2024 |
Elena B Popowitch, Tommy H Tran, Isabel Fernandez Escapa, Eeshta Bhatt, Alp K Sozat, Nashwa Ahmed, Clayton Deming, Ari Q Roberts; NISC Comparative Sequencing Program; Julia A Segre, Heidi H Kong, Sean Conlan, Katherine P Lemon, Matthew S Kelly
Description of two novel Corynebacterium species isolated from human nasal passages and skin
bioRxiv [Preprint]. 2024 Nov 21:2024.11.21.624533. doi: 10.1101/2024.11.21.624533.
39605597 |
Leonardo Gomes de Lima, Andrea Guarracino, Sergey Koren, Tamara Potapova, Sean McKinney, Arang Rhie, Steven J Solar, Chris Seidel, Brandon Fagen, Brian P Walenz, Gerard G Bouffard, Shelise Y Brooks, Michael Peterson, Kate Hall, Juyun Crawford, Alice C Young, Brandon D Pickett, Erik Garrison, Adam M Phillippy, Jennifer L Gerton
The formation and propagation of human Robertsonian chromosomes
bioRxiv [Preprint]. 2024 Sep 26:2024.09.24.614821. doi: 10.1101/2024.09.24.614821.
39386535 |
Joseph W Palmer, Kyrene M Villavicencio, Misgana Idris, Ian J Baranyk, Nunaya Polycarp, Alex D Dawson, Dominique Weddle; NISC Comparative Sequencing Program; William J Pavan, Fabian V Filipp, Melissa L Harris
Quiescence and aging of melanocyte stem cells and a novel association with programmed death-ligand 1
iScience. 2024 Sep 12;27(10):110908. doi: 10.1016/j.isci.2024.110908. eCollection 2024 Oct 18.
39351197 |
Pulak R Nath, Mary Maclean, Vijay Nagarajan, Jung Wha Lee, Mehmet Yakin, Aman Kumar, Hadi Nadali, Brian Schmidt, Koray D Kaya, Shilpa Kodati, Alice Young, Rachel R Caspi, Jonas J W Kuiper, H Nida Sen
Single-cell profiling identifies a CD8bright CD244bright Natural Killer cell subset that reflects disease activity in HLA-A29-positive birdshot chorioretinopathy
Nat Commun. 2024 Jul 31;15(1):6443. doi: 10.1038/s41467-024-50472-0.
39085199 |
Pilar Alvarez Jerez, Kensuke Daida, Francis P Grenn, Laksh Malik, Abigail Miano-Burkhardt, Mary B Makarious, Jinhui Ding, J Raphael Gibbs, Anni Moore, Xylena Reed, Mike A Nalls, Syed Shah, Medhat Mahmoud, Fritz J Sedlazeck, Egor Dolzhenko, Morgan Park, Hirotaka Iwaki, Bradford Casey, Mina Ryten, Cornelis Blauwendraat, Andrew B Singleton, Kimberley J Billingsley
Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing
NPJ Parkinsons Dis. 2024 Jul 26;10(1):136. doi: 10.1038/s41531-024-00749-4.
39060285 |
Sean Conlan, Poorani Subramanian, Beatriz Plata Barril, Jung-Ho Youn, Pamela J Thomas, Sergey Koren, Gabrielle A Dotson, Morgan Park, Arang Rhie, Julie A Segre, John P Dekker, Adrian M Zelazny
Whole-genome sequence of Mucor velutinosus NIH1002, a strain associated with disseminated disease
Microbiol Resour Announc. 2024 Jun 20:e0006224. doi: 10.1128/mra.00062-24. Online ahead of print.
38899875 |
Kateryna D Makova, Brandon D Pickett, Robert S Harris, Gabrielle A Hartley, Monika Cechova, Karol Pal, Sergey Nurk, DongAhn Yoo, Qiuhui Li, Prajna Hebbar, Barbara C McGrath, Francesca Antonacci, Margaux Aubel, Arjun Biddanda, Matthew Borchers, Erich Bornberg-Bauer, Gerard G Bouffard, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Andrew Carroll, Pi-Chuan Chang, Chen-Shan Chin, Daniel E Cook, Sarah J C Craig, Luciana de Gennaro, Mark Diekhans, Amalia Dutra, Gage H Garcia, Patrick G S Grady, Richard E Green, Diana Haddad, Pille Hallast, William T Harvey, Glenn Hickey, David A Hillis, Savannah J Hoyt, Hyeonsoo Jeong, Kaivan Kamali, Sergei L Kosakovsky Pond, Troy M LaPolice, Charles Lee, Alexandra P Lewis, Yong-Hwee E Loh, Patrick Masterson, Kelly M McGarvey, Rajiv C McCoy, Paul Medvedev, Karen H Miga, Katherine M Munson, Evgenia Pak, Benedict Paten, Brendan J Pinto, Tamara Potapova, Arang Rhie, Joana L Rocha, Fedor Ryabov, Oliver A Ryder, Samuel Sacco, Kishwar Shafin, Valery A Shepelev, Viviane Slon, Steven J Solar, Jessica M Storer, Peter H Sudmant, Sweetalana, Alex Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Mario Ventura, Melissa A Wilson, Alice C Young, Huiqing Zeng, Xinru Zhang, Zachary A Szpiech, Christian D Huber, Jennifer L Gerton, Soojin V Yi, Michael C Schatz, Ivan A Alexandrov, Sergey Koren, Rachel J O'Neill, Evan E Eichler, Adam M Phillippy
The complete sequence and comparative analysis of ape sex chromosomes
Nature. 2024 May 29. doi: 10.1038/s41586-024-07473-2. Online ahead of print.
38811727 |
Christine E Schnitzler, E Sally Chang, Justin Waletich, Gonzalo Quiroga-Artigas, Wai Yee Wong, Anh-Dao Nguyen, Sofia N Barreira, Liam B Doonan, Paul Gonzalez, Sergey Koren, James M Gahan, Steven M Sanders, Brian Bradshaw, Timothy Q DuBuc, Febrimarsa, Danielle de Jong, Eric P Nawrocki, Alexandra Larson, Samantha Klasfeld, Sebastian G Gornik, R Travis Moreland, Tyra G Wolfsberg, Adam M Phillippy, James C Mullikin, Oleg Simakov, Paulyn Cartwright, Matthew Nicotra, Uri Frank, Andreas D Baxevanis
The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
Genome Res. 2024 Apr 15. doi: 10.1101/gr.278382.123. Online ahead of print.
38508693 |
Su Hyun Lee, Michaela E Cooke, Kai Zheng Duan, Sarah K Williams Avram, June Song, Abdel G Elkahloun, George McGrady; NISC Comparative Sequencing Program; Austin Howley, Babru Samal, W Scott Young
Investigation of the Fasciola Cinereum, Absent in BTBR mice, and Comparison with the Hippocampal Area CA2
bioRxiv [Preprint]. 2024 Mar 26:2024.03.21.586108. doi: 10.1101/2024.03.21.586108.
38883723 |
Kai Yu, Natalie Deuitch, Matthew Merguerian, Lea Cunningham, Joie Davis, Erica Bresciani, Jamie Diemer, Elizabeth Andrews, Alice Young, Frank Donovan, Raman Sood, Kathleen Craft, Shawn Chong, Settara Chandrasekharappa, Jim Mullikin, Paul P Liu
Genomic landscape of patients with germline RUNX1 variants and familial platelet disorder with myeloid malignancy
Blood Adv. 2024 Jan 23;8(2):497-511. doi: 10.1182/bloodadvances.2023011165.
38019014 |
2023 |
Nashwa M. Ahmed, Payal Joglekar, Clayton Deming, NISC Comparative Sequencing Program, Katherine P. Lemon, Heidi H. Kong, Julia A. Segre, Sean Conlan
Genomic characterization of the C. tuberculostearicum species complex, a prominent member of the human skin microbiome
mSystems. 2023 Dec 21;8(6):e0063223. doi: 10.1128/msystems.00632-23. Epub 2023 Nov 10.
38126779 |
Payal Joglekar, Sean Conlan, Shih-Queen Lee-Lin, Clay Deming, Sara Saheb Kashaf, NISC Comparative Sequencing Program, Heidi H. Kong, Julia A. Segre
Integrated genomic and functional analyses of human skin-associated Staphylococcus reveal extensive inter- and intra-species diversity
Proc Natl Acad Sci U S A. 2023 Nov 21;120(47):e2310585120. doi: 10.1073/pnas.2310585120. Epub 2023 Nov 13.
37956283 |
Zeyang Shen, Lukian Robert, Milan Stolpman, You Che, Katrina J Allen, Richard Saffery, Audrey Walsh, Angela Young, Jana Eckert, Clay Deming, Qiong Chen, Sean Conlan, Karen Laky, Jenny Min Li, Lindsay Chatman, Sara Saheb Kashaf; NISC Comparative Sequencing Program; VITALITY team; Heidi H Kong, Pamela A Frischmeyer-Guerrerio, Kirsten P Perrett, Julia A Segre
A genome catalog of the early-life human skin microbiome
Genome Biol. 2023 Nov 10;24(1):252. doi: 10.1186/s13059-023-03090-w.
37946302 |
Claire C Homan, Michael W Drazer, Kai Yu, David M Lawrence, Jinghua Feng, Luis Arriola-Martinez, Matthew J Pozsgai, Kelsey E McNeely, Thuong Ha, Parvathy Venugopal, Peer Arts, Sarah L King-Smith, Jesse Cheah, Mark Armstrong, Paul Wang, Csaba Bödör, Alan B Cantor, Mario Cazzola, Erin Degelman, Courtney D DiNardo, Nicolas Duployez, Remi Favier, Stefan Fröhling, Ana Rio-Machin, Jeffery M Klco, Alwin Krämer, Mineo Kurokawa, Joanne Lee, Luca Malcovati, Neil V Morgan, Georges Natsoulis, Carolyn Owen, Keyur P Patel, Claude Preudhomme, Hana Raslova, Hugh Rienhoff, Tim Ripperger, Rachael Schulte, Kiran Tawana, Elvira Velloso, Benedict Yan, Erika Kim, Raman Sood, Amy P Hsu, Steven M Holland, Kerry Phillips, Nicola K Poplawski, Milena Babic, Andrew H Wei, Cecily Forsyth, Helen Mar Fan, Ian D Lewis, Julian Cooney, Rachel Susman, Lucy C Fox, Piers Blombery, Deepak Singhal, Devendra Hiwase, Belinda Phipson, Andreas W Schreiber, Christopher N Hahn, Hamish S Scott, Paul Liu, Lucy A Godley, Anna L Brown; NISC Comparative Sequencing Program
Somatic mutational landscape of hereditary hematopoietic malignancies caused by germline variants in RUNX1, GATA2, and DDX41
Blood Adv. 2023 Oct 24;7(20):6092-6107. doi: 10.1182/bloodadvances.2023010045.
37406166 |
Ryan A Blaustein, Zeyang Shen, Sara Saheb Kashaf, ShihQueen Lee-Lin, Sean Conlan; NISC Comparative Sequencing Program; Marita Bosticardo, Ottavia M Delmonte, Cassandra J Holmes, Monica E Taylor, Glenna Banania, Keisuke Nagao, Dimana Dimitrova, Jennifer A Kanakry, Helen Su, Steven M Holland, Jenna R E Bergerson, Alexandra F Freeman, Luigi D Notarangelo, Heidi H Kong, Julia A Segre
Expanded microbiome niches of RAG-deficient patients
Cell Rep Med. 2023 Oct 17;4(10):101205. doi: 10.1016/j.xcrm.2023.101205. Epub 2023 Sep 26.
37757827 |
Henoke K Shiferaw, Celine S Hong, David Cooper, Jennifer J Johnston; NISC; Leslie G Biesecker
Genome-wide identification of dominant polyadenylation hexamers for use in variant classification
Hum Mol Genet. 2023 Aug 22;ddad136. doi: 10.1093/hmg/ddad136. Online ahead of print.
37606238 |
Claire L Simpson, Danielle C Kimble, Settara C Chandrasekharappa; NISC Comparative Sequencing Program; Khalid Alqosayer, Emily Holzinger, Blake Carrington, John McElderry, Raman Sood, Ghiath Al-Souqi, Hasan Albacha-Hejazi, Joan E Bailey-Wilson
A novel de novo TP63 mutation in whole-exome sequencing of a Syrian family with Oral cleft and ectrodactyly
Mol Genet Genomic Med. 2023 Aug;11(8):e2179. doi: 10.1002/mgg3.2179. Epub 2023 Apr 18.
