UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
                                  SCHEDULE 13D
                   Under the Securities Exchange Act of 1934
                               (Amendment No. 3)*


                                  AEROGEN, INC.
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                                (Name of Issuer)

                     Common Stock, par value $0.001 per share
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                         (Title of Class of Securities)

                                    007779309
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                                 (CUSIP Number)

   Mitchell D. Kaye, Manager                        with a copy to:
   Xmark Asset Management, LLC                      Steven E. Siesser, Esq.
   301 Tresser Blvd.                                Lowenstein Sandler PC
   Suite 1320                                       65 Livingston Avenue
   Stamford, Connecticut 06901                      Roseland, New Jersey  07068
   (203) 653-2511                                   (973) 597-2506
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                 (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                 March 29, 2005
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             (Date of Event which Requires Filing of this Statement)


If the filing person has previously  filed a statement on Schedule l3G to report
the  acquisition  that is the subject of this  Schedule  13D, and is filing this
schedule  because of Sections 240.13d-1(e),  240.13d-1(f) or 240.13d-1(g), check
the following box. [ ]

Note:  Schedules  filed in paper format shall include a signed original and five
copies of the schedule, including all exhibits.  See Section 240.13d-7 for other
parties to whom copies are to be sent.

* The remainder of this cover page shall be filled out for a reporting  person's
initial filing on this form with respect to the subject class of securities, and
for  any  subsequent   amendment   containing   information  which  would  alter
disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed
to be "filed" for the purpose of Section 18 of the  Securities  Exchange  Act of
1934 ("Act") or otherwise  subject to the liabilities of that section of the Act
but  shall be  subject  to all other  provisions  of the Act  (however,  see the
Notes).




Cusip No.         007779309
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1.  Names of Reporting Persons.  I.R.S. Identification Nos. of above persons
   (entities only):
                       Xmark Asset Management, LLC
                               13-3954392
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2.  Check the Appropriate Box if a Member of a Group (See Instructions):
         (a)                  Not
         (b)               Applicable
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3.  SEC Use Only
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4.  Source of Funds (See Instructions):  WC
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5.  Check if  Disclosure  of  Legal  Proceedings Is  Required Pursuant  to Items
    2(d) or 2(e):                 Not Applicable
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6.  Citizenship or Place of Organization:  New York, United States
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    Number of                      7. Sole Voting Power:                  *
                                      ------------------------------------------
    Shares Beneficially            8. Shared Voting Power:                *
                                      ------------------------------------------
    Owned by
    Each Reporting                 9. Sole Dispositive Power:             *
                                      ------------------------------------------
    Person With                   10. Shared Dispositive Power:           *
                                      ------------------------------------------
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11. Aggregate Amount Beneficially Owned by Each Reporting Person:   1,133,330*
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12. Check if the Aggregate Amount in Row (11) Excludes Certain Shares
    (See Instructions):          Not Applicable
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13. Percent of Class Represented by Amount in Row (11):   18.8%*
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14. Type of Reporting Person (See Instructions):  IA
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* Xmark Asset  Management,  LLC, a New York limited  liability  company ("XAM"),
serves as investment  manager for each of Xmark Fund,  L.P., a Delaware  limited
partnership  ("Xmark  LP"),  and Xmark Fund,  Ltd.,  a Cayman  Islands  exempted
company  ("Xmark Ltd").  In such  capacity,  XAM possesses the power to vote and
direct the  disposition of all securities  held by Xmark LP and Xmark Ltd. As of
March  29,  2005,  Xmark LP is the  holder  of  50,337  shares  (the  "Xmark  LP
Preferred") of the Series A-1 Preferred  Stock,  par value $0.001 per share (the
"Preferred  Stock") of Aerogen,  Inc., a Delaware  corporation  (the "Company"),
which are presently  convertible  into 503,370  shares of the  Company's  common
stock,  par value $0.001 per share (the "Common  Stock").  As of March 29, 2005,
Xmark  Ltd is the  holder  of 62,996  shares  (the  "Xmark  Ltd  Preferred")  of
Preferred Stock,  which are presently  convertible into 629,960 shares of Common
Stock.  The  terms  of the  Xmark  LP  Preferred  and the  Xmark  Ltd  Preferred
originally precluded each of Xmark LP and Xmark Ltd from converting the Xmark LP
Preferred and the Xmark Ltd Preferred if the conversion  thereof would result in
Xmark LP, Xmark Ltd and/or  their  affiliates  beneficially  owning in excess of
4.99% of the Company's  outstanding  Common Stock  following any such conversion
(the "Issuance Limitation"). Each such Issuance Limitation was waivable by Xmark
LP and Xmark Ltd, respectively, providing 61 days' advance written notice to the
Company.  On  November 3, 2004,  Xmark LP and Xmark Ltd each  provided a written
waiver of the  Issuance  Limitation  to the Company with respect to the Xmark LP
Preferred  and the Xmark Ltd  Preferred.  As a result  of this  waiver  and as a
result of the fact that XAM  possesses  the sole  power to vote and  direct  the
disposition  of the securities  described  above,  for purposes of Reg.  Section
240.13d-3,  XAM may be deemed to  beneficially  own  1,133,330  shares of Common
Stock,  or  approximately  18.8% of the shares of Common Stock deemed issued and
outstanding as of March 29, 2005.





