XH*, Ai X, Cunningham JM. Computational prognostic indicators for breast cancer (Review). Cancer Management and Research. 2014 July; 6:301-312.

3. van den Boogaard M, Smemo S, Burnicka-Turek O, Arnolds DE, van de Werken HJ, Klous P, McKean D, Muehlschlegel JD, Toka O, Yang X, Koopmann T, Adriaens M, Bezzina C, de Laat W, Seidman C, Seidman JG, Christoffels VM, Nobrega MA, Barnett P, Moskowitz IP. Common genetic variant in SCN10A modulates cardiac SCN5A expression. J Clin Invest. 2014 Mar 18. pii: 73140. doi: 10.1172/JCI73140

4. Yang XH, Huang Y, Lee Y, Gardeux V, Achour I, Regan K, Rebman E, Li H, Lussier YA. In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment. PLoS ONE 8(2): e56195. doi:10.1371/journal.pone.0056195

1.  Lee Y, Li H, Li J, Rebman E, Achour I, Regan KE, Gamazon E, Chen J, Yang XH, Cox NJ, Lussier Y. Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases.  J Am Med Inform Assoc. 20(4): 619-629

2. Li Z, Herold T, He C, Valk PJM, Chen P, Jurinovic V, Mansmann U, Radmacher M, Maharry K, Sun M, Yang X, Huang H, Jiang X, Sauerland MC, Büchner T, Hiddemann V, Elkahloun A, Neilly MB, Zhang Y, Larson RA, Beau MML, Caligiuri MA, Dohner K, Bullinger L, Liu PP, Delwel R, Marcucci G, Lowenberg B, Bloomfield CD, Rowley JD, Bohlander SK, Chen J. Identification of a 24-Gene Prognostic Signature That Improves the European LeukemiaNet Risk Classification of Acute Myeloid Leukemia: An International Collaborative Study of 1,324 Patients. J Clin Oncol. 2013 Mar 20;31(9):1172-81.

3. Chen J, Hsu A, Yang X, Li J, Lee Y, Parinandi G, Li H, Lussier YA. Curation-free biomodules mechanisms in prostate cancer predict recurrent disease. BMC Medical Genetics 2013 6(Suppl 2):S4

4. Yang XH*, Vasudevan P, Parekh V, Penev A, Cunningham JM. Bridging Cancer Biology with the Clinic: Relative Expression of a GRHL2-Mediated Gene-Set Pair Predicts Breast Cancer Metastasis. PLoS ONE 8(2): e56195. doi:10.1371/journal.pone.0056195

1. Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EE, Xing HR, Lussier YA. Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer. PLoS Computational Biology. 8(1):e1002350

• The ISCB/ECCB 2011 Highlights paper, July 19, Vienna, Austria

2. Ferreira CM, Chen JL, Li J, Shimomura K, Yang X, Lussier YA, Pinto LH, Solway J.
Genetic interactions between chromosomes 11 and 18 contribute to
airway hyperresponsiveness in mice. PLoS One. 7(1):e29579.

3. Li Z, Huang H, Li Y, Jiang X, Chen P, Arnovitz S, Radmacher MD, Maharry K, Elkahloun A, Yang X, He C, He M, Zhang Z, Dohner K, Neilly MB, Shen C, Price C, Lussier YA, Zhang Y, Larson RA, Le Beau MM, Caligiuri MA, Bullinger L, Valk PJ, Delwel R, Lowenberg B, Liu PP, Marcucci G, Bloomfield CD, Rowley JD, and Chen J. Up-regulation of a HOXA-PBX3 homeobox-gene signature following down-regulation of miR-181 is associated with adverse prognosis in patients with cytogenetically abnormal AML. Blood. 119(10):2314-24.

4. Yang X, Li H, Regan K, Li J, Huang Y, Lussier Y. Towards Mechanism Classifiers: Expression-anchored Gene Ontology Signature Predicts Clinical Outcome in Lung Adenocarcinoma Patients. AMIA 2012 Annual Symposium processing:1040

1. Yang X, Li J, Lee Y, Lussier YA. GO-Module: functional synthesis and improved interpretation of Gene Ontology patterns. Bioinformatics. 27: 1444-146

2. Lussier YA, Xing HR, Salam JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE, Malik R, Fan H, Perakis S, Filippo M, Corbin K, Lee Y, Posner MC, Chmura SJ, Hellman S, Weichselbaum RR. MicroRNA expression characterizes oligometastases. PLoS One. 6(12):e28650.

