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2. Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes

Author

Hurtado, Jonathan, primary, Rogers, Thomas F., additional, Jaffe, David B., additional, Adams, Bruce A., additional, Bangaru, Sandhya, additional, Garcia, Elijah, additional, Capozzola, Tazio, additional, Messmer, Terrence, additional, Sharma, Pragati, additional, Song, Ge, additional, Beutler, Nathan, additional, He, Wanting, additional, Dueker, Katharina, additional, Musharrafieh, Rami, additional, Burbach, Sarah, additional, Truong, Alina, additional, Stubbington, Michael J.T., additional, Burton, Dennis R., additional, Andrabi, Raiees, additional, Ward, Andrew B., additional, McDonnell, Wyatt J., additional, and Briney, Bryan, additional

Published
2024
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3. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octávio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F.

Subjects
Quantitative Biology - Genomics
Abstract

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets

Published
2013
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4. The genomic substrate for adaptive radiation in African cichlid fish.

Author

Brawand, David, Wagner, Catherine E, Li, Yang I, Malinsky, Milan, Keller, Irene, Fan, Shaohua, Simakov, Oleg, Ng, Alvin Y, Lim, Zhi Wei, Bezault, Etienne, Turner-Maier, Jason, Johnson, Jeremy, Alcazar, Rosa, Noh, Hyun Ji, Russell, Pamela, Aken, Bronwen, Alföldi, Jessica, Amemiya, Chris, Azzouzi, Naoual, Baroiller, Jean-François, Barloy-Hubler, Frederique, Berlin, Aaron, Bloomquist, Ryan, Carleton, Karen L, Conte, Matthew A, D'Cotta, Helena, Eshel, Orly, Gaffney, Leslie, Galibert, Francis, Gante, Hugo F, Gnerre, Sante, Greuter, Lucie, Guyon, Richard, Haddad, Natalie S, Haerty, Wilfried, Harris, Rayna M, Hofmann, Hans A, Hourlier, Thibaut, Hulata, Gideon, Jaffe, David B, Lara, Marcia, Lee, Alison P, MacCallum, Iain, Mwaiko, Salome, Nikaido, Masato, Nishihara, Hidenori, Ozouf-Costaz, Catherine, Penman, David J, Przybylski, Dariusz, Rakotomanga, Michaelle, Renn, Suzy CP, Ribeiro, Filipe J, Ron, Micha, Salzburger, Walter, Sanchez-Pulido, Luis, Santos, M Emilia, Searle, Steve, Sharpe, Ted, Swofford, Ross, Tan, Frederick J, Williams, Louise, Young, Sarah, Yin, Shuangye, Okada, Norihiro, Kocher, Thomas D, Miska, Eric A, Lander, Eric S, Venkatesh, Byrappa, Fernald, Russell D, Meyer, Axel, Ponting, Chris P, Streelman, J Todd, Lindblad-Toh, Kerstin, Seehausen, Ole, and Di Palma, Federica

Subjects
Animals, Cichlids, MicroRNAs, DNA Transposable Elements, Genomics, Evolution, Molecular, Phylogeny, Gene Expression Regulation, Gene Duplication, Polymorphism, Genetic, Genome, Africa, Eastern, Genetic Speciation, Lakes, Africa, Eastern, Evolution, Molecular, Polymorphism, Genetic, General Science & Technology
Abstract

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.

Published
2014

5. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F

Abstract

Abstract Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Published
2013

6. Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing

Author

Kirby, Andrew, Gnirke, Andreas, Jaffe, David B, Barešová, Veronika, Pochet, Nathalie, Blumenstiel, Brendan, Ye, Chun, Aird, Daniel, Stevens, Christine, Robinson, James T, Cabili, Moran N, Gat-Viks, Irit, Kelliher, Edward, Daza, Riza, DeFelice, Matthew, Hůlková, Helena, Sovová, Jana, Vylet'al, Petr, Antignac, Corinne, Guttman, Mitchell, Handsaker, Robert E, Perrin, Danielle, Steelman, Scott, Sigurdsson, Snaevar, Scheinman, Steven J, Sougnez, Carrie, Cibulskis, Kristian, Parkin, Melissa, Green, Todd, Rossin, Elizabeth, Zody, Michael C, Xavier, Ramnik J, Pollak, Martin R, Alper, Seth L, Lindblad-Toh, Kerstin, Gabriel, Stacey, Hart, P Suzanne, Regev, Aviv, Nusbaum, Chad, Kmoch, Stanislav, Bleyer, Anthony J, Lander, Eric S, and Daly, Mark J

Subjects
Biotechnology, Kidney Disease, Genetics, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Cytosine, Female, Genetic Linkage, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Male, Minisatellite Repeats, Mucin-1, Mutation, Polycystic Kidney, Autosomal Dominant, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (∼1.5-5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.

Published
2013

7. The genomic basis of adaptive evolution in threespine sticklebacks.

Author

Jones, Felicity C, Grabherr, Manfred G, Chan, Yingguang Frank, Russell, Pamela, Mauceli, Evan, Johnson, Jeremy, Swofford, Ross, Pirun, Mono, Zody, Michael C, White, Simon, Birney, Ewan, Searle, Stephen, Schmutz, Jeremy, Grimwood, Jane, Dickson, Mark C, Myers, Richard M, Miller, Craig T, Summers, Brian R, Knecht, Anne K, Brady, Shannon D, Zhang, Haili, Pollen, Alex A, Howes, Timothy, Amemiya, Chris, Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Jaffe, David B, Nicol, Robert, Wilkinson, Jane, Lander, Eric S, Di Palma, Federica, Lindblad-Toh, Kerstin, and Kingsley, David M

Subjects
Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team, Chromosomes, Animals, Smegmamorpha, Sequence Analysis, DNA, Genomics, Fresh Water, Seawater, Adaptation, Physiological, Conserved Sequence, Genome, Molecular Sequence Data, Alaska, Female, Genetic Variation, Chromosome Inversion, Biological Evolution, Aquatic Organisms, Ecotype, General Science & Technology
Abstract

Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.