37070724 |
Michael J Tisza, Derek D N Smith, Andrew E Clark, Jung-Ho Youn; NISC Comparative Sequencing Program; Pavel P Khil, John P Dekker
Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group
Nat Commun. 2023 Jul 10;14(1):4082. doi: 10.1038/s41467-023-39892-6.
37429841 |
Eliza M Gordon-Lipkin, Payal Banerjee, Jose Luis Marin Franco, Tatiana Tarasenko, Shannon Kruk, Elizabeth Thompson, Derek E Gildea, Suiyuan Zhang, Tyra G Wolfsberg; NISC Comparative Sequencing Program; Willy A Flegel, Peter J McGuire
Primary oxidative phosphorylation defects lead to perturbations in the human B cell repertoire
Front Immunol. 2023 Jul 7;14:1142634. doi: 10.3389/fimmu.2023.1142634. eCollection 2023.
37483601 |
Stacie K Loftus, Meredith F Gillis, Linnea Lundh, Laura L Baxter, Julia C Wedel, Dawn E Watkins-Chow, Frank X Donovan; NISC Comparative Sequencing Program; Yuri V Sergeev, William S Oetting, William J Pavan, David R Adams
Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B
Am J Hum Genet. 2023 Jun 12;S0002-9297(23)00169-6. doi: 10.1016/j.ajhg.2023.05.012. Online ahead of print.
37327787 |
Pagna Sok, Aniko Sabo, Lynn M Almli, Mary M Jenkins, Wendy N Nembhard, A J Agopian, Michael J Bamshad, Elizabeth E Blue, Lawrence C Brody, Austin L Brown, Marilyn L Browne, Mark A Canfield, Suzan L Carmichael, Jessica X Chong, Shannon Dugan-Perez, Marcia L Feldkamp, Richard H Finnell, Richard A Gibbs, Denise M Kay, Yunping Lei, Qingchang Meng, Cynthia A Moore, James C Mullikin, Donna Muzny, Andrew F Olshan, Faith Pangilinan, Jennita Reefhuis, Paul A Romitti, Jeremy M Schraw, Gary M Shaw, Martha M Werler, Sanjiv Harpavat, Philip J Lupo; University of Washington Center for Mendelian Genomics, NISC Comparative Sequencing Program, the National Birth Defects Prevention Study
Exome-wide assessment of isolated biliary atresia: A report from the National Birth Defects Prevention Study using child-parent trios and a case-control design to identify novel rare variants
Am J Med Genet A. 2023 Jun;191(6):1546-1556. doi: 10.1002/ajmg.a.63185. Epub 2023 Mar 21.
36942736 |
Tatiana N. Tarasenko, Payal Banerjee, Julio Gomez-Rodriguez, Derek Gildea, Suiyuan Zhang, Tyra Wolfsberg, Lisa M. Jenkins, NISC Comparative Sequencing Program, Peter J. McGuire
Pyruvate dehydrogenase complex integrates the metabolome and epigenome in CD8+ memory T cell differentiation in vitro
Res Sq . 2023 May 10;rs.3.rs-2838359. doi: 10.21203/rs.3.rs-2838359/v1. Preprint
37215014 |
Cory A Weller, Ilya Andreev, Michael J Chambers, Morgan Park; NISC Comparative Sequencing Program; Joshua S Bloom, Meru J Sadhu
Highly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity
Genome Res. 2023 May;33(5):729-740. doi: 10.1101/gr.277515.122. Epub 2023 May 1.
37127330 |
Sara Saheb Kashaf, Catriona P Harkins, Clay Deming, Payal Joglekar, Sean Conlan, Cassandra J Holmes; NISC Comparative Sequencing Program; Alexandre Almeida, Robert D Finn, Julia A Segre, Heidi H Kong
Staphylococcal diversity in atopic dermatitis from an individual to a global scale
Cell Host Microbe . 2023 Apr 12;31(4):578-592.e6. doi: 10.1016/j.chom.2023.03.010.
37054678 |
2022 |
Drazer MW, Homan CC, Yu K, Cavalcante de Andrade Silva M, McNeely KE, Pozsgai MJ, Acevedo-Mendez MG, Segal JP, Wang P, Feng J, King-Smith SL, Kim E, Korotev S, Lawrence DM, Schreiber AW, Hahn CN, Scott HS, Sood R;
NISC Comparative Sequencing Program, Velloso EDRP, Brown AL, Liu PP, Godley LA.
Clonal hematopoiesis in patients with ANKRD26 or ETV6 germline mutations.
Blood Adv. 2022 Aug 9;6(15):4357-4359. doi: 10.1182/bloodadvances.2022007211.
35537115 |
Jingjing Li, Wei Yang, Yuejun Jessie Wang, Chen Ma, Cynthia J Curry, Daniel McGoldrick, Deborah A Nickerson, Jessica X Chong, Elizabeth E Blue, James C Mullikin, Jennita Reefhuis, Wendy N Nembhard, Paul A Romitti, Martha M Werler, Marilyn L Browne, Andrew F Olshan, Richard H Finnell, Marcia L Feldkamp, Faith Pangilinan, Lynn M Almli, Mike J Bamshad, Lawrence C Brody, Mary M Jenkins, Gary M Shaw, NISC Comparative Sequencing Program; University of Washington Center for Mendelian Genomics; National Birth Defects Prevention Study
Exome sequencing identifies genetic variants in anophthalmia and microphthalmia
Am J Med Genet A . 2022 Jun 18. doi: 10.1002/ajmg.a.62874. Online ahead of print.
35716026 |
Nicolas Altemose, Glennis A Logsdon, Andrey V Bzikadze, Pragya Sidhwani, Sasha A Langley, Gina V Caldas, Savannah J Hoyt, Lev Uralsky, Fedor D Ryabov, Colin J Shew, Michael E G Sauria, Matthew Borchers, Ariel Gershman, Alla Mikheenko, Valery A Shepelev, Tatiana Dvorkina, Olga Kunyavskaya, Mitchell R Vollger, Arang Rhie, Ann M McCartney, Mobin Asri, Ryan Lorig-Roach, Kishwar Shafin, Julian K Lucas, Sergey Aganezov, Daniel Olson, Leonardo Gomes de Lima, Tamara Potapova, Gabrielle A Hartley, Marina Haukness, Peter Kerpedjiev, Fedor Gusev, Kristof Tigyi, Shelise Brooks, Alice Young, Sergey Nurk, Sergey Koren, Sofie R Salama, Benedict Paten, Evgeny I Rogaev, Aaron Streets, Gary H Karpen, Abby F Dernburg, Beth A Sullivan, Aaron F Straight, Travis J Wheeler, Jennifer L Gerton, Evan E Eichler, Adam M Phillippy, Winston Timp, Megan Y Dennis, Rachel J O'Neill, Justin M Zook, Michael C Schatz, Pavel A Pevzner, Mark Diekhans, Charles H Langley, Ivan A Alexandrov, Karen H Miga
Complete genomic and epigenetic maps of human centromeres
Science. 2022 Apr;376(6588):eabl4178. doi: 10.1126/science.abl4178. Epub 2022 Apr 1.
35357911 |
Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V Bzikadze, Alla Mikheenko, Mitchell R Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J Hoyt, Mark Diekhans, Glennis A Logsdon, Michael Alonge, Stylianos E Antonarakis, Matthew Borchers, Gerard G Bouffard, Shelise Y Brooks, Gina V Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G de Lima, Philip C Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T Fiddes, Giulio Formenti, Robert S Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G S Grady, Tina A Graves-Lindsay, Ira M Hall, Nancy F Hansen, Gabrielle A Hartley, Marina Haukness, Kerstin Howe, Michael W Hunkapiller, Chirag Jain, Miten Jain, Erich D Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V Maduro, Tobias Marschall, Ann M McCartney, Jennifer McDaniel, Danny E Miller, James C Mullikin, Eugene W Myers, Nathan D Olson, Benedict Paten, Paul Peluso, Pavel A Pevzner, David Porubsky, Tamara Potapova, Evgeny I Rogaev, Jeffrey A Rosenfeld, Steven L Salzberg, Valerie A Schneider, Fritz J Sedlazeck, Kishwar Shafin, Colin J Shew, Alaina Shumate, Ying Sims, Arian F A Smit, Daniela C Soto, Ivan Sović, Jessica M Storer, Aaron Streets, Beth A Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P Walenz, Aaron Wenger, Jonathan M D Wood, Chunlin Xiao, Stephanie M Yan, Alice C Young, Samantha Zarate, Urvashi Surti, Rajiv C McCoy, Megan Y Dennis, Ivan A Alexandrov, Jennifer L Gerton, Rachel J O'Neill, Winston Timp, Justin M Zook, Michael C Schatz, Evan E Eichler, Karen H Miga, Adam M Phillippy
The complete sequence of a human genome
Science. 2022 Apr;376(6588):44-53. doi: 10.1126/science.abj6987. Epub 2022 Mar 31.
35357919 |
Choon K Sim, Sara Saheb Kashaf, Apollo Stacy, Diana M Proctor, Alexandre Almeida, Nicolas Bouladoux, Mark Chen, NISC Comparative Sequencing Program; Robert D Finn, Yasmine Belkaid, Sean Conlan, Julia A Segre
A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
Microbiome. 2022 Mar 10;10(1):43. doi: 10.1186/s40168-021-01207-6.
35272717 |
Georgia Pitsava, Marcia L Feldkamp, Nathan Pankratz, John Lane, Denise M Kay, Kristin M Conway, Charlotte Hobbs, Gary M Shaw, Jennita Reefhuis, Mary M Jenkins, Lynn M Almli, Cynthia Moore, Martha Werler, Marilyn L Browne, Chris Cunniff, Andrew F Olshan, Faith Pangilinan, Lawrence C Brody, Robert J Sicko, Richard H Finnell, Michael J Bamshad, Daniel McGoldrick, Deborah A Nickerson, James C Mullikin, Paul A Romitti, James L Mills, UW Center for Mendelian Genomics, NISC Comparative Sequencing Program and the National Birth Defects Prevention Study
Exome sequencing identifies variants in infants with sacral agenesis
Birth Defects Res. 2022 Mar 10. doi: 10.1002/bdr2.1987. Online ahead of print.
35274497 |
Meghan L Rudd, Nancy F Hansen, Xiaolu Zhang, Mary Ellen Urick, Suiyuan Zhang, Maria J Merino, National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program; James C Mullikin, Lawrence C Brody, Daphne W Bell
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas
PLoS One. 2022 Jan 26;17(1):e0251286. doi: 10.1371/journal.pone.0251286. eCollection 2022. 35081118 |
Sara Saheb Kashaf, Diana M Proctor, Clay Deming, Paul Saary, Martin Hölzer, NISC Comparative Sequencing Program; Monica E Taylor, Heidi H Kong, Julia A Segre, Alexandre Almeida, Robert D Finn
Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions
Nat Microbiol. 2022 Jan;7(1):169-179. doi: 10.1038/s41564-021-01011-w. Epub 2021 Dec 24.
34952941 |
2021 |
Jay-Hyun Jo, Catriona P Harkins, Nicole H Schwardt, Jessica A Portillo, NISC Comparative Sequencing Program; Matthew D Zimmerman, Claire L Carter, Md Amir Hossen, Cody J Peer, Eric C Polley, Véronique Dartois, William D Figg, Niki M Moutsopoulos, Julia A Segre, Heidi H Kong
Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics
Sci Transl Med. 2021 Dec 22;13(625):eabd8077. doi: 10.1126/scitranslmed.abd8077. Epub 2021 Dec 22.