Item 4.   Purpose of Transaction.
          ----------------------

          Item 4 of the  Schedule  13D is hereby  amended  and  restated  in its
entirety as follows:

          As the beneficial owner of the percentage of the Company's outstanding
Common Stock  described in Item 5 of this  Schedule  13D, XAM can  influence the
outcome  of  matters  that  may be  submitted  to  the  vote  of  the  Company's
stockholders  at annual or special  meetings  of  stockholders.  Such  corporate
actions may  include,  and are not limited to, the approval of each of the types
of actions  described in clauses (a) through (g) of Item 4 of Schedule 13D under
the Securities Exchange Act of 1934, or any similar actions.

          XAM also has the power to  influence  the  strategic  direction of the
Company as a result of  restrictive  covenants  contained in the  Certificate of
Designations  of the Series A-1 Preferred  Stock,  par value $0.001 per share of
the Company (the "Preferred Stock") described in Item 6 of this Schedule 13D. In
addition,  under the terms of the Purchase Agreement described in Item 6 of this
Schedule  13D,  Xmark  LP and  Xmark  Ltd  have the  right  (which  has not been
exercised to date) to designate two members to the Company's Board of Directors,
and to remove or replace their designees,  until they no longer collectively own
at least  80,000  shares  of  Preferred  Stock in the  aggregate  (appropriately
adjusted for any stock dividend, split, combination or other recapitalization).

          Since the  completion of the Financing,  XAM has repeatedly  contacted
the  Company  and its Board of  Directors  expressing  strong  concern  with the
Company's  strategic  direction.  In  particular,  XAM has  expressed  that  the
Company's greater than expected  dissipation of cash since the completion of the
Financing,  combined with management's inability to lead the Company responsibly
and to  properly  administer  its  financial  resources,  has  compelled  XAM to
question  the  continuing  efficacy of current  management.  XAM has  repeatedly
requested  that  the  Company's  management  and  Board  implement  cost-cutting
measures  and retain an  investment  banker to explore the  Company's  strategic
alternatives.   In  response,   the  Company   rebuffed  XAM's  concerns  as  an
unintelligent  misunderstanding  of the Company's  business model, while stating
that it was indeed responsibly managing the Company.

          On March 29, 2005,  XAM sent a letter to the Company's  Board to, once
again,  express its deepening  concern with the  increasing  degradation  of the
Company's  financial  condition and its continued terrible  performance,  and to
provide  the  Company  with  notice  that it will  not  consent  to any  Company
financing  transaction  presented  to it  unless  the  Company  effects: (i)  an
immediate  change in management,  including the  replacement of the Chairman and
Chief Executive Officer and the Chief Financial  Officer of the Company,  (ii) a
sale of all  non-therapeutic  assets  (e.g.,  the  device  business),  (iii) the
immediate  implementation  of a  plan  to  reduce  expenditures,  and  (iv)  the
retention  of a  qualified  investment  banking  firm to assist  the  Company in
exploring alternatives to maximize shareholder value, including a potential sale
of the Company.  This letter is  attached as an Exhibit to this  Amendment No. 3
to Schedule 13D pursuant to Item 7 hereof, and the description of this letter is
qualified in its entirety by this reference thereto.

          XAM may,  from time to time,  further  utilize  its  voting  and other
rights to change or influence control of, and to influence the corporate affairs
of, the Company,  including  through the use of its influence on the approval of
any of the events referred to above.  XAM may take additional  steps intended to
replace  management,  including without limitation Dr. Jane Shaw, and/or certain
members of the Board of Directors.  XAM may seek to acquire additional shares of
the  Company's  Common  Stock in the open  market or  through  private  purchase





transactions, in an effort to increase its position and its voting strength. XAM
also may decide to dispose of all or part of its position if it determines  that
it no  longer  desires  to be,  or it  desires  to  reduce  its  position  as, a
stockholder of the Company.

          XAM  intends  to  continue  to  evaluate  the  business  and  business
prospects of the Company and its present and future  interest in, and intentions
with respect to, the Company,  and in connection therewith may from time to time
consult with other stockholders of the Company.