Published
2012

8. A high-resolution map of human evolutionary constraint using 29 mammals.

Author

Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F, Parker, Brian J, Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D, Lowe, Craig B, Holloway, Alisha K, Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J, Jaffe, David B, Jungreis, Irwin, Kent, W James, Kostka, Dennis, Lara, Marcia, Martins, Andre L, Massingham, Tim, Moltke, Ida, Raney, Brian J, Rasmussen, Matthew D, Robinson, Jim, Stark, Alexander, Vilella, Albert J, Wen, Jiayu, Xie, Xiaohui, Zody, Michael C, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin, Jen, Bloom, Toby, Chin, Chee Whye, Heiman, Dave, Nicol, Robert, Nusbaum, Chad, Young, Sarah, Wilkinson, Jane, Worley, Kim C, Kovar, Christie L, Muzny, Donna M, Gibbs, Richard A, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree, Andrew, Dihn, Huyen H, Fowler, Gerald, Jhangiani, Shalili, Joshi, Vandita, Lee, Sandra, Lewis, Lora R, Nazareth, Lynne V, Okwuonu, Geoffrey, Santibanez, Jireh, Warren, Wesley C, Mardis, Elaine R, Weinstock, George M, Wilson, Richard K, Genome Institute at Washington University, Delehaunty, Kim, Dooling, David, Fronik, Catrina, Fulton, Lucinda, Fulton, Bob, Graves, Tina, Minx, Patrick, Sodergren, Erica, Birney, Ewan, Margulies, Elliott H, Herrero, Javier, Green, Eric D, Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S, Pedersen, Jakob S, Lander, Eric S, and Kellis, Manolis

Subjects
Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Animals, Mammals, Humans, Disease, RNA, Sequence Alignment, Sequence Analysis, DNA, Genomics, Evolution, Molecular, Phylogeny, Genome, Genome, Human, Exons, Health, Selection, Genetic, Molecular Sequence Annotation, Sequence Analysis, DNA, Evolution, Molecular, Human, Selection, Genetic, General Science & Technology
Abstract

The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Published
2011

10. New results on binary linear codes

Author

Jaffe, David B.

Subjects
Mathematics - Combinatorics, Computer Science - Information Theory, 94B65
Abstract

This research announcement describes in very rough terms methods and a computer language under development, which can be used to prove the nonexistence of binary linear codes. Over a hundred new results have been obtained by the author. For example, there is no [29,11,10] code. The proof of this is roughly outlined.

Published
1995

11. A sextic surface cannot have 66 nodes

Author

Jaffe, David B. and Ruberman, Daniel

Subjects
Mathematics - Algebraic Geometry
Abstract

Let S be a surface in complex projective 3-space, having only nodes as singularities. Suppose that S has degree 6. We show that the maximum number of nodes which S can have is 65. An abbreviated history of this is as follows. Basset showed that S can have at most 66 nodes. Catanese and Ceresa and Stagnaro constructed sextic surfaces having 64 nodes. Barth has recently exhibited a 65 node sextic surface. We complete the story by showing that S cannot have 66 nodes. Let f: S~ --> S be a minimal resolution of singularities. A set N of nodes on S is even if there exists a divisor Q on S~ such that 2Q ~ f^{-1}(N). We show that a nonempty even set of nodes on S must have size 24, 32, 40, 56, or 64. This result is key to showing the nonexistence of the 66 node sextic. We do not know if a sextic surface can have an even node set of size 56 or 64. The existence or nonexistence of large even node sets is related to the following vanishing problem. Let S be a normal surface of degree s in CP^3. Let D be a Weil divisor on S such that D is Q-rationally equivalent to rH, for some r \in \Q. Under what circumstances do we have H^1(O_S(D)) = 0? For instance, this holds when r < 0. For s=4 and r=0, H^1 can be nonzero. For s=6 and r=0, if a 56 or 64 node even set exists, then H^1 can be nonzero. The vanishing of H^1 is also related to linear normality, quadric normality, etc. of set-theoretic complete intersections in P^3., Comment: 19 pages; the body of the paper is distributed as a compressed postscript file at ftp://mathlab03.unl.edu/pub/faculty/jaffe/sextic.Z The paper will print nicely on a 600 dpi printer; on lower resolution printers, one picture will be blurred. Hard copy is available from the authors: jaffe@cpthree.unl.edu, ruberman@maths.ox.ac.uk

Published
1995

12. On sextic surfaces having only nodes (preliminary report)

Author

Jaffe, David B.

Subjects
Mathematics - Algebraic Geometry
Abstract

Let S be a surface in CP^3, having only nodes as singularities. Let pi: S~ --> S be a minimal resolution of singularities. A set N of nodes on S is EVEN if there exists a divisor Q on S~ such that 2Q ~ pi^{-1}(N). Suppose that S has degree 6. It is known (Basset) that S cannot have 67 or more nodes. It is also known (Barth) that S can have 65 nodes. It is not known if S can have 66 nodes. Likewise, it is not known exactly what sizes can occur for an even set of nodes on S. We show that an nonempty even set of nodes on S must have size 24, 32, 40, 56, or 64. We do not know if the sizes 56 and 64 can occur. We show that if S has 66 nodes, then it must have an even set of 64 nodes, and it cannot have an even set of 56 nodes. THUS IF ONE COULD RULE OUT THE CASE OF A 64 NODE EVEN SET, IT WOULD FOLLOW THAT S CANNOT HAVE 66 NODES. The existence or nonexistence of large even node sets is related to the following vanishing problem. Let S be a normal surface of degree s in CP^3. Let D be a Weil divisor on S such that D is Q-rationally equivalent to rH, for some r \in \Q. Under what circumstances do we have H^1(O_S(D)) = 0? For instance, this holds when r < 0. For s=4 and r=0, H^1 can be nonzero. For s=6 and r=0, if a 56 or 64 node even set exists, then H^1 can be nonzero. The vanishing of H^1 is also related to linear normality, quadric normality, etc. of set-theoretic complete intersections in P^3. Hard copy is available from the author. E-mail to jaffe@cpthree.unl.edu., Comment: 14 pages, AMS-LaTeX

Published
1994

13. Functorial structure of units in a tensor product

Author

Jaffe, David B.

Subjects
Mathematics - Algebraic Geometry
Abstract

We study the units in a tensor product of rings. For example, let k be an algebraically closed field. Let A and B be reduced rings containing k, having connected spectra. Let u \in A tensor_k B be a unit. Then u = a tensor_k b for some units a \in A and b \in B. Here is a deeper result, stated for simplicity in the affine case only. Let k be a field, and let f: R --> S be a homomorphism of f.g. k-algebras such that Spec(f) is dominant. Assume that every irreducible component of Spec(R_red) or Spec(S_red) is geometrically integral and has a rational point. Let B --> C be a faithfully flat homomorphism of reduced k-algebras. For A a k-algebra, define Q(A) to be (S tensor_k A)^*/(R tensor_k A)^*. Then Q satisfies the following sheaf property: the sequence 0 --> Q(B) --> Q(C) --> Q(C tensor_B C) is exact. This and another result are used in the proof of the following statement from "The kernel of the map on Picard groups induced by a faithfully flat homomorphism" by R. Guralnick, D. Jaffe, W. Raskind, R. Wiegand: Let K/k be an algebraic field extension and let A be a f.g. k-algebra. Assume resolution of singularities. Then there is a finite extension E/k contained in K/k such that Pic(A tensor_k E) --> Pic(A tensor_k K) is injective., Comment: 23 pages, AMS-LaTeX. Hard copy is available from the author. E-mail to jaffe@cpthree.unl.edu

Published
1994

14. Applications of iterated curve blowup to set-theoretic complete intersections in P3

Author

Jaffe, David B.

