This is the list of publications from the collaborative projects with other groups. For publications from my independent research, see this list. For full publications, see this list.

  1. Lidia Bosurgi, etc. (2017) Macrophage function in tissue repair requires the coincident detection of IL-4/IL-13 and apoptotic cells, Science, accepted.

  2. Daisy Xin, Kasey J Christopher, Lewie Zeng, Yong Kong, Scott D Weatherbee (2017) IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture, Development, 144, 1544-1553. [doi] [pubmed] [The Company of Biologists]

  3. Otsuka, Taketo; Brauer, Aimee; Kirkham, Charmaine; Sully, Erin; Pettigrew, Melinda; Kong, Yong; Geller, Bruce; Murphy , Timothy (2016) Antimicrobial activity of antisense peptide-peptide nucleic acid conjugates against nontypeable Haemophilus influenzae in planktonic and biofilm forms, Journal of Antimicrobial Chemotherapy, 72, 137-144. [doi] [pubmed] [Oxford]

  4. Melinda Pettigrew, Janneane F Gent, Yong Kong, Martina Wade, Shane Gansebom, Anna M Bramley, Seema Jain, Sandra R Arnold, Jonathan A McCullers (2016) Association of sputum microbiota profiles with severity of community-acquired pneumonia in children, BMC Infectious Diseases, 16, 317. [doi] [pubmed] [BMC]

  5. Melinda Pettigrew, Brian Tsuji, Janneane Gent, Yong Kong, Patricia Holden, Sanjay Sethi, and Timothy Murphy (2016) Effect of Fluoroquinolones and Macrolides on Eradication and Resistance of Haemophilus influenzae in Chronic Obstructive Pulmonary Disease, Antimicrobial Agents and Chemotherapy, 60, 4151-4158. [doi] [pubmed] [ASM]

  6. William Khoury-Hanold, etc. (2016) Viral spread to enteric neurons links genital HSV-1 infection to toxic megacolon and lethality, Cell Host & Microbe, 19, 788-799. [doi] [pubmed] [Sciencedirect]

  7. Jieming Chen, Joel Rozowsky, Timur R. Galeev, Arif Harmanci, Robert Kitchen, Jason Bedford, Alexej Abyzov, Yong Kong, Lynne Regan & Mark Gerstein (2016) A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals, Nature Communications, 7, 11101. [doi] [pubmed] [Nature]

  8. Natalie R Powers, John D Eicher, Laura L Miller, Yong Kong, Shelley D Smith, Bruce F Pennington, Erik G Willcutt, Richard K Olson, Susan M Ring, Jeffrey R Gruen (2016) The regulatory element READ1 epistatically influences reading and language, with both deleterious and protective alleles, Journal of Medical Genetics, 53, 163-171. [doi]

  9. Michael Krauthammer, Yong Kong, Antonella Bacchiocchi, Perry Evans, Natapol Pornputtapong, Cen Wu, James P McCusker, Shuangge Ma, Elaine Cheng, Robert Straub, Merdan Serin, Marcus Bosenberg, Stephan Ariyan, Deepak Narayan, Mario Sznol, Harriet M Kluger, Shrikant Mane, Joseph Schlessinger, Richard P Lifton, Ruth Halaban (2015) Exome sequencing identifies recurrent mutations in NF1 and RASopathy genes in sun-exposed melanomas, Nature genetics, 47, 996-1002. [doi] [pubmed] [Nature]

  10. Timothy F Murphy, Charmaine Kirkham, Megan M Jones, Sanjay Sethi, Yong Kong, Melinda M Pettigrew (2015) Expression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease, Journal of Infectious Diseases, 212, 1798-1805. [doi] [pubmed] [Oxford]

  11. Nicole Ali McNeer, Kavitha Anandalingam, Rachel J Fields, Christina Caputo, Sascha Kopic, Anisha Gupta, Elias Quijano, Lee Polikoff, Yong Kong, Raman Bahal, John P Geibel, Peter M Glazer, W Mark Saltzman, Marie E Egan (2015) Nanoparticles that deliver triplex-forming peptide nucleic acid molecules correct F508del CFTR in airway epithelium, Nature communications, 6, 6952. [doi] [pubmed] [Nature]