34936382 |
Deena Iskander, Guanlin Wang, Elisabeth F Heuston, Chrysi Christodoulidou, Bethan Psaila, Kanagaraju Ponnusamy, Hongwei Ren, Zeinab Mokhtari, Mark Robinson, Aristeidis Chaidos, Pritesh Trivedi, Nikolaos Trasanidis, Alexia Katsarou, Richard Szydlo, Carmen G Palii, Mehmood H Zaidi, Qais Al-Oqaily, Valentina S Caputo, Anindita Roy, Yvonne Harrington, Leena Karnik, Kikkeri Naresh, Adam J Mead, Supat Thongjuea, Marjorie Brand, Josu de la Fuente, David M Bodine, Irene Roberts, Anastasios Karadimitris
Single-cell profiling of human bone marrow progenitors reveals mechanisms of failing erythropoiesis in Diamond-Blackfan anemia
Sci Transl Med. 2021 Sep 8;13(610):eabf0113. doi: 10.1126/scitranslmed.abf0113. Epub 2021 Sep 8
34516827 |
Georgia Pitsava, Marcia L Feldkamp, Nathan Pankratz, John Lane, Denise M Kay, Kristin M Conway, Gary M Shaw, Jennita Reefhuis, Mary M Jenkins, Lynn M Almli, Andrew F Olshan, Faith Pangilinan, Lawrence C Brody, Robert J Sicko, Charlotte A Hobbs, Mike Bamshad, Daniel McGoldrick, Deborah A Nickerson, Richard H Finnell, James Mullikin, Paul A Romitti, James L Mills, University of Washington Center for Mendelian Genomics, NISC Comparative Sequencing Program and the National Birth Defects Prevention Study
Exome sequencing of child-parent trios with bladder exstrophy: Findings in 26 children
Am J Med Genet A. 2021 Aug 5. doi: 10.1002/ajmg.a.62439. Online ahead of print.
34355505 |
Xin Huang, Rory M Welsh, Clay Deming, Diana M Proctor, Pamela J Thomas, NISC Comparative Sequencing Program; Gabrielle M Gussin, Susan S Huang, Heidi H Kong, Meghan L Bentz, Snigdha Vallabhaneni, Tom Chiller, Brendan R Jackson, Kaitlin Forsberg, Sean Conlan, Anastasia P Litvintseva, Julia A Segre
Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.
mSphere. 2021 Aug 4:e0028721. doi: 10.1128/mSphere.00287-21. Online ahead of print.
34346704 |
Jorge L Rodriguez-Gil, Laura L Baxter, Dawn E Watkins-Chow, Nicholas L Johnson, Cristin D Davidson, Steven R Carlson, Arturo A Incao, NISC Comparative Sequencing Program; Kerri L Wallom, Nicole Y Farhat, Frances M Platt, Ryan K Dale, Forbes D Porter, William J Pavan.
Transcriptome of HPβCD-treated Niemann-pick disease type C1 cells highlights GPNMB as a biomarker for therapeutics
Hum Mol Genet. 2021 Jul 22;ddab194. doi: 10.1093/hmg/ddab194. Online ahead of print.
34296265 |
Stacie K Loftus, Linnea Lundh, Dawn E Watkins-Chow, Laura L Baxter, Erola Pairo-Castineira, NISC Comparative Sequencing Program, Ian J Jackson, William S Oetting, William J Pavan, David R Adams.
A custom capture sequence approach for oculocutaneous albinism identifies structural variant alleles at the OCA2 locus
Hum Mutat. 2021 Jul 10. doi: 10.1002/humu.24257. Online ahead of print.
34246199 |
Kevin W Currin, Michael R Erdos, Narisu Narisu, Vivek Rai, Swarooparani Vadlamudi, Hannah J Perrin, Jacqueline R Idol, Tingfen Yan, Ricardo D'Oliveira Albanus, K Alaine Broadaway, Amy S Etheridge, Lori L Bonnycastle, Peter Orchard, John P Didion, Amarjit S Chaudhry, NISC Comparative Sequencing Program; Federico Innocenti, Erin G Schuetz, Laura J Scott, Stephen C J Parker, Francis S Collins, Karen L Mohlke
Genetic effects on liver chromatin accessibility identify disease regulatory variants
Am J Hum Genet . 2021 Jul 1;108(7):1169-1189. doi: 10.1016/j.ajhg.2021.05.001. Epub 2021 May 25.
34038741 |
Proctor DM, Dangana T, Sexton DJ, Fukuda C, Yelin RD, Stanley M, Bell PB, Baskaran S, Deming C, Chen Q, Conlan S, Park M; NISC Comparative Sequencing Program, Welsh RM, Vallabhaneni S, Chiller T, Forsberg K, Black SR, Pacilli M, Kong HH, Lin MY, Schoeny ME, Litvintseva AP, Segre JA, Hayden MK.
Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility.
Nat Med. 2021 Jun 21. doi: 10.1038/s41591-021-01383-w. Online ahead of print.
34155414 |
Jeffrey N Dudley, Celine S Hong, Marwan A Hawari, Jasmine Shwetar, Julie C Sapp, Justin Lack, Henoke Shiferaw, NISC Comparative Sequencing Program; Jennifer J Johnston, Leslie G Biesecker
Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach
Am J Hum Genet. 2021 May 20;S0002-9297(21)00185-3. doi: 10.1016/j.ajhg.2021.05.001.
33832433 |
Oskar Schnappauf, Natalia Sampaio Moura, Ivona Aksentijevich, Monique Stoffels, Amanda K Ombrello, Patrycja Hoffmann, Karyl Barron, Elaine F Remmers, Michael Hershfield, Susan J Kelly, NISC Comparative Sequencing Program; David Cuthbertson, Simon Carette, Sharon A Chung, Lindsy Forbess, Nader A Khalidi, Curry L Koening, Carol A Langford, Carol A McAlear, Paul A Monach, Larry Moreland, Christian Pagnoux, Philip Seo, Jason M Springer, Antoine G Sreih, Kenneth J Warrington, Steven R Ytterberg, Daniel L Kastner, Peter C Grayson, Peter A Merkel, Vasculitis Clinical Research Consortium
Sequence-Based Screening of Patients With Idiopathic Polyarteritis Nodosa, Granulomatosis With Polyangiitis, and Microscopic Polyangiitis for Deleterious Genetic Variants in ADA2
Arthritis Rheumatol . 2021 Mar;73(3):512-519. doi: 10.1002/art.41549. Epub 2021 Feb 3.
33021335 |
Yongxing Zhou, Raman Sood, Qun Wang, Blake Carrington, Morgan Park, Alice C Young, Daniel Birnbaum, Zhao Liu, Tetsuo Ashizawa, James C Mullikin, Mohamad Z Koubeissi, Paul Liu
Clinical and genomic analysis of a large Chinese family with familial cortical myoclonic tremor with epilepsy and SAMD12 intronic repeat expansion
Epilepsia Open . 2021 Feb 2;6(1):102-111. doi: 10.1002/epi4.12450. eCollection 2021 Mar.
33681653 |
2020 |
David B Beck, Marcela A Ferrada, Keith A Sikora, Amanda K Ombrello, Jason C Collins, Wuhong Pei, Nicholas Balanda, Daron L Ross, Daniela Ospina Cardona, Zhijie Wu, Bhavisha Patel, Kalpana Manthiram, Emma M Groarke, Fernanda Gutierrez-Rodrigues, Patrycja Hoffmann, Sofia Rosenzweig, Shuichiro Nakabo, Laura W Dillon, Christopher S Hourigan, Wanxia L Tsai, Sarthak Gupta, Carmelo Carmona-Rivera, Anthony J Asmar, Lisha Xu, Hirotsugu Oda, Wendy Goodspeed, Karyl S Barron, Michele Nehrebecky, Anne Jones, Ryan S Laird, Natalie Deuitch, Dorota Rowczenio, Emily Rominger, Kristina V Wells, Chyi-Chia R Lee, Weixin Wang, Megan Trick, James Mullikin, Gustaf Wigerblad, Stephen Brooks, Stefania Dell'Orso, Zuoming Deng, Jae J Chae, Alina Dulau-Florea, May C V Malicdan, Danica Novacic, Robert A Colbert, Mariana J Kaplan, Massimo Gadina, Sinisa Savic, Helen J Lachmann, Mones Abu-Asab, Benjamin D Solomon, Kyle Retterer, William A Gahl, Shawn M Burgess, Ivona Aksentijevich, Neal S Young, Katherine R Calvo, Achim Werner, Daniel L Kastner, Peter C Grayson
Somatic Mutations in UBA1 and Severe Adult-Onset Autoinflammatory Disease
N Engl J Med. 2020 Dec 31;383(27):2628-2638. doi: 10.1056/NEJMoa2026834. Epub 2020 Oct 27.
33108101 |
Maura Manion, Augusto Dulanto Chiang, Luxin Pei, Chun-Shu Wong, Pavel Khil, Dima A Hammoud, Megan Anderson, Elizabeth Laidlaw, Safia Kuriakose, Andrea Lisco, NISC Comparative Sequencing Program; Adrian M Zelazny, John P Dekker, Irini Sereti
Disseminated Mycobacterium marinum in HIV unmasked by Immune Reconstitution Inflammatory Syndrome.
J Infect Dis. 2020 Dec 18;jiaa769. doi: 10.1093/infdis/jiaa769. Online ahead of print.
33336253 |
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Andrey Bzikadze, Shelise Brooks, Edmund Howe, David Porubsky, Glennis A Logsdon, Valerie A Schneider, Tamara Potapova, Jonathan Wood, William Chow, Joel Armstrong, Jeanne Fredrickson, Evgenia Pak, Kristof Tigyi, Milinn Kremitzki, Christopher Markovic, Valerie Maduro, Amalia Dutra, Gerard G Bouffard, Alexander M Chang, Nancy F Hansen, Amy B Wilfert, Françoise Thibaud-Nissen, Anthony D Schmitt, Jon-Matthew Belton, Siddarth Selvaraj, Megan Y Dennis, Daniela C Soto, Ruta Sahasrabudhe, Gulhan Kaya, Josh Quick, Nicholas J Loman, Nadine Holmes, Matthew Loose, Urvashi Surti, Rosa Ana Risques, Tina A Graves Lindsay, Robert Fulton, Ira Hall, Benedict Paten, Kerstin Howe, Winston Timp, Alice Young, James C Mullikin, Pavel A Pevzner, Jennifer L Gerton, Beth A Sullivan, Evan E Eichler, Adam M Phillippy.
Telomere-to-telomere assembly of a complete human X chromosome.
Nature. 2020 Sep;585(7823):79-84. doi: 10.1038/s41586-020-2547-7. Epub 2020 Jul 14.
32663838 |
Oskar Schnappauf, Qing Zhou, Natalia Sampaio Moura, Amanda K Ombrello, Drew G Michael, Natalie Deuitch, Karyl Barron, Deborah L Stone, Patrycja Hoffmann, Michael Hershfield, Carolyn Applegate, Hans T Bjornsson, David B Beck, P Dane Witmer, Nara Sobreira, Elizabeth Wohler, John A Chiorini, The American Genome Center, Clifton L Dalgard, Nih Intramural Sequencing Center, Daniel L Kastner, Ivona Aksentijevich
Deficiency of Adenosine Deaminase 2 (DADA2): Hidden Variants, Reduced Penetrance, and Unusual Inheritance
J Clin Immunol. 2020 Aug;40(6):917-926. doi: 10.1007/s10875-020-00817-3. Epub 2020 Jul 8.
32638197 |
Alexander Pemov, Ramita Dewan, Nancy F Hansen, Settara C Chandrasekharappa, Abhik Ray-Chaudhury, Kristine Jones, Wen Luo, John D Heiss, James C Mullikin, Prashant Chittiboina, Douglas R Stewart, Ashok R Asthagiri
Comparative clinical and genomic analysis of neurofibromatosis type 2-associated cranial and spinal meningiomas
Sci Rep. 2020 Jul 28;10(1):12563. doi: 10.1038/s41598-020-69074-z.
32724039 |
| Psaila B, Wang G, Rodriguez-Meira A, Li R, Heuston EF, Murphy L, Yee D, Hitchcock IS, Sousos N, O'Sullivan J, Anderson S, Senis YA, Weinberg OK, Calicchio ML; NIH Intramural Sequencing Center, Iskander D, Royston D, Milojkovic D, Roberts I, Bodine DM, Thongjuea S, Mead AJ.
Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets.
Mol Cell. 2020 May 7;78(3):477-492.e8. doi: 10.1016/j.molcel.2020.04.008.
32386542 |
| Liu Z, Shriner D, Hansen NF, Rotimi CN, Mullikin JC; NISC Comparative Sequencing Program.
Admixture mapping identifies genetic regions associated with blood pressure phenotypes in African Americans.
PLoS One. 2020 Apr 21;15(4):e0232048. doi: 10.1371/journal.pone.0232048. eCollection 2020.