Subjects
Mathematics - Algebraic Geometry
Abstract

Let S, T be surfaces in P3. Suppose that S intersect T is set-theoretically a smooth curve C of degree d and genus g. Suppose that S and T have no common singular points. Then if C is not a complete intersection, then deg(S), deg(T) < 2d^4. Fixing (d,g), one can form a finite (shorter) list of all possible pairs (deg(S),deg(T)). For instance, when (d,g) = (4,0), and assuming for simplicity that deg(S) <= deg(T): (deg(S), deg(T)) \in {(3,4), (3,8), (4,4), (4,7), (6,26), (9,48), (10,28) (12,18), (13,16), (17,220), (18,118), (19,84), (20,67), (22,50), (28,33)}. Assume characteristic 0. [1] Suppose that S and T have non-overlapping rational singularities. Then d <= g+3. [2] Suppose that S is normal, and that d>deg(S). Then C is linearly normal (and so d <= g+3). [3] Suppose that S is a quartic surface having only rational singularities. Then C is linearly normal. Hard copy is available from the author. E-mail to jaffe@cpthree.unl.edu., Comment: 57 pages, AMS-LaTeX

Published
1994

15. Coherent functors, with application to torsion in the Picard group

Author

Jaffe, David B.

Subjects
Mathematics - Algebraic Geometry
Abstract

Let A be a commutative noetherian ring. Call a functor <> --> <> coherent if it can be built up (via iterated finite limits) from functors of the form B \mapsto M tensor_A B, where M is a f.g. A-module. When such a functor F in fact takes its values in <>, we show that there are only finitely many prime numbers p such that _p F(A) is infinite, and that none of these primes are invertible in A. This (and related statements) yield information about torsion in Pic(A). For example, if A is of finite type over Z, we prove that the torsion in Pic(A) is supported at a finite set of primes, and if _p Pic(A) is infinite, then the prime p is not invertible in A. These results use the (already known) fact that if such an A is normal, then Pic(A) is finitely generated. We obtain a parallel result for a reduced scheme X of finite type over Z. We show that the groups which can occur as the Picard group of a scheme of finite type over a finite field all have the form (finitely generated) + sum_{n=1}^infty F, where F is a finite p-group. Hard copy is available from the author. E-mail to jaffe@cpthree.unl.edu., Comment: 46 pages, AMS-LaTeX

Published
1994

16. Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes

Author

Hurtado, Jonathan, primary, Rogers, Thomas F., additional, Jaffe, David B., additional, Adams, Bruce A., additional, Bangaru, Sandhya, additional, Garcia, Elijah, additional, Capozzola, Tazio, additional, Messmer, Terrence, additional, Sharma, Pragati, additional, Song, Ge, additional, Beutler, Nathan, additional, He, Wanting, additional, Dueker, Katharina, additional, Musharrafieh, Rami, additional, Stubbington, Michael J.T., additional, Burton, Dennis R., additional, Andrabi, Raiees, additional, Ward, Andrew B., additional, McDonnell, Wyatt J., additional, and Briney, Bryan, additional

Published
2023
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19. Dorsal root ganglia control nociceptive input to the central nervous system

Author

Smith, Cody J, Hao, Han, Ramli, Rosmaliza, Wang, Caixue, Liu, Chao, Shah, Shihab, Mullen, Pierce, Lall, Varinder, Jones, Frederick, Shao, Jicheng, Zhang, Hailin, Jaffe, David B, Gamper, Nikita, Du, Xiaona, Smith, Cody J, Hao, Han, Ramli, Rosmaliza, Wang, Caixue, Liu, Chao, Shah, Shihab, Mullen, Pierce, Lall, Varinder, Jones, Frederick, Shao, Jicheng, Zhang, Hailin, Jaffe, David B, Gamper, Nikita, and Du, Xiaona

Abstract

Accumulating observations suggest that peripheral somatosensory ganglia may regulate nociceptive transmission, yet direct evidence is sparse. Here, in experiments on rats and mice, we show that the peripheral afferent nociceptive information undergoes dynamic filtering within the dorsal root ganglion (DRG) and suggest that this filtering occurs at the axonal bifurcations (t-junctions). Using synchronous in vivo electrophysiological recordings from the peripheral and central processes of sensory neurons (in the spinal nerve and dorsal root), ganglionic transplantation of GABAergic progenitor cells, and optogenetics, we demonstrate existence of tonic and dynamic filtering of action potentials traveling through the DRG. Filtering induced by focal application of GABA or optogenetic GABA release from the DRG-transplanted GABAergic progenitor cells was specific to nociceptive fibers. Light-sheet imaging and computer modeling demonstrated that, compared to other somatosensory fiber types, nociceptors have shorter stem axons, making somatic control over t-junctional filtering more efficient. Optogenetically induced GABA release within DRG from the transplanted GABAergic cells enhanced filtering and alleviated hypersensitivity to noxious stimulation produced by chronic inflammation and neuropathic injury in vivo. These findings support "gating" of pain information by DRGs and suggest new therapeutic approaches for pain relief.

Published
2023

21. Dorsal root ganglia control nociceptive input to the central nervous system

Author

Hao, Han, primary, Ramli, Rosmaliza, additional, Wang, Caixue, additional, Liu, Chao, additional, Shah, Shihab, additional, Mullen, Pierce, additional, Lall, Varinder, additional, Jones, Frederick, additional, Shao, Jicheng, additional, Zhang, Hailin, additional, Jaffe, David B., additional, Gamper, Nikita, additional, and Du, Xiaona, additional

Published
2023
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22. Local GABAergic signaling within sensory ganglia controls peripheral nociceptive transmission

Author

Du, Xiaona, Hao, Han, Yang, Yuehui, Huang, Sha, Wang, Caixue, Gigou, Sylvain, Ramli, Rosmaliza, Li, Xinmeng, Jaworska, Ewa, Edwards, Ian, Deuchars, Jim, Yanagawa, Yuchio, Qi, Jinlong, Guan, Bingcai, Jaffe, David B., Zhang, Hailin, and Gamper, Nikita

Subjects
Nociception -- Research, GABA -- Research, Ganglia -- Health aspects -- Research, Cellular signal transduction -- Research, Health care industry
Abstract