  12. Seth Rakoff-Nahoum, Yong Kong, Steven H Kleinstein, Sathish Subramanian, Philip P Ahern, Jeffrey I Gordon, Ruslan Medzhitov (2015) Analysis of gene-environment interactions in postnatal development of the mammalian intestine, Proceedings of the National Academy of Sciences, 112, 1929-1936. [doi] [pubmed] [PNAS]

  13. Melinda M Pettigrew, Laura R Marks, Yong Kong, Janneane F Gent, Hazeline Roche-Hakansson, Anders P Hakansson (2014) Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection, Infection and immunity, 82, 4607-4619. [doi] [pubmed] [ASM]

  14. Yong Kong, Michael Krauthammer, Ruth Halaban (2014) Rare SF3B1 R625 mutations in cutaneous melanoma, Melanoma research, 24, 332-334. [doi] [pubmed] [Springer]

  15. Catherine A Brownstein, Alan H Beggs, Nils Homer, Barry Merriman, W Yu Timothy, Katherine C Flannery, Elizabeth T DeChene, Meghan C Towne, Sarah K Savage, Emily N Price, Ingrid A Holm, Lovelace J Luquette, Elaine Lyon, Joseph Majzoub, Peter Neupert, David McCallie Jr, Peter Szolovits, Huntington F Willard, Nancy J Mendelsohn, Renee Temme, Richard S Finkel, Sabrina W Yum, Livija Medne, Shamil R Sunyaev, Ivan Adzhubey, Christopher A Cassa, Paul IW de Bakker, Hatice Duzkale, Piotr Dworzyński, William Fairbrother, Laurent Francioli, Birgit H Funke, Monica A Giovanni, Robert E Handsaker, Kasper Lage, Matthew S Lebo, Monkol Lek, Ignaty Leshchiner, Daniel G MacArthur, Heather M McLaughlin, Michael F Murray, Tune H Pers, Paz P Polak, Soumya Raychaudhuri, Heidi L Rehm, Rachel Soemedi, Nathan O Stitziel, Sara Vestecka, Jochen Supper, Claudia Gugenmus, Bernward Klocke, Alexander Hahn, Max Schubach, Mortiz Menzel, Saskia Biskup, Peter Freisinger, Mario Deng, Martin Braun, Sven Perner, Richard JH Smith, Janeen L Andorf, Jian Huang, Kelli Ryckman, Val C Sheffield, Edwin M Stone, Thomas Bair, E Ann Black-Ziegelbein, Terry A Braun, Benjamin Darbro, Adam P DeLuca, Diana L Kolbe, Todd E Scheetz, Aiden E Shearer, Rama Sompallae, Kai Wang, Alexander G Bassuk, Erik Edens, Katherine Mathews, Steven A Moore, Oleg A Shchelochkov, Pamela Trapane, Aaron Bossler, Colleen A Campbell, Jonathan W Heusel, Anne Kwitek, Tara Maga, Karin Panzer, Thomas Wassink, Douglas Van Daele, Hela Azaiez, Kevin Booth, Nic Meyer, Michael M Segal, Marc S Williams, Gerard Tromp, Peter White, Donald Corsmeier, Sara Fitzgerald-Butt, Gail Herman, Devon Lamb-Thrush, Kim L McBride, David Newsom, Christopher R Pierson, Alexander T Rakowsky, Aleš Maver, Luca Lovrečić, Anja Palandačić, Borut Peterlin, Ali Torkamani, Anna Wedell, Mikael Huss, Andrey Alexeyenko, Jessica M Lindvall, Måns Magnusson, Daniel Nilsson, Henrik Stranneheim, Fulya Taylan, Christian Gilissen, Alexander Hoischen, Bregje van Bon, Helger Yntema, Marcel Nelen, Weidong Zhang, Jason Sager, Lu Zhang, Kathryn Blair, Deniz Kural, Michael Cariaso, Greg G Lennon, Asif Javed, Saloni Agrawal, Pauline C Ng, Komal S Sandhu, Shuba Krishna, Vamsi Veeramachaneni, Ofer Isakov, Eran Halperin, Eitan Friedman, Noam Shomron, Gustavo Glusman, Jared C Roach, Juan Caballero, Hannah C Cox, Denise Mauldin, Seth A Ament, Lee Rowen, Daniel R Richards, F Anthony S Lucas, Manuel L Gonzalez-Garay, C Thomas Caskey (2014) An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge, Genome biology, 15, R53. [doi] [pubmed] [Genome biology]

