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1

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

Burton, Joshua N, Adey, Andrew, Patwardhan, Rupali P, Qiu, Ruolan, Kitzman, Jacob O, Shendure, Jay

Journal:

Nature Biotechnology

Year:

2013

Language:

english

File:

PDF, 1001 KB

english, 2013

2

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

Amini, Sasan, Pushkarev, Dmitry, Christiansen, Lena, Kostem, Emrah, Royce, Tom, Turk, Casey, Pignatelli, Natasha, Adey, Andrew, Kitzman, Jacob O, Vijayan, Kandaswamy, Ronaghi, Mostafa, Shendure, Jay,

Journal:

Nature Genetics

Year:

2014

Language:

english

File:

PDF, 1.46 MB

english, 2014

3

Haplotype-resolved genome sequencing of a Gujarati Indian individual

Kitzman, Jacob O, MacKenzie, Alexandra P, Adey, Andrew, Hiatt, Joseph B, Patwardhan, Rupali P, Sudmant, Peter H, Ng, Sarah B, Alkan, Can, Qiu, Ruolan, Eichler, Evan E, Shendure, Jay

Journal:

Nature Biotechnology

Year:

2011

Language:

english

File:

PDF, 128 KB

english, 2011

4

Haplotype-resolved genome sequencing: experimental methods and applications

Snyder, Matthew W., Adey, Andrew, Kitzman, Jacob O., Shendure, Jay

Journal:

Nature Reviews Genetics

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

5

Haplotypes drop by drop

Kitzman, Jacob O

Journal:

Nature Biotechnology

Year:

2016

Language:

english

File:

PDF, 765 KB

english, 2016

6

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

Springer, Nathan M., Ying, Kai, Fu, Yan, Ji, Tieming, Yeh, Cheng-Ting, Jia, Yi, Wu, Wei, Richmond, Todd, Kitzman, Jacob, Rosenbaum, Heidi, Iniguez, A. Leonardo, Barbazuk, W. Brad, Jeddeloh, Jeffrey A.

Journal:

Year:

2009

Language:

english

File:

PDF, 1.50 MB

english, 2009

7

Mutation discovery in the mouse using genetically guided array capture and resequencing

Mark D’Ascenzo, Carl Meacham, Jacob Kitzman, Christina Middle, Jim Knight, Roger Winer, Miroslav Kukricar, Todd Richmond, Thomas J. Albert, Anne Czechanski, Leah Rae Donahue, Jason Affourtit, Jeffrey

Journal:

Mammalian Genome

Year:

2009

Language:

english

File:

PDF, 687 KB

english, 2009

8

Repeat subtraction-mediated sequence capture from a complex genome

Yan Fu, Nathan M. Springer, Daniel J. Gerhardt, Kai Ying, Cheng-Ting Yeh, Wei Wu, Ruth Swanson-Wagner, Mark D’Ascenzo, Tracy Millard, Lindsay Freeberg, Natsuyo Aoyama, Jacob Kitzman, Daniel Burgess, T

Journal:

The Plant Journal

Year:

2010

Language:

english

File:

PDF, 558 KB

english, 2010

9

Haplotype-resolved genome sequencing of a Gujarati Indian individual

Kitzman, Jacob O, MacKenzie, Alexandra P, Adey, Andrew, Hiatt, Joseph B, Patwardhan, Rupali P, Sudmant, Peter H, Ng, Sarah B, Alkan, Can, Qiu, Ruolan, Eichler, Evan E

Journal:

Nature Biotechnology

Year:

2010

Language:

english

File:

PDF, 652 KB

english, 2010

10

Personalized copy number and segmental duplication maps using next-generation sequencing

Alkan, Can, Kidd, Jeffrey M, Marques-Bonet, Tomas, Aksay, Gozde, Antonacci, Francesca, Hormozdiari, Fereydoun, Kitzman, Jacob O, Baker, Carl, Malig, Maika, Mutlu, Onur

Journal:

Nature Genetics

Year:

2009

Language:

english

File:

PDF, 794 KB

english, 2009

11

Non-invasive fetal genome sequencing: Opportunities and challenges

Holly K. Tabor, Jeffrey C. Murray, Hilary S. Gammill, Jacob O. Kitzman, Matthew W. Snyder, Mario Ventura, Alexandra P. Lewis, Ruolan Qiu, LaVone E. Simmons, Craig E. Rubens, Mark K. Santillan, Evan E.