The integration of somatosensory information is generally assumed to be a function of the central nervous system (CNS). Here we describe fully functional GABAergic communication within rodent peripheral sensory ganglia and show that it can modulate transmission of pain-related signals from the peripheral sensory nerves to the CNS. We found that sensory neurons express major proteins necessary for GABA synthesis and release and that sensory neurons released GABA in response to depolarization. In vivo focal infusion of GABA or GABA reuptake inhibitor to sensory ganglia dramatically reduced acute peripherally induced nociception and alleviated neuropathic and inflammatory pain. In addition, focal application of GABA receptor antagonists to sensory ganglia triggered or exacerbated peripherally induced nociception. We also demonstrated that chemogenetic or optogenetic depolarization of GABAergic dorsal root ganglion neurons in vivo reduced acute and chronic peripherally induced nociception. Mechanistically, GABA depolarized the majority of sensory neuron somata, yet produced a net inhibitory effect on the nociceptive transmission due to the filtering effect at nociceptive fiber T-junctions. Our findings indicate that peripheral somatosensory ganglia represent a hitherto underappreciated site of somatosensory signal integration and offer a potential target for therapeutic intervention., Introduction Peripheral nerves convey to the central nervous system (CNS) versatile information about the body's environment. An important function of these nerves is informing the brain about ongoing or imminent [...]

Published
2017
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23. LETTERS TO THE EDITOR

Author

Robbins, Ira P., Johnson, Philip McBride, Dobbins, David F., Goddard, Terry, McKenna, Rob, Warshawsky, Ira B., Pinaire, Ben, Jaffe, David B., Campbell, Dave, Petts, James E., Booker, Rita, Goetzl, Thomas, and Lee, Rosalind Manson

Published
2007

26. Functional antibodies exhibit light chain coherence

Author

Jaffe, David B., primary, Shahi, Payam, additional, Adams, Bruce A., additional, Chrisman, Ashley M., additional, Finnegan, Peter M., additional, Raman, Nandhini, additional, Royall, Ariel E., additional, Tsai, FuNien, additional, Vollbrecht, Thomas, additional, Reyes, Daniel S., additional, and McDonnell, Wyatt J., additional

Published
2022
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27. enclone: precision clonotyping and analysis of immune receptors

Author

Jaffe, David B., primary, Shahi, Payam, additional, Adams, Bruce A., additional, Chrisman, Ashley M., additional, Finnegan, Peter M., additional, Raman, Nandhini, additional, Royall, Ariel E., additional, Tsai, FuNien, additional, Vollbrecht, Thomas, additional, Reyes, Daniel S., additional, and McDonnell, Wyatt J., additional

Published
2022
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28. High-quality draft assemblies of mammalian genomes from massively parallel sequence data

Author

Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J., Burton, Joshua N., Walker, Bruce J., Sharpe, Ted, Hall, Giles, Shea, Terrance P., Sykes, Sean, Berlin, Aaron M., Aird, Daniel, Costello, Maura, Daza, Riza, Williams, Louise, Nicol, Robert, Gnirke, Andreas, Nusbaum, Chad, Lander, Eric S., and Jaffe, David B.

Published
2011

34. Dorsal root ganglia control nociceptive input to the central nervous system

Author

Han, Hao, primary, Ramli, Rosmaliza, additional, Wang, Caixue, additional, Liu, Chao, additional, Shah, Shihab, additional, Mullen, Pierce, additional, Lall, Varinder, additional, Jones, Frederick, additional, Shao, Jicheng, additional, Zhang, Hailin, additional, Jaffe, David B, additional, Gamper, Nikita, additional, and Du, Xiaona, additional

Published
2021
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35. Technological advancements in multiomic single cell immune profiling and analysis

Author

Royall, Ariel E, primary, Sukovich, David J, additional, Adams, Bruce A, additional, Chi, Javelin C, additional, Reyes, Daniel, additional, Puleo, Alaina R, additional, Krishnan, Sreenath, additional, Jaffe, David B, additional, McDonnell, Wyatt J, additional, Cheung, Denise, additional, Marrs, Samuel, additional, Chen, Tina, additional, Srinavas, Niranjan, additional, Carli, Natasha, additional, Montesclaros, Luz, additional, Lau, Julia, additional, and Taylor, Sarah E. B., additional

Published
2021
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37. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Author

Zody, Michael C., Garber, Manuel, Adams, David J., Sharpe, Ted, Harrow, Jennifer, Lupski, James R., Nicholson, Christine, Searle, Steven M., Wilming, Laurens, Young, Sarah K., Abouelleil, Amr, Allen, Nicole R., Bi, Weimin, Bloom, Toby, Borowsky, Mark L., Bugalter, Boris E., Butler, Jonathan, Chang, Jean L., Chen, Chao-Kung, Cook, April, Corum, Benjamin, Cuomo, Christina A., de Jong, Pieter J., DeCaprio, David, Dewar, Ken, FitzGerald, Michael, Gilbert, James, Gibson, Richard, Gnerre, Sante, Goldstein, Steven, Grafham, Darren V., Grocock, Russell, Hafez, Nabil, Hagopian, Daniel S., Hart, Elizabeth, Norman, Catherine Hosage, Humphray, Sean, Jaffe, David B., Jones, Matt, Kamal, Michael, Khodiyar, Varsha K., LaButti, Kurt, Laird, Gavin, Lehoczky, Jessica, Liu, Xiaohong, Lokyitsang, Tashi, Loveland, Jane, Lui, Annie, Macdonald, Pendexter, Major, John E., Matthews, Lucy, Mauceli, Evan, McCarroll, Steven A., Mihalev, Atanas H., Mudge, Jonathan, Nguyen, Cindy, Nicol, Robert, O'Leary, Sinéad B., Osoegawa, Kazutoyo, Schwartz, David C., Shaw-Smith, Charles, Stankiewicz, Pawel, Steward, Charles, Swarbreck, David, Venkataraman, Vijay, Whittaker, Charles A., Yang, Xiaoping, Zimmer, Andrew R., Bradley, Allan, Hubbard, Tim, Birren, Bruce W., Rogers, Jane, Lander, Eric S., and Nusbaum, Chad

Published
2006
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38. Evolution of genes and genomes on the Drosophila phylogeny

Author

Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

Published
2007
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39. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigo, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C. J., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu1, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermuller, Jorg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K.G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaoz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A., Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W.H., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Hoon Kim, Tae, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N. S., Yu, Yong, Birney*, Ewan, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I. W., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrimsdottir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, Goncalo R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V.B., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Baylor College of Medicine, Human Genome Sequencing Center, Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): The ENCODE Project Consortium; Analysis Coordination; Ewan Birney (corresponding author) [1]; John A. Stamatoyannopoulos (corresponding author) [2]; Anindya Dutta (corresponding author) [3]; Roderic Guigó (corresponding author) [4, 5]; Thomas [...]