32315356 |
|
Pei W, Xu L, Chen Z, Slevin CC, Pettie KP, Wincovitch S; NISC Comparative Sequencing Program, Burgess SM.
A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation.
NPJ Regen Med. 2020 Mar 25;5:6. doi: 10.1038/s41536-020-0089-0. eCollection 2020.
32218991 |
|
Vijay K Kalaskar, Ramakrishna P Alur, LeeAnn K Li, James W Thomas, Yuri V Sergeev, Delphine Blain, Robert B Hufnagel, Tiziana Cogliati, Brian P Brooks
High-throughput custom capture sequencing identifies novel mutations in coloboma-associated genes: Mutation in DNA-binding domain of retinoic acid receptor beta affects nuclear localization causing ocular coloboma
Hum Mutat. 2020 Mar;41(3):678-695. doi: 10.1002/humu.23954. Epub 2019 Dec 9.
31816153 |
2019 |
|
Fufa TD, Baxter LL, Wedel JC, Gildea DE; NISC Comparative Sequencing Program, Loftus SK, Pavan WJ.
MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells.
Epigenetics Chromatin. 2019 Aug 9;12(1):50. doi: 10.1186/s13072-019-0297-2.
31399133 |
|
Gourh P1, Safran SA, Alexander T, Boyden SE, Morgan ND, Shah AA, Mayes MD, Doumatey A, Bentley AR, Shriner D, Domsic RT, Medsger TA Jr, Ramos PS, Silver RM, Steen VD, Varga J, Hsu V, Saketkoo LA, Schiopu E, Khanna D, Gordon JK, Kron B, Criswell LA, Gladue H, Derk CT, Bernstein EJ, Bridges SL Jr, Shanmugam VK, Kolstad KD, Chung L, Kafaja S, Jan R, Trojanowski M, Goldberg A, Korman BD, Steinbach PJ, Chandrasekharappa SC, Mullikin JC, Adeyemo A, Rotimi C, Wigley FM, Kastner DL, Boin F, Remmers EF.
HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry.
Proc Natl Acad Sci U S A. 2020 Jan 7;117(1):552-562. doi: 10.1073/pnas.1906593116. Epub 2019 Dec 23.
31871193 |
|
Lalaoui N, Boyden SE, Oda H, Wood GM, Stone DL, Chau D, Liu L, Stoffels M, Kratina T, Lawlor KE, Zaal KJM, Hoffmann PM, Etemadi N, Shield-Artin K, Biben C5, Tsai WL, Blake MD, Kuehn HS, Yang D, Anderton H, Silke N, Wachsmuth L, Zheng L, Moura NS, Beck DB, Gutierrez-Cruz G, Ombrello AK, Pinto-Patarroyo GP, Kueh AJ, Herold MJ, Hall C, Wang H, Chae JJ, Dmitrieva NI, McKenzie M, Light A, Barham BK, Jones A, Romeo TM, Zhou Q, Aksentijevich I, Mullikin JC, Gross AJ, Shum AK, Hawkins ED, Masters SL, Lenardo MJ, Boehm M, Rosenzweig SD, Pasparakis M, Voss AK, Gadina M, Kastner DL, Silke J.
Mutations that prevent caspase cleavage of RIPK1 cause autoinflammatory disease.
Nature. 2020 Jan;577(7788):103-108. doi: 10.1038/s41586-019-1828-5. Epub 2019 Dec 11.
31827281 |
|
Coon SL, Fu C, Hartley SW, Holtzclaw L, Mays JC, Kelly MC, Kelley MW, Mullikin JC, Rath MF, Savastano LE, Klein DC.
Single Cell Sequencing of the Pineal Gland: The Next Chapter.
Front Endocrinol (Lausanne). 2019 Sep 20;10:590. doi: 10.3389/fendo.2019.00590. eCollection 2019.
31616371 |
|
Conlan S, Lau AF, Deming C, Spalding CD, Lee-Lin S, Thomas PJ, Park M, Dekker JP, Frank KM, Palmore TN, Segre JA.
Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy.
MBio. 2019 Oct 8;10(5). pii: e00652-19. doi: 10.1128/mBio.00652-19.
31594809 |
|
Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, Gu Y, Jafari AJ, Louder MK, O'Dell S, Rowshan AP, Viox EG, Wang Y, Choi CW, Corcoran MM, Corrigan AR, Dandey VP, Eng ET, Geng H, Foulds KE, Guo Y, Kwon YD, Lin B, Liu K, Mason RD, Nason MC, Ohr TY, Ou L, Rawi R, Sarfo EK, Schön A, Todd JP, Wang S, Wei H, Wu W; NISC Comparative Sequencing Program, Mullikin JC, Bailer RT, Doria-Rose NA, Karlsson Hedestam GB, Scorpio DG, Overbaugh J, Bloom JD, Carragher B, Potter CS, Shapiro L, Kwong PD, Mascola JR.
Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Cell. 2019 Jul 25;178(3):567-584.e19. doi: 10.1016/j.cell.2019.06.030.
31348886 |
|
Jenkins MM, Almli LM, Pangilinan F, Chong JX, Blue EE, Shapira SK, White J, McGoldrick D, Smith JD, Mullikin JC, Bean CJ, Nembhard WN, Lou XY, Shaw GM, Romitti PA, Keppler-Noreuil K, Yazdy MM, Kay DM, Carter TC, Olshan AF, Moore KJ, Nascone-Yoder N, Finnell RH, Lupo PJ, Feldkamp ML; NISC Comparative Sequencing Program; University of Washington Center for Mendelian Genomics, Nickerson DA, Bamshad MJ, Brody LC, Reefhuis J; National Birth Defects Prevention Study.
Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data.
Birth Defects Res. 2019 Jul 21. doi: 10.1002/bdr2.1554. [Epub ahead of print]
31328417 |
Chen Z, Omori Y, Koren S, Shirokiya T, Kuroda T, Miyamoto A, Wada H, Fujiyama A, Toyoda A, Zhang S, Wolfsberg TG, Kawakami K, Phillippy AM; NISC Comparative Sequencing Program, Mullikin JC, Burgess SM.
De novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole-genome duplication.
Sci Adv. 2019 Jun 26;5(6):eaav0547. doi: 10.1126/sciadv.aav0547. eCollection 2019 Jun.
31249862 |
Pemov A, Hansen NF, Sindiri S, Patidar R, Higham CS, Dombi E, Miettinen MM, Fetsch P, Brems H, Chandrasekharappa S, Jones K, Zhu B, Wei JS; NISC Comparative Sequencing Program; NCI DCEG Cancer Genomics Research Laboratory, Mullikin JC, Wallace MR, Khan J, Legius E, Widemann BC, Stewart DR.
Low mutation burden and frequent loss of CDKN2A/B and SMARCA2, but not PRC2, define pre-malignant neurofibromatosis type 1-associated atypical neurofibromas.
Neuro Oncol. 2019 Feb 5. doi: 10.1093/neuonc/noz028. [Epub ahead of print]
30722027 |
|
Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li J, Merrick BA, Tice RR, Wang T, Xu X; NISC Comparative Sequencing Program, Bushel PR, Fargo DC, Mullikin JC, Wade PA.
DNA methylation in mice is influenced by genetics as well as sex and life experience.
Nat Commun. 2019 Jan 18;10(1):305. doi: 10.1038/s41467-018-08067-z.
30659182 |
2018 |
|
Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, Piecuch E, Luo O, Chines PS, Fuchbserger C; NIH Intramural Sequencing Center, Sethupathy P, Aiden AP, Ruan Y, Aiden EL, Collins FS, Ucar D, Parker SCJ, Stitzel ML.
Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function.
Cell Rep. 2019 Jan 15;26(3):788-801.e6. doi: 10.1016/j.celrep.2018.12.083.
30650367 |
|
Johnson RC, Deming C, Conlan S, Zellmer CJ, Michelin AV, Lee-Lin S, Thomas PJ, Park M, Weingarten RA, Less J, Dekker JP, Frank KM, Musser KA, McQuiston JR, Henderson DK, Lau AF, Palmore TN, Segre JA.
Investigation of a Cluster of Sphingomonas koreensis Infections.
N Engl J Med. 2018 Dec 27;379(26):2529-2539. doi: 10.1056/NEJMoa1803238.
30586509 |
|
Tirosh O, Conlan S, Deming C, Lee-Lin SQ, Huang X; NISC Comparative Sequencing Program, Su HC, Freeman AF, Segre JA, Kong HH.
Expanded skin virome in DOCK8-deficient patients.
Nat Med. 2018 Dec;24(12):1815-1821. doi: 10.1038/s41591-018-0211-7. Epub 2018 Nov 5.
30397357 |
|
Zhang T, Choi J, Kovacs MA, Shi J, Xu M; NISC Comparative Sequencing Program; Melanoma Meta-Analysis Consortium, Goldstein AM, Trower AJ, Bishop DT, Iles MM, Duffy DL, MacGregor S, Amundadottir LT, Law MH, Loftus SK, Pavan WJ, Brown KM.
Cell-type-specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes.
Genome Res. 2018 Nov;28(11):1621-1635. doi: 10.1101/gr.233304.117. Epub 2018 Oct 17.
30333196 |
|
Sapp JC, Johnston JJ, Driscoll K, Heidlebaugh AR, Miren Sagardia A, Dogbe DN, Umstead KL, Turbitt E, Alevizos I, Baron J, Bönnemann C, Brooks B, Donkervoort S, Jee YH, Linehan WM, McMahon FJ, Moss J, Mullikin JC, Nielsen D, Pelayo E, Remaley AT, Siegel R, Su H, Zarate C; NISC Comparative Sequencing Program, Manolio TA, Biesecker BB, Biesecker LG.
Evaluation of Recipients of Positive and Negative Secondary Findings Evaluations in a Hybrid CLIA-Research Sequencing Pilot.
Am J Hum Genet. 2018 Sep 6;103(3):358-366. doi: 10.1016/j.ajhg.2018.07.018. Epub 2018 Aug 16.
30122538 |
|
Brooks BP, Zein WM, Thompson AH, Mokhtarzadeh M, Doherty DA, Parisi M, Glass IA, Malicdan MC, Vilboux T, Vemulapalli M, Mullikin JC, Gahl WA, Gunay-Aygun M.
Joubert Syndrome: Ophthalmological Findings in Correlation with Genotype and Hepatorenal Disease in 99 Patients Prospectively Evaluated at a Single Center.
Ophthalmology. 2018 Dec;125(12):1937-1952. doi: 10.1016/j.ophtha.2018.05.026. Epub 2018 Jul 25.
30055837 |
|
Roessler E, Hu P, Marino J, Hong S, Hart R, Berger S, Martinez A, Abe Y, Kruszka P, Thomas JW, Mullikin JC; NISC Comparative Sequencing Program, Wang Y, Wong WSW, Niederhuber JE, Solomon BD, Richieri-Costa A, Ribeiro-Bicudo LA, Muenke M.
Common genetic causes of holoprosencephaly are limited to a small set of evolutionarily conserved driver genes of midline development coordinated by TGF-β, hedgehog, and FGF signaling.
Hum Mutat. 2018 Oct;39(10):1416-1427. doi: 10.1002/humu.23590. Epub 2018 Jul 26.
29992659 |
|
Duncan CG, Grimm SA, Morgan DL, Bushel PR, Bennett BD; NISC Comparative Sequencing Program, Roberts JD, Tyson FL, Merrick BA, Wade PA.
Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver.
Sci Rep. 2018 Jul 4;8(1):10138. doi: 10.1038/s41598-018-28356-3.
29973619 |
|
Elisabeth F Heuston, Cheryl A Keller, Jens Lichtenberg, Belinda Giardine, Stacie M Anderson, NIH Intramural Sequencing Center; Ross C Hardison, David M Bodine
Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points
Epigenetics Chromatin. 2018 May 28;11(1):22. doi: 10.1186/s13072-018-0195-z.
29807547 |
|
Gourh P, Remmers EF, Boyden SE, Alexander T, Morgan ND, Shah AA, Mayes MD, Doumatey A, Bentley AR, Shriner D, Domsic RT, Medsger TA Jr, Steen VD, Ramos PS, Silver RM, Korman B, Varga J, Schiopu E, Khanna D, Hsu V, Gordon JK, Saketkoo LA, Gladue H, Kron B, Criswell LA, Derk CT, Bridges SL Jr, Shanmugam VK, Kolstad KD, Chung L, Jan R, Bernstein EJ, Goldberg A, Trojanowski M, Kafaja S, Maksimowicz-McKinnon KM, Mullikin JC; NISC Comparative Sequencing Program, Adeyemo A, Rotimi C, Boin F, Kastner DL, Wigley FM.