1. Lee Y#, Yang X# (equally contributed 1st author), Huang Y, Fan HL, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen M, Gerstein M, Weichselbaum R, Xing HR, Lussier YA. Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Computational Biology. 6(4):e1000730

• One of the 24 best translational bioinformatics reports of 2009-2010, by Russ Altman, in his review presented at the 2010 AMIA Summit on Translational Bioinformatics and on his blog (page 36 of the PDF file): Selected as ‘late breaking news’ (5 selected) for highlight in the 2010 AMIA Summit on Translational Bioinformatics; S12, p.17.

2. Yang X, Lee Y, Huang Y, Chen JL, Xing HR, Lussier YA. Stromal Microenvironment Processes Unveiled by Biological Component Analysis of Gene Expression in Xenograft Tumor Models. BMC Bioinformatics. 11:S9

• Outstanding Paper Award, American Medical Informatics Association.

• 12 selected for this award among about 100 submitted manuscripts (top 12%).

3. Yang X, Huang Y, Crowson M, Li JR, Maitland ML, Lussier YA. Kinase inhibition- related adverse events predicted from in vitro kinome and clinical trial data. J. Biomedical Informatics. 43(3):376-84

4. Yang X, Lee Y, Fan H, Sun X, Lussier YA. Identification of common microRNA- mRNA regulatory biomodules in human epithelial cancers. Chinese Science Bulletin. 55 (31): 3576-3589

1. Wu J, Liu H, Yang X, Xie J, Sun S. A SVM-based Approach for Predicting DNA-binding Residues in Proteins from Amino Acid Sequences. International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. (IJCBS '09.):225-229

2. Yang X, Huang Y, Chen JL, Xie JM, Sun X, Lussier YA. Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. BMC Bioinformatics. 10(S9):S6

• Outstanding Paper Award, American Medical Informatics Association.
• More than 350 attendees, from 18 countries attended AMIA2009 Summit on Translational Bioinformatics. Among 175 submitted works, six papers (top 3.4%) further received the outstanding paper award.

1. Yang X*, Sun X, Xie JM, Lu ZH. Comparability of gene expression in human blood, immune and carcinoma cells. Applied Mathematics and Computation 205:178-18

• The conference “received a total of 1383 full paper submissions from 21 countries”, summarized by M. Warerman on ‘Lecture Notes inBioinformatics’. The best paper among 35 good quality papers out of 333 (top 2.5%) that were recommend for journal publication. The Best Paper Award, International Conference on Life System Modeling and Simulation sponsored by IEEE (2007).

2. Liu H, Wu J, Xie J, Yang X, Lu Z, Sun X. Characteristics of nucleosome core DNA and their applications in predicting nucleosome positions. Biophys. J. 94(12):4597-4604

3. Liu H, Wu J, Xie J, Yang X, Xu Z, Sun X. Applications of signal processing techniques in analysis of bimolecular sequences. China Journal of Bioinformatics. 6(4): 180-182 [review in Chinese].

4. Xu Z, Xie J, Yang X, Sun X. Genome-Scale Simulation Analysis: The Impact of Gene Deletion on the Metabolic Flux of E.coli and Its Flux-backbone. International Conference on BioMedical Engineering and Informatics. (BMEI '08), (1):695-699

2001

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2007

1. Yang X and Sun X. 2001. Bioinformatics Visualization of gene [Chinese]. Computers and Applied Chemistry. 18(5): 403-410.

2. Yang X, Bentink S, Spang R. 2005. Detecting common gene expression patterns in multiple cancer outcome entities. Biomedical Microdevices. 7(3): 247-251.

3. Yang X, Bentink S, Scheid S, Spang R. 2006. Similarities of ordered gene lists. J Bioinform Comput Biol. 4(3):693-708

4. Yang X, Sun X, Lu ZH. 2006. Meta-Analysis gene lists about subtypes of leukemia based on gene expression data. J Southeast University. 22(2): 248-255

5. Lottaz C, Yang X, Scheid S, Spang R. 2006. OrderedList — a Bioconductor package for detecting similarity in ordered gene lists. Bioinformatics. 22(18): 2315-2316

6. Yang X* and Sun X. 2007. Meta-analysis of several gene lists for distinct types of cancer: A simple way to reveal common prognostic markers. BMC Bioinformatics. 6; 8(1):118

• “Highly accessed stamp” in BMC bioinformatics