Published
2007
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40. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Author

Mikkelsen, Tarjei S., Wakefield, Matthew J., Aken, Bronwen, Amemiya, Chris T., Chang, Jean L., Duke, Shannon, Garber, Manuel, Gentles, Andrew J., Goodstadt, Leo, Heger, Andreas, Jurka, Jerzy, Kamal, Michael, Mauceli, Evan, Searle, Stephen M. J., Sharpe, Ted, Baker, Michelle L., Batzer, Mark A., Benos, Panayiotis V., Belov, Katherine, Clamp, Michele, Cook, April, Cuff, James, Das, Radhika, Davidow, Lance, Deakin, Janine E., Fazzari, Melissa J., Glass, Jacob L., Grabherr, Manfred, Greally, John M., Gu, Wanjun, Hore, Timothy A., Huttley, Gavin A., Kleber, Michael, Jirtle, Randy L., Koina, Edda, Lee, Jeannie T., Mahony, Shaun, Marra, Marco A., Miller, Robert D., Nicholls, Robert D., Oda, Mayumi, Papenfuss, Anthony T., Parra, Zuly E., Pollock, David D., Ray, David A., Schein, Jacqueline E., Speed, Terence P., Thompson, Katherine, VandeBerg, John L., Wade, Claire M., Walker, Jerilyn A., Waters, Paul D., Webber, Caleb, Weidman, Jennifer R., Xie, Xiaohui, Zody, Michael C., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Acer, St Christophe, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Husby, M. Erii, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Jaffe, David B., Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Gnerre, Sante, MacCallum, Iain, Graves, Jennifer A. Marshall, Ponting, Chris P., Breen, Matthew, Samollow, Paul B., Lander, Eric S., and Lindblad-Toh, Kerstin

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Tarjei S. Mikkelsen (corresponding author) [1, 2]; Matthew J. Wakefield [3]; Bronwen Aken [4]; Chris T. Amemiya [5]; Jean L. Chang [1]; Shannon Duke [6]; Manuel Garber [1]; Andrew [...]

Published
2007
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41. Two Deans Answer the Wellness Questions They Hear the Most: It's not an exaggeration to say that your career success depends in large part on how you handle the challenges the profession presents over the next decades

Author

Jaffe, David B. and Stearns, Janet E.

Subjects
Career development -- Psychological aspects -- Research, Stress management -- Influence -- Methods -- Research, Health behavior -- Influence -- Methods -- Research, Law
Abstract

It's easy in law school to get so focused on torts and the Uniform Commercial Code that you lose sight of the big picture. Law school is about learning how [...]

Published
2018

42. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Author

Kamper, Jorg, Kahmann, Regine, Bolker, Michael, Ma, Li-Jun, Brefort, Thomas, Saville, Barry J., Banuett, Flora, Kronstad, James W., Gold, Scott E., Muller, Olaf, Perlin, Michael H., Wosten, Han A. B., de Vries, Ronald, Ruiz-Herrera, Jose, Reynaga-Pena, Cristina G., Snetselaar, Karen, McCann, Michael, Perez-Martin, Jose, Feldbrugge, Michael, Basse, Christoph W., Steinberg, Gero, Ibeas, Jose I., Holloman, William, Guzman, Plinio, Farman, Mark, Stajich, Jason E., Sentandreu, Rafael, Gonzalez-Prieto, Juan M., Kennell, John C., Molina, Lazaro, Schirawski, Jan, Mendoza-Mendoza, Artemio, Greilinger, Doris, Munch, Karin, Rossel, Nicole, Scherer, Mario, Vraneš, Miroslav, Ladendorf, Oliver, Vincon, Volker, Fuchs, Uta, Sandrock, Bjorn, Meng, Shaowu, Ho, Eric C. H., Cahill, Matt J., Boyce, Kylie J., Klose, Jana, Klosterman, Steven J., Deelstra, Heine J., Ortiz-Castellanos, Lucila, Li, Weixi, Sanchez-Alonso, Patricia, Schreier, Peter H., Hauser-Hahn, Isolde, Vaupel, Martin, Koopmann, Edda, Friedrich, Gabi, Voss, Hartmut, Schluter, Thomas, Margolis, Jonathan, Platt, Darren, Swimmer, Candace, Gnirke, Andreas, Chen, Feng, Vysotskaia, Valentina, Mannhaupt, Gertrud, Guldener, Ulrich, Munsterkotter, Martin, Haase, Dirk, Oesterheld, Matthias, Mewes, Hans-Werner, Mauceli, Evan W., DeCaprio, David, Wade, Claire M., Butler, Jonathan, Young, Sarah, Jaffe, David B., Calvo, Sarah, Nusbaum, Chad, Galagan, James, and Birren, Bruce W.

Abstract

Author(s): Jörg Kämper (corresponding author) [1]; Regine Kahmann (corresponding author) [1]; Michael Bölker (corresponding author) [2]; Li-Jun Ma [3]; Thomas Brefort [1]; Barry J. Saville [4, 27]; Flora Banuett [5]; [...]

Published
2006
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43. Analysis of the DNA sequence and duplication history of human chromosome 15

Author

Zody, Michael C., Garber, Manuel, Sharpe, Ted, Young, Sarah K., Rowen, Lee, O'Neill, Keith, Whittaker, Charles A., Kamal, Michael, Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Kodira, Chinnappa D., Madan, Anup, Qin, Shizhen, Yang, Xiaoping, Abbasi, Nissa, Abouelleil, Amr, Arachchi, Harindra M., Baradarani, Lida, Birditt, Brian, Bloom, Scott, Bloom, Toby, Borowsky, Mark L., Burke, Jeremy, Butler, Jonathan, Cook, April, DeArellano, Kurt, DeCaprio, David, Dorris, III, Lester, Dors, Monica, Eichler, Evan E., Engels, Reinhard, Fahey, Jessica, Fleetwood, Peter, Friedman, Cynthia, Gearin, Gary, Hall, Jennifer L., Hensley, Grace, Johnson, Ericka, Jones, Charlien, Kamat, Asha, Kaur, Amardeep, Locke, Devin P., Madan, Anuradha, Munson, Glen, Jaffe, David B., Lui, Annie, Macdonald, Pendexter, Mauceli, Evan, Naylor, Jerome W., Nesbitt, Ryan, Nicol, Robert, O'Leary, Sinead B., Ratcliffe, Amber, Rounsley, Steven, She, Xinwei, Sneddon, Katherine M. B., Stewart, Sandra, Sougnez, Carrie, Stone, Sabrina M., Topham, Kerri, Vincent, Dascena, Wang, Shunguang, Zimmer, Andrew R., Birren, Bruce W., Hood, Leroy, Lander, Eric S., and Nusbaum, Chad

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Michael C. Zody (corresponding author) [1]; Manuel Garber [1]; Ted Sharpe [1]; Sarah K. Young [1]; Lee Rowen [2]; Keith O'Neill [1]; Charles A. Whittaker [1, 6]; Michael Kamal [...]