Journal:

American Journal of Medical Genetics Part A

Year:

2012

Language:

english

File:

PDF, 68 KB

english, 2012

12

Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses

Elde, Nels C., Child, Stephanie J., Eickbush, Michael T., Kitzman, Jacob O., Rogers, Kelsey S., Shendure, Jay, Geballe, Adam P., Malik, Harmit S.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.32 MB

english, 2012

13

Noninvasive fetal genome sequencing: a primer

Snyder, Matthew W., Simmons, LaVone E., Kitzman, Jacob O., Santillan, Donna A., Santillan, Mark K., Gammill, Hilary S., Shendure, Jay

Journal:

Prenatal Diagnosis

Year:

2013

Language:

english

File:

PDF, 1.44 MB

english, 2013

14

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

Adey, Andrew, Burton, Joshua N., Kitzman, Jacob O., Hiatt, Joseph B., Lewis, Alexandra P., Martin, Beth K., Qiu, Ruolan, Lee, Choli, Shendure, Jay

Journal:

Year:

2013

Language:

english

File:

PDF, 869 KB

english, 2013

15

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-densityin vitrotransposition

Andrew Adey, Hilary G Morrison, Asan, Xu Xun, Jacob O Kitzman…

Journal:

Year:

2010

Language:

english

File:

PDF, 3.66 MB

english, 2010

16

Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains

Salipante, Stephen J., Roach, David J., Kitzman, Jacob O., Snyder, Matthew W., Stackhouse, Bethany, Butler-Wu, Susan M., Lee, Choli, Cookson, Brad T., Shendure, Jay

Journal:

Genome Research

Year:

2015

Language:

english

File:

PDF, 1015 KB

english, 2015

17

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

Adey, Andrew, Kitzman, Jacob O., Burton, Joshua N., Daza, Riza, Kumar, Akash, Christiansen, Lena, Ronaghi, Mostafa, Amini, Sasan, L. Gunderson, Kevin, Steemers, Frank J., Shendure, Jay

Journal:

Genome Research

Year:

2014

Language:

english

File:

PDF, 707 KB

english, 2014

18

Massively parallel single-amino-acid mutagenesis

Kitzman, Jacob O, Starita, Lea M, Lo, Russell S, Fields, Stanley, Shendure, Jay

Journal:

Year:

2015

Language:

english

File:

PDF, 1.21 MB

english, 2015

19

Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes

Kumar, Akash, Boyle, Evan A, Tokita, Mari, Mikheev, Andrei M, Sanger, Michelle C, Girard, Emily, Silber, John R, Gonzalez-Cuyar, Luis F, Hiatt, Joseph B, Adey, Andrew, Lee, Choli, Kitzman, Jacob O, Bo

Journal:

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

20

Copy-Number Variation and False Positive Prenatal Aneuploidy Screening Results

Snyder, Matthew W., Simmons, LaVone E., Kitzman, Jacob O., Coe, Bradley P., Henson, Jessica M., Daza, Riza M., Eichler, Evan E., Shendure, Jay, Gammill, Hilary S.

Journal:

New England Journal of Medicine

Year:

2015

Language:

english

File:

PDF, 512 KB

english, 2015

21

STATINS AND EXERCISE TRAINING RESPONSE IN HEART FAILURE PATIENTS: INSIGHTS FROM THE HF-ACTION TRIAL

Kelly, Jacob P., Mentz, Robert, Schulte, Phillip, Dunning, Allison, Fiuzat, Mona, Keteyian, Steven, Fleg, Jerome, Leifer, Eric, Pina, Ileana, Cooper, Lawton, Kitzman, Dalane, Kraus, William, Whellan,

Journal:

Journal of the American College of Cardiology

Year:

2015

Language:

english

File:

PDF, 643 KB

english, 2015

22

Whole genome prediction for preimplantation genetic diagnosis

Kumar, Akash, Ryan, Allison, Kitzman, Jacob O, Wemmer, Nina, Snyder, Matthew W, Sigurjonsson, Styrmir, Lee, Choli, Banjevic, Milena, Zarutskie, Paul W, Lewis, Alexandra P, Shendure, Jay, Rabinowitz, M

Journal:

Genome Medicine

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

23

Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range

Brennan, Greg, Kitzman, Jacob O., Rothenburg, Stefan, Shendure, Jay, Geballe, Adam P., Condit, Richard C.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.45 MB

english, 2014

24

Statins and Exercise Training Response in Heart Failure Patients

Kelly, Jacob P., Dunning, Allison, Schulte, Phillip J., Fiuzat, Mona, Leifer, Eric S., Fleg, Jerome L., Cooper, Lawton S., Keteyian, Steven J., Kitzman, Dalane W., Pina, Ileana L., Kraus, William E.,

Journal:

Journal of the American College of Cardiology: Heart Failure

Year:

2016

Language:

english

File:

PDF, 396 KB

english, 2016

25

NIH Public Access

Elde, Nels C, Child, Stephanie J, Eickbush, Michael T, Kitzman, Jacob O, Kelsey, S, Shendure, Jay, Geballe, Adam P, Malik, Harmit S

Year:

2013

Language:

english

File:

PDF, 1.79 MB

english, 2013

26

Corrigendum: Massively parallel single-amino-acid mutagenesis

Kitzman, Jacob O, Starita, Lea M, Lo, Russell S, Fields, Stanley, Shendure, Jay

Journal:

Year:

2017

Language:

english

File:

PDF, 51 KB

english, 2017

27

Variant Interpretation: Functional Assays to the Rescue

Starita, Lea M., Ahituv, Nadav, Dunham, Maitreya J., Kitzman, Jacob O., Roth, Frederick P., Seelig, Georg, Shendure, Jay, Fowler, Douglas M.

Journal:

The American Journal of Human Genetics

Year:

2017

Language:

english

File:

PDF, 364 KB

english, 2017

28

Global dynamics of stage-specific transcription factor binding during thymocyte development

Hosoya, Tomonori, D’Oliveira Albanus, Ricardo, Hensley, John, Myers, Greggory, Kyono, Yasuhiro, Kitzman, Jacob, Parker, Stephen C. J., Engel, James Douglas

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 2.50 MB

english, 2018

29

Fragment Length of Circulating Tumor DNA

Underhill, Hunter R., Kitzman, Jacob O., Hellwig, Sabine, Welker, Noah C., Daza, Riza, Baker, Daniel N., Gligorich, Keith M., Rostomily, Robert C., Bronner, Mary P., Shendure, Jay, Kwiatkowski, David

Journal:

Year:

2016

Language:

english

File:

PDF, 7.23 MB

english, 2016

30

Genomic annotation of disease-associated variants reveals shared functional contexts

Kyono, Yasuhiro, Kitzman, Jacob O., Parker, Stephen C. J.

Journal:

Year:

2019

File:

PDF, 1.60 MB

2019

31

Genomic annotation of disease-associated variants reveals shared functional contexts

Kyono, Yasuhiro, Kitzman, Jacob O., Parker, Stephen C. J.

Journal:

Year:

2019

Language:

english

File:

PDF, 1.60 MB

english, 2019

32

CRISPR knockout screen implicates three genes in lysosome function

Lenk, Guy M., Park, Young N., Lemons, Rosemary, Flynn, Emma, Plank, Margaret, Frei, Christen M., Davis, Michael J., Gregorka, Brian, Swanson, Joel A., Meisler, Miriam H., Kitzman, Jacob O.

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 3.31 MB

english, 2019

33

Quantification, Dynamic Visualization, and Validation of Bias in ATAC-Seq Data with ataqv

Orchard, Peter, Kyono, Yasuhiro, Hensley, John, Kitzman, Jacob O., Parker, Stephen C.J.

Journal:

Year:

2020

Language:

english

File:

PDF, 2.27 MB

english, 2020

34

Elevated exopolysaccharide levels in Pseudomonas aeruginosa flagellar mutants have implications for biofilm growth and chronic infections

Harrison, Joe J., Almblad, Henrik, Irie, Yasuhiko, Wolter, Daniel J., Eggleston, Heather C., Randall, Trevor E., Kitzman, Jacob O., Stackhouse, Bethany, Emerson, Julia C., Mcnamara, Sharon, Larsen, Ty

Journal:

Year:

2020

File:

PDF, 10.99 MB

2020

35

SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells

Fogarty, Elizabeth A., Kitzman, Jacob O., Antonellis, Anthony

Journal:

Year:

2020

File:

PDF, 3.33 MB

2020