          The descriptions of the documents set forth in this Amendment No. 3 to
Schedule  13D are  qualified  in their  entirety by  reference  to the  complete
documents governing such matters, each of which are incorporated by reference to
this Amendment No. 3 to Schedule 13D as exhibits pursuant to Item 7 hereof.


Item 7.   Material to be Filed as Exhibits.
          --------------------------------

          Item 7 of the Schedule 13D is hereby amended by adding the following:

          11.  Letter  dated March 29, 2005 from XAM to the  Company's  Board of
Directors.





                                    Signature
                                    ---------

          After reasonable inquiry and to the best of my knowledge and belief, I
certify that the information  set forth in this statement is true,  complete and
correct.


                                            March 29, 2005

                                            XMARK ASSET MANAGEMENT, LLC


                                            /s/ Mitchell D. Kaye
                                            ------------------------------------
                                            Mitchell D. Kaye, Manager


Attention:  Intentional  misstatements  or omissions of fact constitute  Federal
criminal violations (See 18 U.S.C. 1001).






                                                                      Exhibit 11



March 29, 2005



Board of Directors
Aerogen, Inc.
2071 Stierlin Court
Mountain View, California  94043


Ladies and Gentlemen of the Board:

Once  again we find it  necessary  to write the Board to express  our  deepening
concern with the increasing degradation of the Company's financial condition and
its continuing terrible performance.

In past  correspondence  with us,  you  argued  that your view of the  Company's
business is superior to our view and that you understand the business far better
than we do. You asserted that our approach to maximizing  shareholder  value was
not only incorrect under the circumstances,  but also unnecessary.  We requested
that you  implement  cost-cutting  measures and retain an  investment  banker to
explore the  Company's  strategic  alternatives.  In response,  you attempted to
assuage our concerns with  assurances that you were acting to contain and manage
the Company's adversities.  We have seen no evidence of this activity, let alone
any positive  impact on the Company.  On the contrary,  the  Company's  downward
spiral has increased at an alarming  pace.  The Company's  public  announcements
about Fast Track status for Amakacin and its recent co-development deal have not
had any  sustainable  positive  impact on the Company's  financial  condition or
market performance.  Neither the Board nor management can continue to claim that
success is on the  horizon;  those  claims are  proving to be  illusory  and are
quickly rising to the point of negligently delusional.

At some point, the Board must face the realization that management has failed to
achieve your goals and that the current team is not capable of generating  value
for this Company's  shareholders.  That point needs to come immediately,  before
the  shareholders  of this Company seek redress  against both you and management
for your  egregious  and  actionable  misdeeds.  It is time  for you to  finally
recognize that the Company cannot continue on its current path.

We are hereby  putting you on notice that Xmark will not  consent  to--and  will
exercise its "veto" with respect to--any financing  transaction presented to us,
unless the Company has first made substantial changes. In a recent discussion, a
member of the Company's  senior  management  suggested that he expected we would






Board of Directors of Aerogen, Inc.
March 29, 2005
Page 2 of 2




"act  rationally"  if and  when  the  Company  presents  us with a  proposal  to
restructure  the  preferred  stock in  order  to  permit  the  Company  to raise
additional capital. We were astounded by that suggestion, coming as it does from
a  management  team that brought the Company to the brink of  bankruptcy  in the
past and is currently on course to repeat that  catastrophe.  It is reckless for
the  Board  and  management  to  rely  on  our  cooperation  given  the  current
circumstances under which the Company is operating.

We will use our voting power against any additional capital raising  transaction
presented to us, unless the Board meets the following  conditions:  (i) there is
an immediate change in management, including the replacement of the Chairman and
Chief Executive Officer as well as the Chief Financial  Officer;  (ii) a sale of
all  non-therapeutic  assets (e.g.,  the device  business);  (iii) the immediate
implementation  of a plan to reduce  expenditures;  and (iv) the retention of an
investment  banker to assist the Company in exploring  alternatives  to maximize
shareholder value, including a sale of the Company.

We expect to see the Board take the steps outlined above. A clever or "lawyered"
response to this letter is not going to resolve  the current  crisis  facing the
Company.  Only  decisive  action by the Board on the items we are  proposing can
save the Company at this point.  As the  Company's  stock  price  confirms,  the
Company's dire situation is becoming more and more apparent to the public.

We intend to remain  vigilant in the protection of our investment and we will no
longer accept empty promises and hollow assurances.

Very truly yours,

Xmark Asset Management, LLC

/s/ Michell D. Kaye

Mitchell D. Kaye,
Chief Investment Officer