Published
2006
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44. Human chromosome 11 DNA sequence and analysis including novel gene identification

Author

Taylor, Todd D., Noguchi, Hideki, Totoki, Yasushi, Toyoda, Atsushi, Kuroki, Yoko, Dewar, Ken, Lloyd, Christine, Itoh, Takehiko, Takeda, Tadayuki, Kim, Dae-Won, She, Xinwei, Barlow, Karen F., Bloom, Toby, Bruford, Elspeth, Chang, Jean L., Cuomo, Christina A., Eichler, Evan, FitzGerald, Michael G., Jaffe, David B., LaButti, Kurt, Nicol, Robert, Park, Hong-Seog, Seaman, Christopher, Sougnez, Carrie, Yang, Xiaoping, Zimmer, Andrew R., Zody, Michael C., Birren, Bruce W., Nusbaum, Chad, Fujiyama, Asao, Hattori, Masahira, Rogers, Jane, Lander, Eric S., and Sakaki, Yoshiyuki

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Todd D. Taylor (corresponding author) [1]; Hideki Noguchi [1, 10]; Yasushi Totoki [1]; Atsushi Toyoda [1]; Yoko Kuroki [1]; Ken Dewar [2, 10]; Christine Lloyd [3]; Takehiko Itoh [4]; [...]

Published
2006
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45. DNA sequence and analysis of human chromosome 8

Author

Nusbaum, Chad, Mikkelsen, Tarjei S., Zody, Michael C., Asakawa, Shuichi, Taudien, Stefan, Garber, Manuel, Kodira, Chinnappa D., Schueler, Mary G., Shimizu, Atsushi, Whittaker, Charles A., Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Yang, Xiaoping, Allen, Nicole R., Anderson, Scott, Asakawa, Teruyo, Blechschmidt, Karin, Bloom, Toby, Borowsky, Mark L., Butler, Jonathan, Cook, April, Corum, Benjamin, DeArellano, Kurt, DeCaprio, David, Dooley, Kathleen T., Dorris, III, Lester, Engels, Reinhard, Glockner, Gernot, Hafez, Nabil, Hagopian, Daniel S., Hall, Jennifer L., Ishikawa, Sabine K., Jaffe, David B., Kamat, Asha, Kudoh, Jun, Lehmann, Rudiger, Lokitsang, Tashi, Macdonald, Pendexter, Major, John E., Matthews, Charles D., Mauceli, Evan, Menzel, Uwe, Mihalev, Atanas H., Minoshima, Shinsei, Murayama, Yuji, Naylor, Jerome W., Nicol, Robert, Nguyen, Cindy, O'Leary, Sinead B., O'Neill, Keith, Parker, Stephen C. J., Polley, Andreas, Raymond, Christina K., Reichwald, Kathrin, Rodriguez, Joseph, Sasaki, Takashi, Schilhabel, Markus, Siddiqui, Roman, Smith, Cherylyn L., Sneddon, Tam P., Talamas, Jessica A., Tenzin, Pema, Topham, Kerri, Venkataraman, Vijay, Wen, Gaiping, Yamazaki, Satoru, Young, Sarah K., Zeng, Qiandong, Zimmer, Andrew R., Rosenthal, Andre, Birren, Bruce W., Platzer, Matthias, Shimizu, Nobuyoshi, and Lander, Eric S.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Chad Nusbaum (corresponding author) [1]; Tarjei S. Mikkelsen [1]; Michael C. Zody [1]; Shuichi Asakawa [2]; Stefan Taudien [3]; Manuel Garber [1]; Chinnappa D. Kodira [1]; Mary G. Schueler [...]

Published
2006
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46. Genome sequence, comparative analysis and haplotype structure of the domestic dog