Whole-Exome Sequencing to Identify Rare Variants and Gene Networks that Increase Susceptibility to Scleroderma in African Americans.
Arthritis Rheumatol. 2018 May 6. doi: 10.1002/art.40541. [Epub ahead of print]
29732714 |
|
Harris ML, Fufa TD, Palmer JW, Joshi SS, Larson DM, Incao A, Gildea DE, Trivedi NS, Lee AN, Day CP, Michael HT, Hornyak TJ, Merlino G; NISC Comparative Sequencing Program, Pavan WJ.
A direct link between MITF, innate immunity, and hair graying.
PLoS Biol. 2018 May 3;16(5):e2003648. doi: 10.1371/journal.pbio.2003648. eCollection 2018 May.
29723194 |
|
Zhou T, Zheng A, Baxa U, Chuang GY, Georgiev IS, Kong R, O'Dell S, Shahzad-Ul-Hussan S, Shen CH, Tsybovsky Y, Bailer RT, Gift SK, Louder MK, McKee K, Rawi R, Stevenson CH, Stewart-Jones GBE, Taft JD, Waltari E, Yang Y, Zhang B, Shivatare SS, Shivatare VS, Lee CD, Wu CY; NISC Comparative Sequencing Program, Mullikin JC, Bewley CA, Burton DR, Polonis VR, Shapiro L, Wong CH, Mascola JR, Kwong PD, Wu X.
A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.
Immunity. 2018 Mar 20;48(3):500-513.e6. doi: 10.1016/j.immuni.2018.02.013. Epub 2018 Mar 13.
29548671 |
|
Weingarten RA, Johnson RC, Conlan S, Ramsburg AM, Dekker JP, Lau AF, Khil P, Odom RT, Deming C, Park M, Thomas PJ; NISC Comparative Sequencing Program, Henderson DK, Palmore TN, Segre JA, Frank KM.
Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance.
MBio. 2018 Feb 6;9(1). pii: e02011-17. doi: 10.1128/mBio.02011-17.
29437920 |
|
Thomas A Randall, James C Mullikin, Geoffrey A Mueller
The Draft Genome Assembly of Dermatophagoides pteronyssinus Supports Identification of Novel Allergen Isoforms in Dermatophagoides Species
Int Arch Allergy Immunol. 2018;175(3):136-146. doi: 10.1159/000481989. Epub 2018 Jan 11.
29320781 |
2017 |
|
Fleming LR, Doherty DA, Parisi MA, Glass IA, Bryant J, Fischer R, Turkbey B, Choyke P, Daryanani K, Vemulapalli M, Mullikin JC, Malicdan MC, Vilboux T, Sayer JA, Gahl WA, Gunay-Aygun M.
Prospective Evaluation of Kidney Disease in Joubert Syndrome.
Clin J Am Soc Nephrol. 2017 Dec 7;12(12):1962-1973. doi: 10.2215/CJN.05660517. Epub 2017 Nov 16.
29146704 |
|
Rajalakshmi S. Asur, Danielle C. Kimble, Francis P. Lach, Moonjung Jung, Frank X. Donovan, Aparna Kamat, Raymond J. Noonan, James W. Thomas, Morgan Park, Peter Chines, Adrianna Vlachos, Arleen D. Auerbach, Agata Smogorzewska, and Settara C. Chandrasekharappa
Somatic mosaicism of an intragenic FANCB duplication in both fibroblast and peripheral blood cells observed in a Fanconi anemia patient leads to milder phenotype
Mol Genet Genomic Med. 2018 Jan;6(1):77-91. doi: 10.1002/mgg3.350. Epub 2017 Nov 30.
29193904 |
|
Strongin A, Heller T, Doherty D, Glass IA, Parisi MA, Bryant J, Choyke P, Turkbey B, Daryanani K, Yildirimli D, Vemulapalli M, Mullikin JC; NISC Comparative Sequencing Program, Malicdan MC, Vilboux T, Gahl WA, Gunay-Aygun M.
Characteristics of Liver Disease in 100 Individuals With Joubert Syndrome Prospectively Evaluated At A Single Center.
J Pediatr Gastroenterol Nutr. 2017 Nov 3. doi: 10.1097/MPG.0000000000001816. [Epub ahead of print]
29112083 |
|
Kimble DC, Lach FP, Gregg SQ, Donovan FX, Flynn EK, Kamat A, Young A, Vemulapalli M, Thomas JW, Mullikin JC, Auerbach AD, Smogorzewska A, Chandrasekharappa SC.
A comprehensive approach to identification of pathogenic FANCA variants in Fanconi anemia patients and their families.
Hum Mutat. 2017 Nov 2. doi: 10.1002/humu.23366. [Epub ahead of print]
29098742 |
|
Le Gallo M, Rudd ML, Urick ME, Hansen NF; National Institutes of Health Intramural Sequencing Center Comparative Sequencing Program, Merino MJ, Mutch DG, Goodfellow PJ, Mullikin JC, Bell DW.
The FOXA2 transcription factor is frequently somatically mutated in uterine carcinosarcomas and carcinomas.
Cancer. 2018 Jan 1;124(1):65-73. doi: 10.1002/cncr.30971. Epub 2017 Sep 21.
28940304 |
|
Chandrasekharappa SC, Chinn SB, Donovan FX, Chowdhury NI, Kamat A, Adeyemo AA, Thomas JW, Vemulapalli M, Hussey CS, Reid HH, Mullikin JC, Wei Q, Sturgis EM.
Assessing the spectrum of germline variation in Fanconi anemia genes among patients with head and neck carcinoma before age 50.
Cancer. 2017 Oct 15;123(20):3943-3954. doi: 10.1002/cncr.30802. Epub 2017 Jul 5.
28678401 |
|
Sheng Z, Schramm CA, Kong R; NISC Comparative Sequencing Program, Mullikin JC, Mascola JR, Kwong PD, Shapiro L.
Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.
Front Immunol. 2017 May 10;8:537. doi: 10.3389/fimmu.2017.00537. eCollection 2017.
28539926 |
|
Crawford NG, Kelly DE, Hansen MEB, Beltrame MH, Fan S, Bowman SL, Jewett E, Ranciaro A, Thompson S, Lo Y, Pfeifer SP, Jensen JD, Campbell MC, Beggs W, Hormozdiari F, Mpoloka SW, Mokone GG, Nyambo T, Meskel DW, Belay G, Haut J; NISC Comparative Sequencing Program, Rothschild H, Zon L, Zhou Y, Kovacs MA, Xu M, Zhang T, Bishop K, Sinclair J, Rivas C, Elliot E, Choi J, Li SA, Hicks B, Burgess S, Abnet C, Watkins-Chow DE, Oceana E, Song YS, Eskin E, Brown KM, Marks MS, Loftus SK, Pavan WJ, Yeager M, Chanock S, Tishkoff SA.
Loci associated with skin pigmentation identified in African populations.
Science. 2017 Nov 17;358(6365). pii: eaan8433. doi: 10.1126/science.aan8433. Epub 2017 Oct 12.
29025994 |
|
Summers AC, Snow J, Wiggs E, Liu AG, Toro C, Poretti A, Zein WM, Brooks BP, Parisi MA, Inati S, Doherty D, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Vilboux T, Gahl WA, Gunay-Aygun M.
Neuropsychological phenotypes of 76 individuals with Joubert syndrome evaluated at a single center.
Am J Med Genet A. 2017 May 12. doi: 10.1002/ajmg.a.38272.
28497568 |
|
Le Gallo M, Rudd ML, Urick ME, Hansen NF, Zhang S, NISC Comparative Sequencing Program, Lozy F, Sgroi DC, Vidal Bel A, Matias-Guiu X, Broaddus RR, Lu KH, Levine DA, Mutch DG, Goodfellow PJ, Salvesen HB, Mullikin JC, Bell DW.
Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing.
Cancer. 2017 May 9. doi: 10.1002/cncr.30745.
2848515 |
|
Shahrour MA, Staretz-Chacham O, Dayan D, Stephen J, Weech A, Damseh N, Pri Chen H, Edvardson S, Mazaheri S, Saada A, NISC Intramural Sequencing, Hershkovitz E, Shaag A, Huizing M, Abu-Libdeh B, Gahl WA, Azem A, Anikster Y, Vilboux T, Elpeleg O, Malicdan MC.
Mitochondrial epileptic encephalopathy, 3-methylglutaconic aciduria and variable complex V deficiency associated with TIMM50 mutations. Clin Genet. 2017 May;91(5):690-696. doi: 10.1111/cge.12855.
27573165 |
|
Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MC, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M.
Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability.
Am J Hum Genet. 2017 Feb 2;100(2):257-266. doi: 10.1016/j.ajhg.2017.01.002.
28132689 |
|
Bryan MM, Tolman NJ, Simon KL, Huizing M, Hufnagel RB, Brooks BP, Speransky V, Mullikin JC, Gahl WA, Malicdan MC, Gochuico BR.
Clinical and molecular phenotyping of a child with Hermansky-Pudlak syndrome-7, an uncommon genetic type of HPS.
Mol Genet Metab. 2017 Feb 27. pii: S1096-7192(16)30413-9. doi: 10.1016/j.ymgme.2017.02.007.
28259707 |
|
Stephen J, Vilboux T, Mian L, Kuptanon C, Sinclair CM, Yildirimli D, Maynard DM, Bryant J, Fischer R, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Huizing M, Gahl WA, Malicdan MC, Gunay-Aygun M.
Mutations in KIAA0753 cause Joubert syndrome associated with growth hormone deficiency.
Hum Genet. 2017 Feb 20. doi: 10.1007/s00439-017-1765-z.
28220259 |
|
Berger SI, Ciccone C, Simon KL, Malicdan MC, Vilboux T, Billington C, Fischer R, Introne WJ, Gropman A, Blancato JK, Mullikin JC, NISC Comparative Sequencing Program, Gahl WA, Huizing M, Smith AC.
Exome analysis of Smith-Magenis-like syndrome cohort identifies de novo likely pathogenic variants.
Hum Genet. 2017 Feb 17. doi: 10.1007/s00439-017-1767-x.
28213671 |
|
Varshney A, Scott LJ, Welch RP, Erdos MR, Chines PS, Narisu N, Albanus RD, Orchard P, Wolford BN, Kursawe R, Vadlamudi S, Cannon ME, Didion JP, Hensley J, Kirilusha A, NISC Comparative Sequencing Program, Bonnycastle LL, Taylor DL, Watanabe R, Mohlke KL, Boehnke M, Collins FS, Parker SC, Stitzel ML.
Genetic regulatory signatures underlying islet gene expression and type 2 diabetes.
Proc Natl Acad Sci U S A. 2017 Feb 13. pii: 201621192. doi: 10.1073/pnas.1621192114.
28193859 |
|
Dewan R, Pemov A, Dutra AS, Pak ED, Edwards NA, Ray-Chaudhury A, Hansen NF, Chandrasekharappa SC, Mullikin JC, Asthagiri AR, NISC Comparative Sequencing Program, Heiss JD, Stewart DR, Germanwala AV.
First insight into the somatic mutation burden of neurofibromatosis type 2-associated grade I and grade II meningiomas: a case report comprehensive genomic study of two cranial meningiomas with vastly different clinical presentation.
BMC Cancer. 2017 Feb 13;17(1):127. doi: 10.1186/s12885-017-3127-6.
28193203 |
|
Kwon EM, Connelly JP, Hansen NF, Donovan FX, Winkler T, Davis BW, Alkadi H, Chandrasekharappa SC, Dunbar CE, Mullikin JC, Liu P.
iPSCs and fibroblast subclones from the same fibroblast population contain comparable levels of sequence variations.
Proc Natl Acad Sci U S A. 2017 Feb 6. pii: 201616035. doi: 10.1073/pnas.1616035114.
28167771 |
|
Loftus SK, Baxter LL, Cronin JC, Fufa TD, NISC Comparative Sequencing Program, Pavan WJ.