  16. Perry Evans, Yong Kong, Michael Krauthammer (2014) Computational Analysis in Cancer Exome Sequencing, Methods in Molecular Biology, 1176, 219-227. [doi] [pubmed] [Springer]

  17. Emily K Mis, Karel F Liem, Yong Kong, Nancy B Schwartz, Miriam Domowicz, Scott D Weatherbee (2014) Forward genetics defines Xylt1 as a key, conserved regulator of early chondrocyte maturation and skeletal length, Developmental biology, 385, 67-82. [doi] [pubmed] [Elsevier]

  18. Sunjin Lee, Yong Kong, Scott D Weatherbee (2013) Forward genetics identifies Kdf1/1810019J16Rik as an essential regulator of the proliferation-differentiation decision in epidermal progenitor cells, Developmental biology, 383, 201-213. [doi] [pubmed] [Elsevier]

  19. Ekta Khurana, Yao Fu, Vincenza Colonna, Xinmeng Jasmine Mu, Hyun Min Kang, Tuuli Lappalainen, Andrea Sboner, Lucas Lochovsky, Jieming Chen, Arif Harmanci, Jishnu Das, Alexej Abyzov, Suganthi Balasubramanian, Kathryn Beal, Dimple Chakravarty, Daniel Challis, Yuan Chen, Declan Clarke, Laura Clarke, Fiona Cunningham, Uday S Evani, Paul Flicek, Robert Fragoza, Erik Garrison, Richard Gibbs, Zeynep H Gümüş, Javier Herrero, Naoki Kitabayashi, Yong Kong, Kasper Lage, Vaja Liluashvili, Steven M Lipkin, Daniel G MacArthur, Gabor Marth, Donna Muzny, Tune H Pers, Graham RS Ritchie, Jeffrey A Rosenfeld, Cristina Sisu, Xiaomu Wei, Michael Wilson, Yali Xue, Fuli Yu, Emmanouil T Dermitzakis, Haiyuan Yu, Mark A Rubin, Chris Tyler-Smith, Mark Gerstein (2013) Integrative annotation of variants from 1092 humans: application to cancer genomics, Science, 342, 1235587. [doi] [pubmed] [Science]

  20. Perry Evans, Stefan Avey, Yong Kong, Michael Krauthammer (2013) Adjusting for background mutation frequency biases improves the identification of cancer driver genes, IEEE Transactions on NanoBioscience, 12, 150-157. [doi] [pubmed] [IEEE]

  21. Natalie R Powers, John D Eicher, Falk Butter, Yong Kong, Laura L Miller, Susan M Ring, Matthias Mann, Jeffrey R Gruen (2013) Alleles of a polymorphic ETV6 binding site in DCDC2 confer risk of reading and language impairment, The American Journal of Human Genetics, 93, 19-28. [doi] [pubmed] [Cell]