Author

Lindblad-Toh, Kerstin, Wade, Claire M., Mikkelsen, Tarjei S., Karlsson, Elinor K., Jaffe, David B., Kamal, Michael, Clamp, Michele, Chang, Jean L., Kulbokas, III, Edward J., Zody, Michael C., Mauceli, Evan, Xie, Xiaohui, Breen, Matthew, Wayne, Robert K., Ostrander, Elaine A., Ponting, Chris P., Galibert, Francis, Smith, Douglas R., deJong, Pieter J., Kirkness, Ewen, Alvarez, Pablo, Biagi, Tara, Brockman, William, Butler, Jonathan, Chin, Chee-Wye, Cook, April, Cuff, James, Daly, Mark J., DeCaprio, David, Gnerre, Sante, Grabherr, Manfred, Kellis, Manolis, Kleber, Michael, Bardeleben, Carolyne, Goodstadt, Leo, Heger, Andreas, Hitte, Christophe, Kim, Lisa, Koepfli, Klaus-Peter, Parker, Heidi G., Pollinger, John P., Searle, Stephen M. J., Sutter, Nathan B., Thomas, Rachael, Webber, Caleb, Baldwin, Jennifer, Abebe, Adal, Abouelleil, Amr, Aftuck, Lynne, Ait-zahra, Mostafa, Aldredge, Tyler, Allen, Nicole, An, Peter, Anderson, Scott, Antoine, Claudel, Arachchi, Harindra, Aslam, Ali, Ayotte, Laura, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Benamara, Mostafa, Berlin, Aaron, Bessette, Daniel, Blitshteyn, Berta, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Brown, Adam, Cahill, Patrick, Calixte, Nadia, Camarata, Jody, Cheshatsang, Yama, Chu, Jeffrey, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Dawoe, Tenzin, Daza, Riza, Decktor, Karin, DeGray, Stuart, Dhargay, Norbu, Dooley, Kimberly, Dooley, Kathleen, Dorje, Passang, Dorjee, Kunsang, Dorris, Lester, Duffey, Noah, Dupes, Alan, Egbiremolen, Osebhajajeme, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Ferreira, Patricia, Fisher, Sheila, FitzGerald, Mike, Foley, Karen, Foley, Chelsea, Franke, Alicia, Friedrich, Dennis, Gage, Diane, Garber, Manuel, Gearin, Gary, Giannoukos, Georgia, Goode, Tina, Goyette, Audra, Graham, Joseph, Grandbois, Edward, Gyaltsen, Kunsang, Hafez, Nabil, Hagopian, Daniel, Hagos, Birhane, Hall, Jennifer, Healy, Claire, Hegarty, Ryan, Honan, Tracey, Horn, Andrea, Houde, Nathan, Hughes, Leanne, Hunnicutt, Leigh, Husby, M., Jester, Benjamin, Jones, Charlien, Kamat, Asha, Kanga, Ben, Kells, Cristyn, Khazanovich, Dmitry, Kieu, Alix Chinh, Kisner, Peter, Kumar, Mayank, Lance, Krista, Landers, Thomas, Lara, Marcia, Lee, William, Leger, Jean-Pierre, Lennon, Niall, Leuper, Lisa, LeVine, Sarah, Liu, Jinlei, Liu, Xiaohong, Lokyitsang, Yeshi, Lokyitsang, Tashi, Lui, Annie, Macdonald, Jan, Major, John, Marabella, Richard, Maru, Kebede, Matthews, Charles, McDonough, Susan, Mehta, Teena, Meldrim, James, Melnikov, Alexandre, Meneus, Louis, Mihalev, Atanas, Mihova, Tanya, Miller, Karen, Mittelman, Rachel, Mlenga, Valentine, Mulrain, Leonidas, Munson, Glen, Navidi, Adam, Naylor, Jerome, Nguyen, Tuyen, Nguyen, Nga, Nguyen, Cindy, Nguyen, Thu, Nicol, Robert, Norbu, Nyima, Norbu, Choe, Novod, Nathaniel, Nyima, Tenchoe, Olandt, Peter, O'Neill, Barry, O'Neill, Keith, Osman, Sahal, Oyono, Lucien, Patti, Christopher, Perrin, Danielle, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Rachupka, Anthony, Raghuraman, Sujaa, Rameau, Rayale, Ray, Verneda, Raymond, Christina, Rege, Filip, Rise, Cecil, Rogers, Julie, Rogov, Peter, Sahalie, Julie, Settipalli, Sampath, Sharpe, Theodore, Shea, Terrance, Sheehan, Mechele, Sherpa, Ngawang, Shi, Jianying, Shih, Diana, Sloan, Jessie, Smith, Cherylyn, Sparrow, Todd, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Stone, Sabrina, Sykes, Sean, Tchuinga, Pierre, Tenzing, Pema, Tesfaye, Senait, Thoulutsang, Dawa, Thoulutsang, Yama, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Venkataraman, Vijay, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Yang, Shuli, Yang, Xiaoping, Young, Geneva, Yu, Qing, Zainoun, Joanne, Zembek, Lisa, Zimmer, Andrew, and Lander, Eric S.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Kerstin Lindblad-Toh (corresponding author) [1]; Claire M Wade [1, 2]; Tarjei S. Mikkelsen [1, 3]; Elinor K. Karlsson [1, 4]; David B. Jaffe [1]; Michael Kamal [1]; Michele Clamp [...]

Published
2005
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47. DNA sequence and analysis of human chromosome 18

Author

Nusbaum, Chad, Zody, Michael C., Borowsky, Mark L., Kamal, Michael, Kodira, Chinnappa D., Taylor, Todd D., Whittaker, Charles A., Chang, Jean L., Cuomo, Christina A., Dewar, Ken, FitzGerald, Michael G., Yang, Xiaoping, Abouelleil, Amr, Allen, Nicole R., Anderson, Scott, Bloom, Toby, Bugalter, Boris, Butler, Jonathan, Cook, April, DeCaprio, David, Engels, Reinhard, Garber, Manuel, Gnirke, Andreas, Hafez, Nabil, Hall, Jennifer L., Norman, Catherine Hosage, Itoh, Takehiko, Jaffe, David B., Kuroki, Yoko, Lehoczky, Jessica, Lui, Annie, Macdonald, Pendexter, Mauceli, Evan, Mikkelsen, Tarjei S., Naylor, Jerome W., Nicol, Robert, Nguyen, Cindy, Noguchi, Hideki, O'Leary, Sinead B., Piqani, Bruno, L Smith, Cherylyn, Talamas, Jessica A., Topham, Kerri, Totoki, Yasushi, Toyoda, Atsushi, Wain, Hester M., Young, Sarah K., Zeng, Qiandong, Zimmer, Andrew R., Fujiyama, Asao, Hattori, Masahira, Birren, Bruce W., Sakaki, Yoshiyuki, and Lander, Eric S.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Chad Nusbaum (corresponding author) [1]; Michael C. Zody [1]; Mark L. Borowsky [1]; Michael Kamal [1]; Chinnappa D. Kodira [1]; Todd D. Taylor [2]; Charles A. Whittaker [1, 8]; [...]

Published
2005
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48. The African coelacanth genome provides insights into tetrapod evolution

Author

Amemiya, Chris T., Alföldi, Jessica J, Lee, Alison P., Fan, Shaohua S, Philippe, Hervé H, MacCallum, Iain I, Braasch, Ingo I, Manousaki, Tereza T, Schneider, Igor I, Rohner, Nicolas N, Organ, Chris C, Chalopin, Domitille D, Smith, Jeramiah J., Robinson, Mark M, Dorrington, Rosemary A., Gerdol, Marco M, Aken, Bronwen B, Biscotti, Maria Assunta, Barucca, Marco M, Baurain, Denis D, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco F, Burmester, Thorsten T, Campbell, Michael S., Canapa, Adriana A, Cannon, John P., Christoffels, Alan A, De Moro, Gianluca G, Edkins, Adrienne L., Fan, Lin L, Fausto, Anna Maria, Feiner, Nathalie N, Forconi, Mariko M, Gamieldien, Junaid J, Gnerre, Sante S, Gnirke, Andreas A, Goldstone, Jared V., Haerty, Wilfried W, Hahn, Mark E., Hesse, Uljana U, Hoffmann, Steve S, Johnson, Jeremy J, Karchner, Sibel I., Kuraku, Shigehiro S, Lara, Marcia M, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan E, Miyake, Tsutomu T, Mueller, Gail M., Nelson, David R., Nitsche, Anne A, Olmo, Ettore E, Ota, Tatsuya T, Pallavicini, Alberto A, Panji, Sumir S, Picone, Barbara B, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz D, Saha, Nil Ratan, Ravi, Vydianathan V, Ribeiro, Filipe J., Sauka-Spengler, Tatjana T, Scapigliati, Giuseppe G, Searle, Stephen M. J., Sharpe, Ted T, Simakov, Oleg O, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta K, Tabbaa, Diana D, Tafer, Hakim H, Turner-Maier, Jason J, van Heusden, Peter P, White, Simon S, Williams, Louise L, Yandell, Mark M, Brinkmann, Henner H, Volff, Jean-Nicolas J, Tabin, Clifford J., Shubin, Neil N, Schartl, Manfred M, Jaffe, David B., Postlethwait, John H., Venkatesh, Byrappa B, Di Palma, Federica F, Lander, Eric S., Meyer, Axel A, and Lindblad-Toh, Kerstin K