Hypoxia-induced HIF1α targets in melanocytes reveal a molecular profile associated with poor melanoma prognosis.
Pigment Cell Melanoma Res. 2017 Feb 6. doi: 10.1111/pcmr.12579.
28168807 |
|
Vilboux T, Doherty DA, Glass IA, Parisi MA, Phelps IG, Cullinane AR, Zein W, Brooks BP, Heller T, Soldatos A, Oden NL, Yildirimli D, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Malicdan MC, Gahl WA, Gunay-Aygun M.
Molecular genetic findings and clinical correlations in 100 patients with Joubert syndrome and related disorders prospectively evaluated at a single center.
Genet Med. 2017 Jan 26. doi: 10.1038/gim.2016.204.
28125082 |
|
Poretti A, Snow J, Summers AC, Tekes A, Huisman TA, Aygun N, Carson KA, Doherty D, Parisi MA, Toro C, Yildirimli D, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program , Cullinane AR, Vilboux T, Gahl WA, Gunay-Aygun M.
Joubert syndrome: neuroimaging findings in 110 patients in correlation with cognitive function and genetic cause.
J Med Genet. 2017 Jan 13. pii: jmedgenet-2016-104425. doi: 10.1136/jmedgenet-2016-104425.
28087721 |
|
Pemov A, Li H, Patidar R, Hansen NF, Sindiri S, Hartley SW, Wei JS, Elkahloun A, Chandrasekharappa SC, NISC Comparative Sequencing Program, Boland JF, Bass S, NCI DCEG Cancer Genomics Research Laboratory, Mullikin JC, Khan J, Widemann BC, Wallace MR, Stewart DR.
The primacy of NF1 loss as the driver of tumorigenesis in neurofibromatosis type 1-associated plexiform neurofibromas.
Oncogene. 2017 Jan 9. doi: 10.1038/onc.2016.464.
28068329 |
|
Vilboux T, Malicdan MC, Roney JC, Cullinane AR, Stephen J, Yildirimli D, Bryant J, Fischer R, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Steinbach PJ, Gahl WA, Gunay-Aygun M.
CELSR2, encoding a planar cell polarity protein, is a putative gene in Joubert syndrome with cortical heterotopia, microophthalmia, and growth hormone deficiency.
Am J Med Genet A. 2017 Jan 4. doi: 10.1002/ajmg.a.38005.
28052552 |
2016 |
|
Falik Zaccai TC, Savitzki D, Zivony-Elboum Y, Vilboux T, Fitts EC, Shoval Y, Kalfon L, Samra N, Keren Z, Gross B, Chasnyk N, Straussberg R, Mullikin JC, Teer JK, Geiger D, Kornitzer D, Bitterman-Deutsch O, Samson AO, Wakamiya M, Peterson JW, Kirtley ML, Pinchuk IV, Baze WB, Gahl WA, Kleta R, Anikster Y, Chopra AK.
Phospholipase A2-activating protein is associated with a novel form of leukoencephalopathy.
Brain. 2016 Dec 21. pii: aww295. doi: 10.1093/brain/aww295.
28007986 |
|
Kambouris M, Thevenon J, Soldatos A, Cox A, Stephen J, Ben-Omran T, Al-Sarraj Y, Boulos H, Bone W, Mullikin JC, NISC Comparative Sequencing Program, Masurel-Paulet A, St-Onge J, Dufford Y, Chantegret C, Thauvin-Robinet C, Al-Alami J, Faivre L, Riviere JB, Gahl WA, Bassuk AG, Malicdan MC, El-Shanti H.
Biallelic SCN10A mutations in neuromuscular disease and epileptic encephalopathy.
Ann Clin Transl Neurol. 2016 Dec 20;4(1):26-35. doi: 10.1002/acn3.372.
28078312 |
|
Gopinath C, Law WD, Rodríguez-Molina JF, Prasad AB, Song L, Crawford GE, Mullikin JC, Svaren J, Antonellis A.
Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation. BMC Genomics. 2016 Nov 7;17(1):887. doi: 10.1186/s12864-016-3167-3
27821050 |
|
Winter JM, Gildea DE, Andreas JP, Gatti DM, Williams KA, Lee M, Hu Y, Zhang S, NISC Comparative Sequencing Program, Mullikin JC, Wolfsberg TG, McDonnell SK, Fogarty ZC, Larson MC, French AJ, Schaid DJ, Thibodeau SN, Churchill GA, Crawford NP.
Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer.
Cell Syst. 2016 Nov 25. pii: S2405-4712(16)30361-1. doi: 10.1016/j.cels.2016.10.018.
27916600 |
|
O'Brien KJ, Lozier J, Cullinane AR, Osorio B, Nghiem K, Speransky V, Zein WM, Mullikin JC, Neff AT, Simon KL, Malicdan MC, Gahl WA, Young LR, Gochuico BR.
Identification of a novel mutation in HPS6 in a patient with hemophilia B and oculocutaneous albinism.
Mol Genet Metab. 2016 Nov;119(3):284-287. doi: 10.1016/j.ymgme.2016.08.009.
27641950 |
|
Hartley SW, Mullikin JC, Klein DC, Park M, NISC Comparative Sequencing Program, Coon SL.
Alternative Isoform Analysis of Ttc8 Expression in the Rat Pineal Gland Using a Multi-Platform Sequencing Approach Reveals Neural Regulation.
PLoS One. 2016 Sep 29;11(9):e0163590. doi: 10.1371/journal.pone.0163590.
27684375 |
|
Török A, Schiffer PH, Schnitzler CE, Ford K, Mullikin JC, Baxevanis AD, Bacic A, Frank U, Gornik SG.
The cnidarian Hydractinia echinata employs canonical and highly adapted histones to pack its DNA.
Epigenetics Chromatin. 2016 Sep 6;9(1):36. doi: 10.1186/s13072-016-0085-1.
27602058 |
|
Ng D, Hong CS, Singh LN, Johnston JJ, Mullikin JC, Biesecker LG.
Assessing the capability of massively parallel sequencing for opportunistic pharmacogenetic screening.
Genet Med. 2016 Aug 18. doi: 10.1038/gim.2016.105.
27537706 |
|
Hong CS, Singh LN, Mullikin JC, Biesecker LG.
Assessing the reproducibility of exome copy number variations predictions.
Genome Med. 2016 Aug 8;8(1):82. doi: 10.1186/s13073-016-0336-6.
27503473 |
|
Conlan S, Lau AF, NISC Comparative Sequencing Program, Palmore TN, Frank KM, Segre JA.
Complete Genome Sequence of a Klebsiella pneumoniae Strain Carrying blaNDM-1 on a Multidrug Resistance Plasmid.
Genome Announc. 2016 Jul 14;4(4). pii: e00664-16. doi: 10.1128/genomeA.00664-16.
27417839 |
|
Margolin G, Petrykowska HM, Jameel N, Bell DW, Young AC, Elnitski L.
Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development.
J Mol Diagn. 2016 Mar;18(2):283-98. doi: 10.1016/j.jmoldx.2015.11.004. Epub 2016 Feb 5.
26857064 |
|
Zhou Q, Yu X, Demirkaya E, Deuitch N, Stone D, Tsai WL, Kuehn HS, Wang H, Yang D, Park YH, Ombrello AK, Blake M, Romeo T, Remmers EF, Chae JJ, Mullikin JC, Güzel F, Milner JD, Boehm M, Rosenzweig SD, Gadina M, Welch SB, Özen S, Topaloglu R, Abinun M, Kastner DL, Aksentijevich I.
Biallelic hypomorphic mutations in a linear deubiquitinase define otulipenia, an early-onset autoinflammatory disease.
Proc Natl Acad Sci U S A. 2016 Aug 24. pii: 201612594.
27559085 |
|
Jo JH, Deming C, Kennedy EA, Conlan S, Polley EC, Ng WL; NISC Comparative Sequencing Program, Segre JA, Kong HH.
Diverse human skin fungal communities in children converge in adulthood.
J Invest Dermatol. 2016 Jul 28. pii: S0022-202X(16)32231-X. doi: 10.1016/j.jid.2016.05.130
27476723 |
|
Joyce MG, Wheatley AK, Thomas PV, Chuang GY, Soto C, Bailer RT, Druz A, Georgiev IS, Gillespie RA, Kanekiyo M, Kong WP, Leung K, Narpala SN, Prabhakaran MS, Yang ES, Zhang B, Zhang Y, Asokan M, Boyington JC, Bylund T, Darko S, Lees CR, Ransier A, Shen CH, Wang L, Whittle JR, Wu X, Yassine HM, Santos C, Matsuoka Y, Tsybovsky Y, Baxa U, NISC Comparative Sequencing Program, Mullikin JC, Subbarao K, Douek DC, Graham BS, Koup RA, Ledgerwood JE, Roederer M, Shapiro L, Kwong PD, Mascola JR, McDermott AB.
Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses.
Cell. 2016 Jul 28;166(3):609-23. doi: 10.1016/j.cell.2016.06.043. Epub 2016 Jul 21.
27453470 |
|
Maglic D, Stephen J, Malicdan MC, Guo J, Fischer R, Konzman D, NISC Comparative Sequencing Program, Mullikin JC, Gahl WA, Vilboux T, Gunay-Aygun M. TMEM231 Gene Conversion Associated with Joubert and Meckel-Gruber Syndromes in the Same Family.
Hum Mutat. 2016 Jul 23. doi: 10.1002/humu.23054.
27449316 |
|
Conlan S, Park M, Deming C, Thomas PJ, Young AC, Coleman H, Sison C, NISC Comparative Sequencing Program, Weingarten RA, Lau AF, Dekker JP, Palmore TN, Frank KM, Segre JA. Plasmid Dynamics in KPC-Positive Klebsiella pneumoniae during Long-Term Patient Colonization. MBio. 2016 Jun 28;7(3). pii: e00742-16.
27353756 |
|
Soto C, Ofek G, Joyce MG, Zhang B, McKee K, Longo NS, Yang Y, Huang J, Parks R, Eudailey J, Lloyd KE, Alam SM, Haynes BF; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Mascola JR, Shapiro L, Kwong PD. Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8. PLoS One. 2016 Jun 14;11(6):e0157409.
27299673 |
| Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF. Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. Orphanet J Rare Dis. 2016 May 14;11(1):62. doi: 10.1186/s13023-016-0439-6.
27179618 |
| Justice CM, Bishop K, Carrington B, Mullikin JC, Swindle K, Marosy B, Sood R, Miller NH, Wilson AF. Evaluation of IRX Genes and Conserved Non-coding Elements in a Region on 5p13.3 Linked to Families with Familial Idiopathic Scoliosis and Kyphosis. G3 (Bethesda). 2016 Apr 13. pii: g3.116.029975. doi: 10.1534/g3.116.029975.
27172222 |
| Oh J, Byrd AL, Park M, NISC Comparative Sequencing Program, Kong HH, Segre JA. Temporal Stability of the Human Skin Microbiome. Cell. 2016 May 5;165(4):854-66. doi: 10.1016/j.cell.2016.04.008. 27153496 |
| Vilboux T, Malicdan MC, Chang YM, Guo J, Zerfas PM, Stephen J, Cullinane AR, Bryant J, Fischer R, Brooks BP, Zein WM, Wiggs EA, Zalewski CK, Poretti A, Bryan MM, Vemulapalli M, Mullikin JC, Kirby M, Anderson SM, NISC Comparative Sequencing Program, Huizing M, Toro C, Gahl WA, Gunay-Aygun M.
Cystic cerebellar dysplasia and biallelic LAMA1 mutations: a lamininopathy associated with tics, obsessive compulsive traits and myopia due to cell adhesion and migration defects. J Med Genet. 2016 Jan 13. pii: jmedgenet-2015-103416. doi: 10.1136/jmedgenet-2015-103416.
27095636 |
| Bonsignori M, Zhou T, Sheng Z, Chen L, Gao F, Joyce MG, Ozorowski G, Chuang GY, Schramm CA, Wiehe K, Alam SM, Bradley T, Gladden MA, Hwang KK, Iyengar S, Kumar A, Lu X, Luo K, Mangiapani MC, Parks RJ, Song H, Acharya P, Bailer RT, Cao A, Druz A, Georgiev IS, Kwon YD, Louder MK, Zhang B, Zheng A, Hill BJ, Kong R, Soto C; NISC Comparative Sequencing Program, Mullikin JC, Douek DC, Montefiori DC, Moody MA, Shaw GM, Hahn BH, Kelsoe G, Hraber PT, Korber BT, Boyd SD, Fire AZ, Kepler TB, Shapiro L, Ward AB4, Mascola JR, Liao HX, Kwong PD, Haynes BF.
Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody. Cell. 2016 Apr 7;165(2):449-63. doi: 10.1016/j.cell.2016.02.022. Epub 2016 Mar 3. 26949186 |
| Dotson GA; NISC Comparative Sequencing Program, Dekker JP, Palmore TN, Segre JA, Conlan S. Draft Genome Sequence of a Klebsiella pneumoniae Carbapenemase-Positive Sequence Type 111 Pseudomonas aeruginosa Strain. Genome Announc. 2016 Feb 11;4(1). pii: e01663-15. doi: 10.1128/genomeA.01663-15. 26868386 |
| Tsai YC, Conlan S, Deming C; NISC Comparative Sequencing Program, Segre JA, Kong HH, Korlach J, Oh J. Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing. MBio. 2016 Feb 9;7(1). pii: e01948-15. doi: 10.1128/mBio.01948-15. 26861018 |
| de Filippo C, Key FM, Ghirotto S, Benazzo A, Meneu JR, Weihmann A; NISC Comparative Sequence Program, Parra G, Green ED, Andrés AM. Recent Selection Changes in Human Genes under Long-Term Balancing Selection. Mol Biol Evol. 2016 Feb 1. pii: msw023. [Epub ahead of print] 26831942 |
| Kane MS, Davids M, Adams C, Wolfe LA, Cheung HW, Gropman A, Huang Y; NISC Comparative Sequencing Program, Ng BG, Freeze HH, Adams DR, Gahl WA, Boerkoel CF. Mitotic Intragenic Recombination: A Mechanism of Survival for Several Congenital Disorders of Glycosylation. Am J Hum Genet. 2016 Feb 4;98(2):339-46. doi: 10.1016/j.ajhg.2015.12.007. Epub 2016 Jan 21. 26805780 |
| Boyden SE, Desai A, Cruse G, Young ML, Bolan HC, Scott LM, Eisch AR, Long RD, Lee CC, Satorius CL, Pakstis AJ, Olivera A, Mullikin JC, Chouery E, Mégarbané A, Medlej-Hashim M, Kidd KK, Kastner DL, Metcalfe DD, Komarow HD. Vibratory Urticaria Associated with a Missense Variant in ADGRE2. Engl J Med. 2016 Feb 18;374(7):656-63. doi: 10.1056/NEJMoa1500611. Epub 2016 Feb 3. 26841242 |
| Beck TF, Mullikin JC, NISC Comparative Sequencing Program, Biesecker LG. Systematic Evaluation of Sanger Validation of NextGen Sequencing Variants. Clin Chem. 2016 Feb 4. pii: clinchem.2015.249623. [Epub ahead of print] 26847218 |
| Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, Joyce MG, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, NISC Comparative Sequencing Program, Mullikin JC, Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L, Mascola JR, Kwong PD. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nat Struct Mol Biol. 2016 Jan;23(1):81-90. doi: 10.1038/nsmb.3144. Epub 2015 Dec 21.
26689967 |
2015 |
| Baran-Gale J, Kurtz CL, Erdos MR, Sison C, Young A, Fannin EE, Chines PS, Sethupathy P. Addressing Bias in Small RNA Library Preparation for Sequencing: A New Protocol Recovers MicroRNAs that Evade Capture by Current Methods. Front Genet. 2015 Dec 22;6:352. doi: 10.3389/fgene.2015.00352. eCollection 2015.
26734062 |
|
Zhou Q, Wang H, Schwartz DM, Stoffels M, Park YH, Zhang Y, Yang D, Demirkaya E, Takeuchi M, Tsai WL, Layons JJ, Yu X, Ouyang C, Chen C, Chin DT, Zaal K, Chandrasekharappa SC, P Hanson E, Yu Z, Mullikin JC, Hasni SA, Wertz IE, Ombrello AK, Stone DL, Hoffmann P, Jones A, Barham BK, Leavis HL, van Royen-Kerkof A, Sibley C, Batu ED, Gül A, Siegel RM, Boehm M, Milner JD, Ozen S, Gadina M, Chae J, Laxer RM, Kastner DL, Aksentijevich I. Loss-of-function mutations in TNFAIP3 leading to A20 haploinsufficiency cause an early-onset autoinflammatory disease. Nat Genet. 2015 Dec 7. doi: 10.1038/ng.3459
26642243 |
|
Cherukuri PF, Maduro V, Fuentes-Fajardo KV, Lam K; NISC Comparative Sequencing Program, Adams DR, Tifft CJ, Mullikin JC, Gahl WA, Boerkoel CF. Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data. BMC Genomics. 2015 Nov 25;16(1):998. 26602380 |
| Lee M, Beggs SM, Gildea D, Bupp S, Lichtenberg J, Trivedi NS; NISC Comparative Sequencing Program, Hu Y, Bodine DM, Crawford NP. Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc. Oncotarget. 2015 Oct 13;6(31):31557-68. 26384308 |
| Kruszka P, Uwineza A, Mutesa L, Martinez AF, Abe Y, Zackai EH, Ganetzky R, Chung B, Stevenson RE, Adelstein RS, Ma X, Mullikin JC, Hong SK, Muenke M. Limb body wall complex, amniotic band sequence, or new syndrome caused by mutation in IQ Motif containing K (IQCK)? Mol Genet Genomic Med. 2015 Sep;3(5):424-32. 26436108 |
| Malicdan MC, Vilboux T, Stephen J, Maglic D, Mian L, Konzman D, Guo J, Yildirimli D, Bryant J, Fischer R, Zein WM, Snow J, Vemulapalli M, Mullikin JC, Toro C7 Solomon BD, Niederhuber JE; NISC Comparative Sequencing Program, Gahl WA, Gunay-Aygun M. Mutations in human homologue of chicken talpid3 gene (KIAA0586) cause a hybrid ciliopathy with overlapping features of Jeune and Joubert syndromes. J Med Genet. 2015 Sep 18. pii: jmedgenet-2015-103316. 2638604 |
| Hartley SW, Coon SL, Savastano LE, Mullikin JC, NISC Comparative Sequencing Program, Fu C2, Klein DC2. Neurotranscriptomics: The Effects of Neonatal Stimulus Deprivation on the Rat Pineal Transcriptome. PLoS One. 2015 Sep 14;10(9):e0137548. 26367423 |
| Huang HW, NISC Comparative Sequencing Program, Mullikin JC, Hansen NF. Evaluation of variant detection software for pooled next-generation sequence data. BMC Bioinformatics. 2015 Jul 29;16:235. 26220471 |
| Sood R, Hansen NF, Donovan FX, Carrington B, Bucci D, Maskeri B, Young A, Trivedi NS, Kohlschmidt J, Stone RM, Caligiuri MA, Chandrasekharappa SC, Marcucci G, Mullikin JC, Bloomfield CD5, Liu P. Somatic mutational landscape of AML with inv(16) or t(8;21) identifies patterns of clonal evolution in relapse leukemia. Leukemia. 2015 Jun 15. doi: 10.1038/leu.2015.141. 26139325 |
| Johnston JJ, Lewis KL, Ng D, Singh LN, Wynter J, Brewer C, Brooks BP, Brownell I, Candotti F, Gonsalves SG, Hart SP, Kong HH, Rother KI, Sokolic R, Solomon BD, Zein WM, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG. Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations. Am J Hum Genet. 2015 Jun 4;96(6):913-25. 26046366 |
| Francica JR, Sheng Z, Zhang Z, Nishimura Y, Shingai M, Ramesh A, Keele BF, Schmidt SD, Flynn BJ, Darko S, Lynch RM, Yamamoto T, Matus-Nicodemos R, Wolinsky D; NISC Comparative Sequencing Program, Nason M, Valiante NM, Malyala P, De Gregorio E, Barnett SW, Singh M, O'Hagan DT, Koup RA, Mascola JR, Martin MA, Kepler TB, Douek DC, Shapiro L, Seder RA. Analysis of immunoglobulin transcripts and hypermutation following SHIV(AD8) infection and protein-plus-adjuvant immunization. Nat Commun. 2015 Apr 10;6:6565. 25858157 |
| Zhou T, Lynch RM, Chen L, Acharya P, Wu X, Doria-Rose NA, Joyce MG, Lingwood D, Soto C, Bailer RT, Ernandes MJ, Kong R, Longo NS, Louder MK, McKee K, O'Dell S, Schmidt SD, Tran L, Yang Z, Druz A, Luongo TS, Moquin S, Srivatsan S, Yang Y, Zhang B, Zheng A, Pancera M, Kirys T, Georgiev IS, Gindin T, Peng HP, Yang AS; NISC Comparative Sequencing Program, Mullikin JC, Gray MD, Stamatatos L, Burton DR, Koff WC, Cohen MS, Haynes BF, Casazza JP, Connors M, Corti D, Lanzavecchia A, Sattentau QJ, Weiss RA, West AP Jr, Bjorkman PJ, Scheid JF, Nussenzweig MC, Shapiro L, Mascola JR, Kwong PD. Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell. 2015 May 20. pii: S0092-8674(15)00554-1. 26004070 |
| Saldana-Caboverde A, Perera EM, Watkins-Chow D, Hansen NF, Vemulapalli M, Mullikin JC, NISC Comparative Sequencing Program, Pavan WJ, Kos L. The transcription factors Ets1 and Sox10 interact during murine melanocyte development. Dev Biol. 2015 Apr 23. pii: S0012-1606(15)00212-2. 25912689 |
| Wu X, Zhang Z, Schramm CA, Joyce MG, Do Kwon Y, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, Soto C, Srivatsan S, Yang Y, Bailer RT, Louder MK; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Kwong PD, Mascola JR, Shapiro L. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell. 2015 Apr 23;161(3):470-85. 25865483 |
2014 |
| Callicrate T, Dikow R, Thomas JW, Mullikin JC, Jarvis ED, Fleischer RC1; NISC Comparative Sequencing Program. Genomic resources for the endangered Hawaiian honeycreepers. BMC Genomics. 2014 Dec 12;15:1098. 25496081 |
| Rudd ML, Mohamed H, Price JC, O'Hara AJ, Le Gallo M, Urick ME, NISC Comparative Sequencing Program, Cruz P, Zhang S, Hansen NF, Godwin AK, Sgroi DC, Wolfsberg TG, Mullikin JC, Merino MJ, Bell DW1. Mutational analysis of the tyrosine kinome in serous and clear cell endometrial cancer uncovers rare somatic mutations in TNK2 and DDR1. BMC Cancer. 2014 Nov 26;14:884.