  22. Karen A Hunt, Vanisha Mistry, Nicholas A Bockett, Tariq Ahmad, Maria Ban, Jonathan N Barker, Jeffrey C Barrett, Hannah Blackburn, Oliver Brand, Oliver Burren, Francesca Capon, Alastair Compston, Stephen CL Gough, Luke Jostins, Yong Kong, James C Lee, Monkol Lek, Daniel G MacArthur, John C Mansfield, Christopher G Mathew, Charles A Mein, Muddassar Mirza, Sarah Nutland, Suna Onengut-Gumuscu, Efterpi Papouli, Miles Parkes, Stephen S Rich, Steven Sawcer, Jack Satsangi, Matthew J Simmonds, Richard C Trembath, Neil M Walker, Eva Wozniak, John A Todd, Michael A Simpson, Vincent Plagnol, David A van Heel (2013) Negligible impact of rare autoimmune-locus coding-region variants on missing heritability, Nature, 498, 232-235. [doi] [pubmed] [Nature]

  23. Florencia del Viso, Dipankan Bhattacharya, Yong Kong, Michael J Gilchrist, Mustafa K Khokha (2012) Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing, BMC genomics, 13, 649. [doi] [pubmed] [Biomed Central]

  24. Melinda M Pettigrew, Alison S Laufer, Janneane F Gent, Yong Kong, Kristopher P Fennie, Joshua P Metlay (2012) Upper Respiratory Tract Microbial Communities, Acute Otitis Media Pathogens, and Antibiotic Use in Healthy and Sick Children, Applied and Environmental Microbiology, 78, 6262-6270. [doi] [pubmed] [ASM]

  25. Michael Krauthammer, Yong Kong, Byung Hak Ha, Perry Evans, Antonella Bacchiocchi, James P McCusker, Elaine Cheng, Matthew J Davis, Gerald Goh, Murim Choi, Stephan Ariyan, Deepak Narayan, Ken Dutton-Regester, Ana Capatana, Edna C Holman, Marcus Bosenberg, Mario Sznol, Harriet M Kluger, Douglas E Brash, David F Stern, Miguel A Materin, Roger S Lo, Shrikant Mane, Shuangge Ma, Kenneth K Kidd, Nicholas K Hayward, Richard P Lifton, Joseph Schlessinger, Titus J Boggon, Ruth Halaban (2012) Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma, Nature genetics, 44, 1006-1014. [doi] [pubmed] [Nature]

  26. Kasey J Christopher, Baolin Wang, Yong Kong, Scott D Weatherbee (2012) Forward genetics uncovers Transmembrane protein 107 as a novel factor required for ciliogenesis and Sonic Hedgehog signaling, Developmental Biology, 368, 382-92. [doi] [pubmed] [Elsevier]

  27. Xinmeng Jasmine Mu, Zhi John Lu, Yong Kong, Hugo YK Lam, Mark B Gerstein (2011) Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project, Nucleic acids research, 39, 7058-7076. [doi] [pubmed] [Oxford]

  28. Jonathan C Thomas, Yong Kong, Vishakha Sabharwal, Stephen I Pelton, Melinda M Pettigrew (2011) Streptococcus pneumoniae serotype 6C: an intra-and interclonal complex comparison, Journal of bacteriology, 193, 3409-3410. [doi] [pubmed] [ASM]

  29. Jonathan C Thomas, Marisol Figueira, Kristopher P Fennie, Alison S Laufer, Yong Kong, Michael E Pichichero, Stephen I Pelton, Melinda M Pettigrew (2011) Streptococcus pneumoniae clonal complex 199: genetic diversity and tissue-specific virulence, PLoS One, 6, e18649. [doi] [pubmed] [PLOS]

  30. Alison S Laufer, Joshua P Metlay, Janneane F Gent, Kristopher P Fennie, Yong Kong, Melinda M Pettigrew (2011) Microbial communities of the upper respiratory tract and otitis media in children, MBio, 2, e00245-10. [doi] [pubmed] [ASM]

  31. Vijay Garla, Yong Kong, Sebastian Szpakowski, Michael Krauthammer (2011) MU2A—reconciling the genome and transcriptome to determine the effects of base substitutions, Bioinformatics, 27, 416-418. [doi] [pubmed] [Oxford]