Published
2013
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49. Initial sequencing and comparative analysis of the mouse genome

Author

Chinwalla, Asif T., Cook, Lisa L., Delehaunty, Kimberly D., Fewell, Ginger A., Fulton, Lucinda A., Fulton, Robert S., Graves, Tina A., Hillier, LaDeana W., Mardis, Elaine R., McPherson, John D., Miner, Tracie L., Nash, William E., Nelson, Joanne O., Nhan, Michael N., Pepin, Kymberlie H., Pohl, Craig S., Ponce, Tracy C., Schultz, Brian, Thompson, Johanna, Trevaskis, Evanne, Waterston, Robert H., Wendl, Michael C., Wilson, Richard K., Yang, Shiaw-Pyng, An, Peter, Berry, Eric, Birren, Bruce, Bloom, Toby, Brown, Daniel G., Butler, Jonathan, Daly, Mark, David, Robert, Deri, Justin, Dodge, Sheila, Foley, Karen, Gage, Diane, Gnerre, Sante, Holzer, Timothy, Jaffe, David B., Kamal, Michael, Karlsson, Elinor K., Kells, Cristyn, Kirby, Andrew, Kulbokas, III, Edward J., Lander, Eric S., Landers, Tom, Leger, J. P., Levine, Rosie, Lindblad-Toh, Kerstin, Mauceli, Evan, Mayer, John H., McCarthy, Megan, Meldrim, Jim, Mesirov, Jill P., Nicol, Robert, Nusbaum, Chad, Seaman, Steven, Sharpe, Ted, Sheridan, Andrew, Singer, Jonathan B., Santos, Ralph, Spencer, Brian, Stange-Thomann, Nicole, Vinson, Jade P., Wade, Claire M., Wierzbowski, Jamey, Wyman, Dudley, Zody, Michael C., Birney, Ewan, Goldman, Nick, Kasprzyk, Arkadiusz, Mongin, Emmanuel, Rust, Alistair G., Slater, Guy, Stabenau, Arne, Ureta-Vidal, Abel, Whelan, Simon, Ainscough, Rachel, Attwood, John, Bailey, Jonathon, Barlow, Karen, Beck, Stephan, Burton, John, Clamp, Michele, Clee, Christopher, Coulson, Alan, Cuff, James, Curwen, Val, Cutts, Tim, Davies, Joy, Eyras, Eduardo, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Hunt, Adrienne, Jones, Matthew, Joy, Ann, Leonard, Steven, Lloyd, Christine, Matthews, Lucy, McLaren, Stuart, McLay, Kirsten, Meredith, Beverley, Mullikin, James C., Ning, Zemin, Oliver, Karen, Overton-Larty, Emma, Plumb, Robert, Potter, Simon, Quail, Michael, Rogers, Jane, Scott, Carol, Searle, Steve, Shownkeen, Ratna, Sims, Sarah, Wall, Melanie, West, Anthony P., Willey, David, Williams, Sophie, Abril, Josep F., Guigo, Roderic, Parra, Genis, Agarwal, Pankaj, Agarwala, Richa, Church, Deanna M., Hlavina, Wratko, Maglott, Donna R., Sapojnikov, Victor, Alexandersson, Marina, Pachter, Lior, Antonarakis, Stylianos E., Dermitzakis, Emmanouil T., Reymond, Alexandre, Ucla, Catherine, Baertsch, Robert, Diekhans, Mark, Furey, Terrence S., Hinrichs, Angela, Hsu, Fan, Karolchik, Donna, Kent, W. James, Roskin, Krishna M., Schwartz, Matthias S., Sugnet, Charles, Weber, Ryan J., Bork, Peer, Letunic, Ivica, Suyama, Mikita, Torrents, David, Zdobnov, Evgeny M., Botcherby, Marc, Brown, Stephen D., Campbell, Robert D., Jackson, Ian, Bray, Nicolas, Couronne, Olivier, Dubchak, Inna, Poliakov, Alex, Rubin, Edward M., Brent, Michael R., Flicek, Paul, Keibler, Evan, Korf, Ian, Batalov, S., Bult, Carol, Frankel, Wayne N., Carninci, Piero, Hayashizaki, Yoshihide, Kawai, Jun, Okazaki, Yasushi, Cawley, Simon, Kulp, David, Wheeler, Raymond, Chiaromonte, Francesca, Collins, Francis S., Felsenfeld, Adam, Guyer, Mark, Peterson, Jane, Wetterstrand, Kris, Copley, Richard R., Mott, Richard, Dewey, Colin, Dickens, Nicholas J., Emes, Richard D., Goodstadt, Leo, Ponting, Chris P., Winter, Eitan, Dunn, Diane M., von Niederhausern, Andrew C., Weiss, Robert B., Eddy, Sean R., Johnson, L. Steven, Jones, Thomas A., Elnitski, Laura, Kolbe, Diana L., Eswara, Pallavi, Miller, Webb, O'Connor, Michael J., Schwartz, Scott, Muzny, Donna M., Glusman, Gustavo, Smit, Arian, Green, Eric D., Hardison, Ross C., Yang, Shan, Haussler, David, Hua, Axin, Roe, Bruce A., Kucherlapati, Raju S., Montgomery, Kate T., Li, Jia, Li, Ming, Lucas, Susan, Ma, Bin, McCombie, W. Richard, Morgan, Michael, Pevzner, Pavel, Tesler, Glenn, Schultz, Jorg, Smith, Douglas R., Tromp, John, and Worley, Kim C.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Mouse Genome Sequencing Consortium ; Genome Sequencing Center: ; Asif T. Chinwalla [1, 47]; Lisa L. Cook [1]; Kimberly D. Delehaunty [1]; Ginger A. Fewell [1]; Lucinda A. Fulton [...]

Published
2002
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50. Profiling the immune infiltrate in tumor samples at single cell resolution

Author

Cheung, Denise, primary, Adams, Bruce A., additional, McDonnell, Wyatt J., additional, Jaffe, David B., additional, Puleo, Alaina R., additional, Sukovich, David J, additional, Reyes, Daniel J, additional, Royall, Ariel J, additional, Chi, Javelin C., additional, Srinavas, Niranjan J, additional, Krishnan, Sreenath J, additional, Carli, Natasha J, additional, Montesclaros, Luz J, additional, Lau, Julia J, additional, Stubbington, Michael J.T., additional, and Taylor, Sarah E.B., additional

Published
2020
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