Research Publications:
● G Chorn, M Klein-McDowell, L Zhao, MA Saunders, WM Flanagan, AT Willingham, LP Lim. ”Single-Stranded microRNA Mimics”. RNA 2012 Oct 1, v.18, p.1796-1804.
● RV Fucini, HJ Haringsma, P Deng, WM Flanagan, AT Willingham*. "Adenosine Modification May Be Preferred for Reducing siRNA Immune Stimulation". Nucleic Acid Therapeutics 2012 Jun, v.22, p205-10. (* corresponding author)
● HJ Haringsma, JJ Li, F Soriano, DM Kenski, WM Flanagan, AT Willingham*. "mRNA Knockdown by Single Strand RNA is Improved by Chemical Modifications". Nucleic Acids Research 2012 May, v.40, p.4125-36. (* corresponding author)
● DM Kenski, AT Willingham, HJ Haringsma, JJ Li, WM Flanagan. "In Vivo Activity and Duration of siRNAs Containing a Synthetic 5'-Phosphate". Nucleic Acid Therapeutics 2012 Apr, v.22, p.90-5.
● DM Kenski, G Butora, AT Willingham, AJ Cooper, W Fu, N Qi, F Soriano, IW Davies, WM Flanagan.  "siRNA-optimized Modifications for Enhanced In Vivo Activity". Molecular Therapy Nucleic Acids 2012. doi:10.1038/mtna.2011.4
● H Peacock, RV Fucini, P Jayalath, J Ibarra-Soza, HJ Haringsma, WM Flanagan, A Willingham*, PA Beal*. "Nucleobase and Ribose Modifications Control Immunostimulation by a MicroRNA-122-mimetic RNA". J Am Chem Soc. 2011 Jun 22, v.133, p.9200-3. (* corresponding authors)
● BR Graveley, AN Brooks, JW Carlson, MO Duff, JM Landolin, L Yang, CG Artieri, MJ van Baren, N Boley, BW Booth, JB Brown, L Cherbas, CA Davis, A Dobin, R Li, W Lin, JH Malone, NR Mattiuzzo, D Miller, D Sturgill, BB Tuch, C Zaleski, D Zhang, M Blanchette, S Dudoit, B Eads, RE Green, A Hammonds, L Jiang, P Kapranov, L Langton, N Perrimon, JE Sandler, KH Wan, A Willingham, Y Zhang, Y Zou, J Andrews, PJ Bickel, SE Brenner, MR Brent, P Cherbas, TR Gingeras, RA Hoskins, TC Kaufman, B Oliver & SE Celniker. "The developmental transcriptome of Drosophila melanogaster". Nature 2011 Mar 24, v.471, p.473-479.
● L Cherbas, A Willingham, D Zhang, L Yang, Y Zou, BD Eads, JW Carlson, JM Landolin, P Kapranov, J Dumais, A Samsonova, JH Choi, J Roberts, CA Davis, H Tang, MJ van Baren, S Ghosh, A Dobin, K Bell, W Lin, L Langton, MO Duff, AE Tenney, C Zaleski, MR Brent, RA Hoskins, TC Kaufman, J Andrews, BR Graveley, N Perrimon, SE Celniker, TR Gingeras, P Cherbas. “The Transcriptional Diversity of 25 Drosophila Cell Lines”. Genome Research 2011 Feb. v21, p. 301-314.
● "Identification of functional elements and regulatory circuits by Drosophila modENCODE". Science 2010 Dec. 24. v330, p. 1787-1797. (An author as a member of the modENCODE Consortium)
● DM Kenski, AJ Cooper, JJ Li, AT Willingham, HJ Haringsma, TA Young, NA Kuklin, JJ Jones, MT Cancilla, DR McMasters, M Mathur, AB Sachs, WM Flanagan. “Analysis of acyclic nucleoside modifications in siRNAs finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo”. Nucleic Acids Research. 2010 Jan. v38, p.660-71.
● Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project (P Kapranov, S Foissac, AT Willingham, R Duttagupta, E Dumais & TR Gingeras for Affymetrix & K Fejes-Toth, V Sotirova, R Sachidanandam, G Assaf & GJ Hannon for Cold Spring Harbor Laboratory). “Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs”. Nature. 2009 Feb 19. v.457, p.1028-1028.
● P Kapranov, J Cheng, S Dike, D Nix, R Duttagupta, AT Willingham, P Stadler, J Hertel, J Hackermueller, IL Hofacker, I Bell, E Cheung, J Drenkow, E Dumais, S Patel, G Helt, G Madhavan, S Ghosh, A Piccolboni, V Sementchenko, H Tammana, TR Gingeras. “RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription”. Science. 2007 Jun 8. v.316, p.1494-1488.
● AT Willingham, S Dike , J Cheng, JR Manak, I Bell, E Cheung, J Drenkow, E Dumais, R Duttagupta, M Ganesh, S Ghosh, G Helt, D Nix, A Piccolboni, V Sementchenko, H Tammana, P Kapranov, TR Gingeras, ENCODE Genes and Transcripts Group. “Transcriptional Landscape of the Human and Fly Genomes: Nonlinear and Multifunctional Modular Model of Transcriptomes”. Cold Spring Harbor Symposia on Quantitative Biology. 2006.v.71, p.101-110.
● AT Willingham, AP Orth, S Batalov, EC Peters, BG Wen, P Aza-Blanc, JB Hogenesch, PG Schultz. “A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT”.  Science. 2005 Sep 2. v.309, p.1570-1573.
● AT Willingham#, T Keil. “A tissue specific cytochrome P450 required for the structure and function of Drosophila sensory organs”. Mechanisms of Development. 2004 Oct. v.121 (n.10), p.1289-1297. ( # corresponding author)
● RG Walker, AT Willingham, CS Zuker. “A Drosophila mechanosensory transduction channel”. Science. 2000 Mar 24. v.287, p.2229-2234.
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Review Articles:
● P Kapranov, AT Willingham, TR Gingeras. “Genome-wide transcription and the implications on genome organization”. Nature Reviews Genetics2007 Jun. v.8, p.413-423.
● AT Willingham, TR Gingeras. “TUF Love for “Junk” DNA”.  Cell. 2006 Jun 30. v.125, p.1215-1220 (Leading Edge Essay).
● AT Willingham, QL Deveraux, GM Hampton, P Aza-Blanc.  “RNAi & HTS: Exploring Cancer by Systematic Loss-of-Function”.  Oncogene. 2004 Nov 1. v.23, p.8392-8400.
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Patents:
● WO Patent 2012/058210 A1, M Cancilla, J Cunningham, WM Flanagan, H Haringsma, D Kenski, M Stanton, S Stirdivant, A Willingham, (published May 3, 2012). RNA Interference Mediated Inhibition of Gene Expression Using Short Interfering Nucleic Acid (siNA).
● WO Patent 2012/027206 A1, L Lim, G Chorn, A Willingham, L Zhao, (published Mar 1, 2012). Single-Stranded RNAi Agents Containing An Internal, Non-Nucleic Acid Spacer.
● U.S. Patent No. 7,867,721 B2, CS Zuker, RG Walker, AT Willingham, (issued Jan 11, 2011), “In Vitro Method For Identifying a Compound Using An Eukaryotic Mechanosensory Transduction Channel”.
● U.S. Patent No. 6,537,778 B1, CS Zuker, RG Walker, AT Willingham, (issued March 25, 2003), “Eukaryotic Mechanosensory Transduction Channel”.