25427824 |
| Oh J, Byrd AL, Deming C, Conlan S; NISC Comparative Sequencing Program, Kong HH, Segre JA. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014 Oct 2;514(7520):59-64. 25279917 |
| Conlan S, Thomas PJ, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai YC, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN, Segre JA. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Sci Transl Med. 2014 Sep 17;6(254):254ra126. 25232178 |
| Pemov A, Sung H, Hyland PL, Sloan JL, Ruppert SL, Baldwin AM, Boland JF, Bass SE, Lee HJ, Jones KM, Zhang X, NISC Comparative Sequencing Program, Mullikin JC, Widemann BC, Wilson AF, Stewart DR. Genetic modifiers of neurofibromatosis type 1-associated café-au-lait macule count identified using multi-platform analysis. PLoS Genet. 2014 Oct 16;10(10):e1004575. 25329635 |
| Rudicell RS, Kwon YD, Ko SY, Pegu A, Louder MK, Georgiev IS, Wu X, Zhu J, Boyington JC, Chen X, Shi W, Yang ZY, Doria-Rose NA, McKee K, O'Dell S, Schmidt SD, Chuang GY, Druz A, Soto C, Yang Y, Zhang B, Zhou T, Todd JP, Lloyd KE, Eudailey J, Roberts KE, Donald BR, Bailer RT, Ledgerwood J, NISC Comparative Sequencing Program, Mullikin JC, Shapiro L, Koup RA, Graham BS, Nason MC, Connors M, Haynes BF, Rao SS, Roederer M, Kwong PD, Mascola JR, Nabel GJ. Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo. J Virol. 2014 Nov 1;88(21):12669-82. 25142607 |
| Sen SK, Boelte KC, Barb JJ, Joehanes R, Zhao X, Cheng Q, Adams L, Teer JK, Accame DS, Chowdhury S, Singh LN; NISC Comparative Sequencing Program; CHARGE Consortium, Kavousi M, Peyser PA, Quigley L, Priel DL, Lau K, Kuhns DB, Yoshimura T, Johnson AD, Hwang SJ, Chen MY, Arai AE, Green ED, Mullikin JC, Kolodgie FD, O'Donnell CJ, Virmani R, Munson PJ, McVicar DW, Biesecker LG. Integrative DNA, RNA, and protein evidence connects TREML4 to coronary artery calcification. Am J Hum Genet. 2014 Jul 3;95(1):66-76. 24975946 |
| Pierson TM, Yuan H, Marsh ED, Fuentes-Fajardo K, Adams DR, Markello T, Golas G, Simeonov DR, Holloman C, Tankovic A, Karamchandani MM, Schreiber JM, Mullikin JC; PhD for the NISC Comparative Sequencing Program, Tifft CJ, Toro C, Boerkoel CF, Traynelis SF, Gahl WA. GRIN2A mutation and early-onset epileptic encephalopathy: personalized therapy with memantine. Ann Clin Transl Neurol. 2014 Mar 1;1(3):190-198. 24839611 |
| Lee M, Dworkin AM, Gildea D, Trivedi NS; NISC Comparative Sequencing Program, Moorhead GB, Crawford NP. RRP1B is a metastasis modifier that regulates the expression of alternative mRNA isoforms through interactions with SRSF1. Oncogene. 2014 Apr 3;33(14):1818-27. 23604122 |
| Sen SK, Barb JJ, Cherukuri PF, Accame DS, Elkahloun AG, Singh LN, Lee-Lin SQ; NISC Comparative Sequencing Program, Kolodgie FD, Cheng Q, Zhao X, Chen MY, Arai AE, Green ED, Mullikin JC, Munson PJ, Biesecker LG. Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines. BMC Genomics. 2014 Mar 14;15:198. 24628908 |
| Zhou Q1, Yang D, Ombrello AK, Zavialov AV, Toro C, Zavialov AV, Stone DL, Chae JJ, Rosenzweig SD, Bishop K, Barron KS, Kuehn HS, Hoffmann P, Negro A, Tsai WL, Cowen EW, Pei W, Milner JD, Silvin C, Heller T, Chin DT, Patronas NJ, Barber JS, Lee CC, Wood GM, Ling A, Kelly SJ, Kleiner DE, Mullikin JC, Ganson NJ, Kong HH, Hambleton S, Candotti F, Quezado MM, Calvo KR, Alao H, Barham BK, Jones A, Meschia JF, Worrall BB, Kasner SE, Rich SS, Goldbach-Mansky R, Abinun M, Chalom E, Gotte AC, Punaro M, Pascual V, Verbsky JW, Torgerson TR, Singer NG, Gershon TR, Ozen S, Karadag O, Fleisher TA, Remmers EF, Burgess SM, Moir SL, Gadina M, Sood R, Hershfield MS, Boehm M, Kastner DL, Aksentijevich I. Early-onset stroke and vasculopathy associated with mutations in ADA2. N Engl J Med. 2014 Mar 6;370(10):911-20. 24552284 |
| Doria-Rose NA, Schramm CA, Gorman J, Moore PL, Bhiman JN, Dekosky BJ, Ernandes MJ, Georgiev IS, Kim HJ, Pancera M, Staupe RP, Altae-Tran HR, Bailer RT, Crooks ET, Cupo A, Druz A, Garrett NJ, Hoi KH, Kong R, Louder MK, Longo NS, McKee K, Nonyane M, O'Dell S, Roark RS, Rudicell RS, Schmidt SD, Sheward DJ, Soto C, Wibmer CK, Yang Y, Zhang Z, NISC Comparative Sequencing Program, Mullikin JC, Binley JM, Sanders RW, Wilson IA, Moore JP, Ward AB, Georgiou G, Williamson C, Abdool Karim SS, Morris L, Kwong PD, Shapiro L, Mascola JR. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature. 2014 Mar 2. 24590074 |
| Prickett TD, Zerlanko B, Gartner JJ, Parker SC, Dutton-Regester K, Lin JC, Teer JK, Wei X, Jiang J; NISC Comparative Sequencing Program, Chen G, Davies MA, Gershenwald JE, Robinson W, Robinson S, Hayward NK, Rosenberg SA, Margulies EH, Samuels Y. Somatic mutations in MAP3K5 attenuate its proapoptotic function in melanoma through increased binding to thioredoxin. J Invest Dermatol. 2014 Feb;134(2):452-60. 24008424 |
2013 |
| Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P; NISC Comparative Sequencing Program, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, Mullikin JC, Martindale MQ, Baxevanis AD. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013 Dec 13;342(6164):1242592. 24337300 |
| Oh J, Freeman AF; NISC Comparative Sequencing Program, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH. The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome Res. 2013 Dec;23(12):2103-14. 24170601 |
| Gonsalves SG, Ng D, Johnston JJ, Teer JK, Stenson PD, Cooper DN, Mullikin JC, Biesecker LG; NISC Comparative Sequencing Program. Using exome data to identify malignant hyperthermia susceptibility mutations. Anesthesiology. 2013 Nov;119(5):1043-53. 24195946 |
| Parker SC, Stitzel ML, Taylor DL, Orozco JM, Erdos MR, Akiyama JA, van Bueren KL, Chines PS, Narisu N; NISC Comparative Sequencing Program, Black BL, Visel A, Pennacchio LA, Collins FS. Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A. 2013 Oct 29;110(44):17921-6. 24127591 |
| Zhu J, Wu X, Zhang B, McKee K, O'Dell S, Soto C, Zhou T, Casazza JP; NISC Comparative Sequencing Program, Mullikin JC, Kwong PD, Mascola JR, Shapiro L. De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. Proc Natl Acad Sci U S A. 2013 Oct 22;110(43):E4088-97. 24106303 |
| Landouré G, Zhu PP, Lourenço CM, Johnson JO, Toro C, Bricceno KV, Rinaldi C, Meilleur KG, Sangaré M, Diallo O, Pierson TM, Ishiura H, Tsuji S, Hein N, Fink JK, Stoll M, Nicholson G, Gonzalez MA, Speziani F, Dürr A, Stevanin G, Biesecker LG, NIH Intramural Sequencing Center, Accardi J, Landis DM, Gahl WA, Traynor BJ, Marques W Jr, Züchner S, Blackstone C, Fischbeck KH, Burnett BG. Hereditary spastic paraplegia type 43 (SPG43) is caused by mutation in C19orf12. Hum Mutat. 2013 Oct;34(10):1357-60. 23857908 |
| Johnston JJ, Wen KK, Keppler-Noreuil K, McKane M, Maiers JL, Greiner A, Sapp JC, NIH Intramural Sequencing Center, Demali KA, Rubenstein PA, Biesecker LG. Functional analysis of a de novo ACTB mutation in a patient with atypical Baraitser-Winter syndrome. Hum Mutat. 2013 Sep;34(9):1242-9. 23649928 |
| Zhou T, Zhu J, Wu X, Moquin S, Zhang B, Acharya P, Georgiev IS, Altae-Tran HR, Chuang GY, Joyce MG, Do Kwon Y, Longo NS, Louder MK, Luongo T, McKee K, Schramm CA, Skinner J, Yang Y, Yang Z, Zhang Z, Zheng A, Bonsignori M, Haynes BF, Scheid JF, Nussenzweig MC, Simek M, Burton DR, Koff WC; NISC Comparative Sequencing Program, Mullikin JC, Connors M, Shapiro L, Nabel GJ, Mascola JR, Kwong PD. Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. Immunity. 2013 Aug 22;39(2):245-58. 23911655 |
| Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK; NISC Comparative Sequencing Program, Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13481-6. 23901115 |
| Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG, NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program. Interpreting secondary cardiac disease variants in an exome cohort. Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. 23861362 |
| Snitkin ES, Zelazny AM, Gupta J; NISC Comparative Sequencing Program, Palmore TN, Murray PR, Segre JA. Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment. Genome Res. 2013 Jul;23(7):1155-62. 23564252 |
| Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, NIH Intramural Sequencing Center Comparative Sequencing Program, Kong HH, Segre JA. Topographic diversity of fungal and bacterial communities in human skin. Nature. 2013 Jun 20;498(7454):367-70. 23698366 |
| Chandrasekharappa SC, Lach FP, Kimble DC, Kamat A, Teer JK, Donovan FX, Flynn E, Sen SK, Thongthip S, Sanborn E, Smogorzewska A, Auerbach AD, Ostrander EA; NISC Comparative Sequencing Program. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia. Blood. 2013 May 30;121(22):e138-48. 23613520 |
| Liao HX, Lynch R, Zhou T, Gao F, Alam SM, Boyd SD, Fire AZ, Roskin KM, Schramm CA, Zhang Z, Zhu J, Shapiro L; NISC Comparative Sequencing Program, Mullikin JC, Gnanakaran S, Hraber P, Wiehe K, Kelsoe G, Yang G, Xia SM, Montefiori DC, Parks R, Lloyd KE, Scearce RM, Soderberg KA, Cohen M, Kamanga G, Louder MK, Tran LM, Chen Y, Cai F, Chen S, Moquin S, Du X, Joyce MG, Srivatsan S, Zhang B, Zheng A, Shaw GM, Hahn BH, Kepler TB, Korber BT, Kwong PD, Mascola JR, Haynes BF. Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. 2013 Apr 25;496(7446):469-76. 23552890 |
| Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, Parks R, Eudailey J, Lloyd KE, Blinn J, Alam SM, Haynes BF, Simek M, Burton DR, Koff WC; NISC Comparative Sequencing Program, Mullikin JC, Mascola JR, Shapiro L, Kwong PD. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6470-5. 23536288 |
| Teer JK, Johnston JJ, Anzick SL, Pineda M, Stone G; NISC Comparative Sequencing Program, Meltzer PS, Mullikin JC, Biesecker LG. Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting. BMC Genomics. 2013 Apr 15;14:253. 23586822 |
| Ferreira Z, Seixas S, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Swanson WJ; NISC Comparative Sequencing Program, Clark AG, Green ED, Hurle B. Reproduction and immunity-driven natural selection in the human WFDC locus. Mol Biol Evol. 2013 Apr;30(4):938-50. 23292442 |
| Prasad AB, Mullikin JC; NISC Comparative Sequencing Program, Green ED. A scalable and flexible approach for investigating the genomic landscapes of phylogenetic incongruence. Mol Phylogenet Evol. 2013 Mar;66(3):1067-74. 23247042 |
| Solomon BD, Pineda-Alvarez DE, Hadley DW, Hansen NF, Kamat A, Donovan FX, Chandrasekharappa SC, Hong SK, Roessler E, Mullikin JC; NISC Comparative Sequencing Program. Exome Sequencing and High-Density Microarray Testing in Monozygotic Twin Pairs Discordant for Features of VACTERL Association. Mol Syndromol. 2013 Feb;4(1-2):27-31. 23653574 |
| Ferreira Z, Hurle B, Andrés AM, Kretzschmar WW, Mullikin JC, Cherukuri PF, Cruz P, Gonder MK, Stone AC, Tishkoff S, Swanson WJ; NISC Comparative Sequencing Program, Green ED, Clark AG, Seixas S. Sequence diversity of Pan troglodytes subspecies and the impact of WFDC6 selective constraints in reproductive immunity. Genome Biol Evol. 2013;5(12):2512-23. 24356879 |
| Giannuzzi G, Siswara P, Malig M, Marques-Bonet T; NISC Comparative Sequencing Program, Mullikin JC, Ventura M, Eichler EE. Evolutionary dynamism of the primate LRRC37 gene family. Genome Res. 2013 Jan;23(1):46-59. 23064749 |
| Vester A, Velez-Ruiz G, McLaughlin HM; NISC Comparative Sequencing Program, Lupski JR, Talbot K, Vance JM, Züchner S, Roda RH, Fischbeck KH, Biesecker LG, Nicholson G, Beg AA, Antonellis A. A loss-of-function variant in the human histidyl-tRNA synthetase (HARS) gene is neurotoxic in vivo. Hum Mutat. 2013 Jan;34(1):191-9. 22930593 |