  32. Joel Rozowsky, Alexej Abyzov, Jing Wang, Pedro Alves, Debasish Raha, Arif Harmanci, Jing Leng, Robert Bjornson, Yong Kong, Naoki Kitabayashi, Nitin Bhardwaj, Mark Rubin, Michael Snyder, Mark Gerstein (2011) AlleleSeq: analysis of allele‐specific expression and binding in a network framework, Molecular systems biology, 7, 522. [doi] [pubmed] [EMBO]

  33. Sara A Marlatt, Yong Kong, Tobin J Cammett, Gregory Korbel, James P Noonan, Daniel DiMaio (2011) Construction and maintenance of randomized retroviral expression libraries for transmembrane protein engineering, Protein Engineering Design and Selection, 24, 311-320. [doi] [pubmed] [Oxford]

  34. James W Murphy, Hua Yuan, Yong Kong, Yong Xiong, Elias J Lolis (2010) Heterologous quaternary structure of CXCL12 and its relationship to the CC chemokine family, Proteins: Structure, Function, and Bioinformatics, 78, 1331-1337. [doi] [pubmed] [Wiley]

  35. Jiang Du, Robert D Bjornson, Zhengdong D Zhang, Yong Kong, Michael Snyder, Mark B Gerstein (2009) Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants, PLoS Comput Biol, 5, e1000432. [doi] [pubmed] [PLOS]

  36. Douglas L Sheridan, Yong Kong, Sirlester A Parker, Kevin N Dalby, Benjamin E Turk (2008) Substrate discrimination among mitogen-activated protein kinases through distinct docking sequence motifs, Journal of Biological Chemistry, 283, 19511-19520. [doi] [pubmed] [JBC]

  37. Kathryn L Stone, Robert D Bjornson, Gregory G Blasko, Can Bruce, Renee Cofrancesco, Nicholas J Carriero, Christopher M Colangelo, Janet K Crawford, J Myron Crawford, Nancy C daSilva, Joseph D Deluca, James I Elliott, Margaret M Elliott, P John Flory, Ewa J Folta-Stogniew, Erol Gulcicek, Yong Kong, TuKiet T Lam, Ji Y Lee, Aiping Lin, Mary B LoPresti, Shrikant M Mane, Walter J McMurray, Irina R Tikhonova, Sheila Westman, Nancy A Williams, Terence L Wu, Zhao Hongyu, and Kenneth R Williams (2007) Keck Foundation Biotechnology Resource Laboratory, Yale University, The Yale journal of biology and medicine, 80, 195-211. [pubmed]

  38. Daniele Arosio, Silvia Costantini, Yong Kong, Alessandro Vindigni (2004) Fluorescence Anisotropy Studies on the Ku-DNA Interaction ANION AND CATION EFFECTS, Journal of Biological Chemistry, 279, 42826-42835. [doi] [pubmed] [JBC]

  39. Loic Giot, Joel S Bader, C Brouwer, Amitabha Chaudhuri, Bing Kuang, Y Li, YL Hao, CE Ooi, Brian Godwin, E Vitols, G Vijayadamodar, Philippe Pochart, H Machineni, M Welsh, Y Kong, B Zerhusen, R Malcolm, Z Varrone, A Collis, M Minto, S Burgess, L McDaniel, E Stimpson, F Spriggs, J Williams, Kathryin Neurath, N Ioime, M Agee, E Voss, K Furtak, R Renzulli, N Aanensen, S Carrolla, E Bickelhaupt, Y Lazovatsky, A DaSilva, J Zhong, Clement A Stanyon, Russell L Finley Jr, Kevin P White, M Braverman, T Jarvie, S Gold, M Leach, J Knight, Richard A Shimkets, Michael P McKenna, John Chant, Jonathan M Rothberg (2003) A protein interaction map of Drosophila melanogaster, Science, 302, 1727-1736. [doi] [pubmed] [Science]

  40. Ying Li, Yong Kong, Sergey Korolev, Gabriel Waksman (1998) Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates, Protein science, 7, 1116-1123. [doi] [pubmed] [Wiley]